Abstract
Background
Inherited bleeding, thrombotic, and platelet disorders (BTPDs) are a heterogeneous set of diseases, many of which are globally very rare. Over the past five decades, the genetic basis of some of these disorders has been identified, and recently, high-throughput sequencing has become the primary means of identifying disease-causing genetic variants.
Objectives
Knowledge of the clinical validity of a gene-disease relationship is essential to both providing an accurate diagnosis based on results of diagnostic gene panel tests and informing the construction of such panels. The Scientific and Standardization Committee for Genetics in Thrombosis and Haemostasis undertook a curation process for selecting 96 TIER1 genes for BTPDs. The purpose was to evaluate the evidence supporting each gene-disease relationship and provide an expert-reviewed classification for the clinical validity of genes associated with BTPDs.
Methods
The ClinGen Hemostasis/Thrombosis Gene Curation Expert Panel (HT GCEP) assessed the strength of evidence for TIER1 genes using the semi-quantitative ClinGen gene disease clinical validity framework. ClinGen lumping and splitting guidelines were used to determine the appropriate disease entity, or entities, for each gene and 101 gene-disease relationships were identified for curation.
Results
The final outcome included 68 Definitive (67%), 26 Moderate (26%), and seven Limited (7%) classifications. The summary of each curation is available on the ClinGen website.
Conclusions
Expert-reviewed assignment of gene-disease relationships by the HT GCEP facilitates accurate molecular diagnoses for BTPDs by clinicians and diagnostic laboratories. These curation efforts can allow genetic testing to focus on genes with a validated role in disease.
Keywords: Data Curation, Genetic Disorders, Genetic Variation, Hemostasis, Reliability and Validity, Thrombosis
INTRODUCTION
Inherited disorders of hemostasis and thrombosis are a heterogenous group of conditions that include rare and more common disorders with Mendelian inheritance and a wide spectrum of penetrance, as well as lower penetrance risk alleles. The clinical phenotype of increased bleeding or venous thromboembolism is common to most of these disorders and hence the laboratory phenotype, including blood counts, platelet function assays and specific clotting factor activities, play an important role in defining the unique and specific manifestations of each disease state. Genetic conditions that lead to laboratory abnormalities alone and have no clinical repercussions, such as some specific coagulation factor deficiencies, are also frequently encountered in this area.[1] With broader access to genetic sequencing technologies, including more robust bioinformatics platforms, a large number of genes have been reported in relation to disorders of hemostasis and thrombosis.[2] However, the quantity and quality of data available to support each gene-disease relationship varies greatly, making the process of evaluating the evidence available challenging and difficult to accomplish outside of a multidisciplinary, academic, collaborative context. [3] In response to the need to thoroughly and systematically approach the available data, an international group of clinical, scientific and gene curation specialists was formed to evaluate the evidence supporting each gene-disease relationship within a standardized framework and provide an expert-reviewed classification for the clinical validity of genes associated with inherited bleeding, thrombotic, and platelet disorders.
METHODS
The Clinical Genome Resource (ClinGen) Hemostasis/Thrombosis Gene Curation Expert Panel
In 2018, the ClinGen Hemostasis/Thrombosis Clinical Domain Working Group assembled a committee of clinicians and researchers with expertise in BTPDs who prioritized the curation of genes and variants within several relevant domains. The Hemostasis/Thrombosis Gene Curation Expert Panel (HT GCEP) was formed to curate and adjudicate genes associated with BTPDs using the ClinGen gene-disease validity classification framework. [4] The HT GCEP comprises six biocurators, a coordinator and assistant coordinator, and 13 experts with significant clinical, molecular diagnostic and/or research experience in hemostasis and thrombosis (https://clinicalgenome.org/affiliation/40028/). This international panel includes members from the United States, the United Kingdom, Belgium, China, France, Germany, Ireland and Italy, representing 16 institutions.
Hemostasis/Thrombosis genes and diseases selected for analysis
The Scientific and Standardization Committee for Genetics in Thrombosis and Haemostasis (SSC-GinTH) selected 96 TIER1 core genes for BTPDs. [5] Additionally, they considered genes associated with hereditary hemorrhagic telangiectasia, Ehlers-Danlos syndrome, Gaucher syndrome, or Noonan syndrome to be part of an “extended TIER1 list”; disorders that are associated with primary phenotypes such as arteriovenous malformations, joint hypermobility, skin hyperextensibility, tissue fragility, and complex syndromic features that result in an increased bleeding tendency. In order to meet the urgent need in diagnostic genetic laboratories, the SSC-GinTH previously applied a scoring system to specify the gene-disease pairs relevant for BTPD based on three layers of evidence; genotype-phenotype cosegregation data, supportive molecular assays or laboratory phenotypes, and mouse models. A gene was considered as TIER1 if the literature review identified at least three genetically independent families with robust gene-phenotype association data or if fewer independent families were paired with support from either robust functional studies or a mouse model.
The HT GCEP considered for curation the 96 TIER1 core genes as well as three associated with hereditary hemorrhagic telangiectasia. Of these 99 genes, ten were previously curated (DIAPH1, FLNA, MYH9, NBEA, RUNX1, STIM1, STXBP2, and WAS) by another ClinGen GCEP, or in plans for curation (RNU4ATAC) by a GCEP with a more appropriate scope of work. One further gene-disease relationship, PIGA related paroxysmal nocturnal hemoglobinuria, was considered outside the scope of work as it is not primarily a thrombosis disorder and is the only gene related to a somatic, rather than germline, condition. Thus, 89 genes were finally identified for curation by the HT GCEP.
For genes with assertions relating to multiple diseases in the Online Mendelian Inheritance in Man (OMIM) database or the literature, the HT GCEP evaluated the mode of inheritance, the mechanism of disease, and phenotypic features of each condition to determine whether to lump the diseases into one curation record or to split them into individual records per the guidelines from the ClinGen Lumping and Splitting group.[6] This resulted in the identification of 101 gene-disease relationships for curation by the HT GCEP, with 12 genes requiring two curations for separate disease entities. Genes with two curations are referred to throughout by their difference in inheritance pattern “-AR” or “-AD” (autosomal recessive and autosomal dominant) or mechanisms of disease “-LoF” or “-GoF” (loss of function and gain of function). All disease entities were curated using a unique identifier in the Mondo disease ontology (https://mondo.monarchinitiative.org/).
Implementation of the ClinGen gene clinical validity curation process
The HT GCEP determined the clinical validity for gene-disease relationships using the ClinGen Gene Curation Standard Operating Procedure, Version 6 or 7 (available at https://clinicalgenome.org/site/assets/files/3975/gene-disease_validity_standard_operating_procedures_version_7-1.pdf), based on the framework described in Strande & Riggs et al.[4] This semi-quantitative scoring system uses an evidence-based approach to classify gene-disease relationships based on the strength of supportive evidence as follows: Definitive (12–18 points, with replication over time), Strong (12–18 points), Moderate (7–11 points), and Limited (0.1–6 points). To differentiate a Definitive from Strong classification, the role of the gene in the disease would need to be repeatedly demonstrated in research and clinical diagnostic settings and upheld over time (a minimum of three years). Additionally, the category of No Known Disease Relationship can be applied when no reports have directly implicated the gene in human disease cases, and two classifications, Disputed and Refuted, are available for gene-disease relationships with conflicting evidence.
For each gene-disease relationship a structured evaluation of genetic and experimental evidence available in the published literature was recorded in ClinGen’s gene curation interface, providing a summary published directly to the ClinGen website (https://search.clinicalgenome.org/kb/affiliate/10028) upon expert approval. Genetic evidence includes variants in the gene of interest identified in patients with the disease entity of interest, including case reports, family studies, and case-control studies. Experimental evidence supports the role of the gene in the disease of interest, or phenotypic features associated with the disease entity, incorporating biochemical function, protein interactions, expression, functional alterations in cells, and animal models that recapitulate the disease. A maximum of 12 points can be assigned for genetic evidence and a maximum of 6 points can be assigned for experimental evidence for a combined maximum total of 18 points. The ClinGen gene curation framework is used as a guide and each expert panel must adjust scoring or final classifications based on the particulars of the relevant disease area and their professional judgment, particularly when the curation score is near a classification boundary. For scores between the category thresholds, the semi-quantitative framework allows for expert adjudication, to either the lower or the higher classification. In exceptional cases, the classification may be increased or decreased by, no more than, one level from the calculated classification.
Once the relevant gene-disease relationships were identified, a preliminary evaluation was performed to determine the strategy for curation and review. The preliminary evaluation incorporated expert input and a cursory review of OMIM and the literature to determine the quantity of evidence available for each gene-disease relationship. When there was expert agreement and abundant literature available, spanning at least a three-year period, gene-disease relationships were considered likely to reach a Definitive classification and permitted to undergo an expedited curation process. Those not meeting these criteria underwent the standard curation process. For an expedited curation, each gene-disease relationship was assigned to one curator and two experts; standard curations were assigned to one curator and one expert. For each curation, the biocurator performed a literature review, assessed the genetic and experimental evidence, and made a provisional classification based on the total points. The biocurator then provided a summary of the curation to the assigned expert(s) for review and revision. Once the biocurator and expert(s) agreed that the curation was complete and accurate, the process diverged between expedited and standard curation strategies. Using the expedited strategy, if the preliminary classification was Definitive and both experts agreed, the classification was finalized. If the preliminary classification was non-Definitive, or consensus was not reached between the curator and two experts, the curation was moved to the standard strategy. For the standard curation strategy, the biocurator presented an overview of the curation to the HT GCEP, represented by a quorum of at least three experts from at least two institutions, on a monthly web conference call and the expert-led group approved a final clinical validity classification by a majority vote.
Curation of the 89 BTPD related genes took place from 2019 to 2022. Once all gene-disease relationships were classified, a literature search was performed for all non-Definitive gene-disease relationships in order to identify additional evidence published during the course of the working period. When relevant, new evidence was added to the curations and the classifications were re-evaluated.
RESULTS
Eighty-nine genes were curated in association with a multitude of disorders spanning the spectrum of bleeding, thrombotic, and platelet disorders. Each gene was evaluated to determine the most appropriate gene-disease relationship for curation (Table 1). Of the 89 genes, 77 were evaluated in association with a single disease entity, while 12 underwent two curations for separate disease entities. Overall, the ClinGen HT GCEP curated 101 gene-disease relationships, which resulted in 68 Definitive (67%), 26 Moderate (26%), and seven Limited (7%) (Figure 1A). Those classified as Definitive scored 12–18 points, and included well-known disease genes such as ITGA2B, ITGB3, GP1BA, GP1BB, and GP9 (Figure 2). Genetic evidence reflecting numerous reports from the literature on causative variants was available for all Definitive curations, reaching the maximum of 12 points in 87% of the Definitive classifications (11.5 +/− 1.2 points), and additional experimental evidence (4.4 +/− 1.3 points) was available for all Definitive classifications (Figure 1B). There were no gene-disease relationships classified as Strong, due to the absence of curated genes with a total of ≥12 points without replication over time, which is the only criterion that distinguishes the Strong from Definitive classification.
Table 1.
Clinical validity classifications and scores for gene-disease relationships in hemostasis and thrombosis
| Gene | Classification (points) | Disease (Inheritance-Mechanism) | MonDO ID | OMIM Phenotype(s) Included | Comments |
|---|---|---|---|---|---|
| ABCC4 | Moderate (9.25) | qualitative platelet defect (AR) | MONDO:0001197 | − | − |
| ABCG5 | Definitive (18) | sitosterolemia (AR) | MONDO:0008863 | Sitosterolemia 2 (#618666) | − |
| ABCG8 | Definitive (17) | sitosterolemia (AR) | MONDO:0008863 | Sitosterolemia 1 (#210250) | − |
| ACTB | Moderate (7.6) | thrombocytopenia (AD) | MONDO:0002049 | − | ACTB was curated for its relationship to syndromic thrombocytopenia, not the relationship with Baraitser-Winter syndrome 1, which is clinically distinct and not classically associated with thrombocytopenia. Specific variants, in the region of exons 5 and 6, are associated with the syndromic thrombocytopenia. |
| ACTN1 | Definitive (13) | platelet-type bleeding disorder 15 (AD) | MONDO:0014078 | Bleeding disorder, platelet-type, 15 (#615193) | − |
| ACVRL1 | Definitive (17) | telangiectasia, hereditary hemorrhagic, type 2 (AD) | MONDO:0010880 | Telangiectasia, hereditary hemorrhagic, type 2 (#600376) | − |
| ADAMTS13 | Definitive (17) | congenital thrombotic thrombocytopenic purpura (AR) | MONDO:0010122 | Thrombotic thrombocytopenic purpura, hereditary (#274150) | |
| ANKRD26 | Definitive (13.5) | thrombocytopenia 2 (AD) | MONDO:0008555 | Thrombocytopenia 2 (#188000) | − |
| ANO6 | Moderate (7.5) | Scott syndrome (AR) | MONDO:0009885 | Scott syndrome (#262890) | − |
| AP3B1 | Definitive (17) | Hermansky-Pudlak syndrome 2 (AR) | MONDO:0011997 | Hermansky-Pudlak syndrome 2 (#608233) | − |
| AP3D1 | Limited (8) | Hermansky-Pudlak syndrome 10 (AR) | MONDO:0014885 | Hermansky-Pudlak syndrome 10 (#617050) | − |
| ARPC1B | Definitive (14) | platelet abnormalities with eosinophilia and immune-mediated inflammatory disease (AR) | MONDO:0060583 | Immunodeficiency 71 with inflammatory disease and congenital thrombocytopenia (#617718) | − |
| BLOC1S3 | Moderate (10) | Hermansky-Pudlak syndrome 8 (AR) | MONDO:0013560 | Hermansky-Pudlak syndrome 8 (#614077) | − |
| BLOC1S6 | Definitive (12) | Hermansky-Pudlak syndrome 9 (AR) | MONDO:0013606 | Hermansky-Pudlak syndrome 9 (#614171) | − |
| CDC42 | Definitive (14.5) | macrothrombocytopen ia-lymphedema-developmental delay-facial dysmorphism-camptodactyly syndrome (AD) | MONDO:0014757 | Takenouchi-Kosaki syndrome (#616737) | − |
| CYCS | Limited (6.8) | thrombocytopenia 4 (AD) | MONDO:0012775 | Thrombocytopenia 4 (#612004) | − |
| DIAPH1 * | Definitive (16) | diaph1-related sensorineural hearing loss-thrombocytopenia syndrome (AD) | MONDO:0044635 | Deafness, autosomal dominant 1, with or without thrombocytopenia (#124900) | DIAPH1 was curated by the ClinGen Hearing Loss GCEP (https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_43c017fd-ce70-4fbe-ad30-90f216adaa7d-2018-01-05T170000.000Z). All variants for this gene-disease relationship have been loss of function or truncating variants in exon 27. Of note, variants in other exons of this gene have been implicated in autosomal recessive Seizures, cortical blindness, microcephaly syndrome (MIM #616632), which is not covered by the scope of this curation. |
| DTNBP1 | Definitive (12.5) | Hermansky-Pudlak syndrome 7 (AR) | MONDO:0013559 | Hermansky-Pudlak syndrome 7 (#614076) | − |
| ENG | Definitive (18) | hereditary hemorrhagic telangiectasia (AD) | MONDO:0019180 | Telangiectasia, hereditary hemorrhagic, type 1 (#187300) | − |
| ETV6 | Definitive (17.5) | thrombocytopenia 5 (AD) | MONDO:0014536 | Thrombocytopenia 5 (#616216) | − |
| F10 | Definitive (16.5) | congenital factor X deficiency (AR) | MONDO:0009212 | Factor X deficiency (#227600) | − |
| F11 | Definitive (16.5) | congenital factor XI deficiency (SD) | MONDO:0012897 | Factor XI deficiency, autosomal dominant (#612416) Factor XI deficiency, autosomal recessive (#612416) |
The FXI deficiency results from either biallelic loss of function or monoallelic dominant negative variants, which were considered to cause the same clinical disease and curated jointly. |
| F12 | Moderate (10) | hereditary angioedema type 3 (AD) | MONDO:0012526 | Angioedema, hereditary, 3 (#610618) | Given differences in the phenotype, inheritance pattern, and molecular mechanism (gain of function variants in |
| F12 | Definitive (16.5) | congenital factor XII deficiency (AR) | MONDO:0009315 | Factor XII deficiency (#234000) | exon 9 versus loss of function) underlying the two disease entities, these were curated separately. |
| F13A1 | Definitive (16) | factor XIII, A subunit, deficiency of (AR) | MONDO:0013187 | Factor XIIIA deficiency (#613225) | − |
| F13B | Definitive (12.5) | factor XIII, B subunit, deficiency of (AR) | MONDO:0013190 | Factor XIIIB deficiency (#613235) | − |
| F2 | Definitive (17) | congenital prothrombin deficiency (AR) | MONDO:0013361 | Dysprothrombinemia (#613679) Hypoprothrombinemia (#613679) | Given differences in the phenotype, inheritance pattern, and molecular mechanism (loss of function versus gain of function) underlying the two disease entities, these were curated separately. |
| F2 | Definitive (13) | thrombophilia due to thrombin defect (AD) | MONDO:0008559 | Thrombophilia due to thrombin defect (#188050) | |
| F5 | Definitive (16.5) | congenital factor V deficiency (AR) | MONDO:0009210 | Factor V deficiency (#227400) | Given differences in the phenotype, inheritance pattern, and molecular mechanism (loss of function versus gain of function) underlying the two disease entities, these were curated separately. |
| F5 | Definitive (14.7) | thrombophilia due to activated protein C resistance (AD) | MONDO:0008560 | Thrombophilia due to activated protein C resistance (#188055) | |
| F7 | Definitive (16.5) | factor VII deficiency (AR) | MONDO:0002244 | Factor VII deficiency (#227500) | − |
| F8 | Definitive (16.5) | hemophilia A (XL) | MONDO:0010602 | Hemophilia A (#306700) | − |
| F9 | Definitive (16.5) | hemophilia B (XL-LOF | MONDO:0010604 | Hemophilia B (#306900) | Given differences in the phenotype, inheritance pattern, and molecular mechanism (loss of function versus |
| F9 | Limited (1) | thrombophilia, X-linked, due to factor IX defect (XL-GOF) | MONDO:0010432 | Thrombophilia, X-linked, due to factor IX defect (#300807) | proposed gain of function) underlying the two disease entities, these were curated separately. |
| FERMT3 | Definitive (18) | leukocyte adhesion deficiency 3 (AR) | MONDO:0013016 | Leukocyte adhesion deficiency, type III (#612840) | − |
| FGA | Definitive (18) | congenital fibrinogen deficiency (SD) | MONDO:0018060 | Afibrinogenemia, congenital (#202400) Dysfibrinogenemia, congenital (#616004) Hypodysfibrinogenemia, congenital (#616004) |
Congenital Afibrinogenemia, Congenital Dysfibrinogenemia, and Congenital Hypodysfibrinogenemia represent a spectrum of severity associated with either monoallelic or biallelic loss of function variants and were curated jointly. Of note FGA is also related to Familial Visceral Amyloidosis (#105200), which has a distinct phenotype and molecular mechanism but does not fall under the purview of the HT GCEP. |
| FGB | Definitive (15) | congenital fibrinogen deficiency (SD) | MONDO:0018060 | Afibrinogenemia, congenital (#202400) Dysfibrinogenemia, congenital (#616004) Hypofibrinogenemia, congenital (#202400) |
Congenital Afibrinogenemia, Congenital Dysfibrinogenemia, and Congenital Hypodysfibrinogenemia represent a spectrum of severity associated with either monoallelic or biallelic loss of function variants and were curated jointly. |
| FGG | Definitive (18) | congenital fibrinogen deficiency (SD) | MONDO:0018060 | Afibrinogenemia, congenital (#202400) Dysfibrinogenemia, congenital (#616004) Hypodysfibrinogenemia (#616004) Hypofibrinogenemia, congenital (#202400) |
Congenital Afibrinogenemia, Congenital Dysfibrinogenemia, Hypodysfibrinogenemia, and Congenital Hypodysfibrinogenemia represent a spectrum of severity associated with either monoallelic or biallelic loss of function variants and were curated jointly. |
| FLI1 | Moderate (7.5) | bleeding disorder, platelet-type, 21 (AD) | MONDO:0054577 | Bleeding disorder, platelet-type, 21 (#617443) | A single family with biallelic FLI1 variants [44] has been noted here for posterity but not considered within this curation of autosomal dominant disease. Should additional evidence arise in the future, additional consideration will be made for lumping or splitting these two inheritance patterns. |
| FLNA * | Definitive (13.85) | periventricular nodular heterotopia (XL) | MONDO:002034 | FG syndrome 2 (#300321) Cardiac valvular dysplasia, X-linked (#314400) Congenital short bowel syndrome (#300048) Heterotopia, periventricular, 1 (#300049) Intestinal pseudoobstruction, neuronal (#300048) |
FLNA was curated by the Intellectual Disability and Autism GCEP (https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_80bc6280-7c21-4168-8a98-93c31fead5d7-2020-12-27T231155.213Z). Loss of function variants lead to FG syndrome 2, X-linked cardiac valvular dysplasia, congenital short bowel syndrome, and neuronal intestinal pseudoobstruction, which all share overlapping phenotypes (including thrombocytopenia) with some patients with periventricular nodular heterotopia. Of note gain of function variants cause X-linked otopalatodigital spectrum disorders (https://www.ncbi.nlm.nih.gov/books/NBK1393/) and were not within the scope of this curation. |
| FYB1 | Moderate (12) | thrombocytopenia 3 (AR) | MONDO:0010120 | Thrombocytopenia 3 (#273900) | − |
| GATA1 | Definitive (14.7) | GATA1-Related X-Linked Cytopenia (XLR) | MONDO:0100089 | Anemia, X-linked, with/without neutropenia and/or platelet abnormalities (#300835) Thrombocytopenia with beta-thalassemia, X-linked (#314050) Thrombocytopenia, X-linked, with or without dyserythropoietic anemia (#300367) |
GATA1-related cytopenia is the accepted term to encompass the heterogeneity of this single disorder. [45] |
| GFI1B | Definitive (14.4) | platelet-type bleeding disorder 17 (AD) | MONDO:0008553 | Bleeding disorder, platelet-type, 17 (#187900) | The predominant form of inheritance, autosomal dominant, was considered in this curation, though three homozygous cases have been reported.[46–49] |
| GGCX | Definitive (17) | vitamin K-dependent clotting factors, combined deficiency of, type 1 (AR) | MONDO:0010187 | Pseudoxanthoma elasticum-like disorder with multiple coagulation factor deficiency (#610842) Vitamin K-dependent clotting factors, combined deficiency of, 1 (#277450) |
Overlapping phenotypes, autosomal recessive inheritance pattern, and molecular mechanism (inactivating variants) resulted in these phenotypes being curated jointly. |
| GNE | Moderate (8.1) | isolated hereditary giant platelet disorder (AR) | MONDO:0016361 | − | Of note, this gene has also been implicated in both Nonaka myopathy (MIM#605820) and sialuria (MIM#269921). However, only this distinct phenotype was curated. |
| GP1BA | Definitive (17) | Bernard-Soulier syndrome (AR) | MONDO:0009276 | Bernard-Soulier syndrome, type A1 (recessive) (#231200) Bernard-Soulier syndrome, type A2 (dominant) (#153670) | Interfamilial phenotypic variability is observed between individuals harboring the same genetic variant between different inheritance patterns and the difference in the inheritance pattern for the disease entities is representative of a continuum of disease, i.e. mild carrier phenotypic features are observed in recessive disease. [50] Thus the disease entities were lumped and the well-established autosomal recessive inheritance pattern has been curated here. |
| GP1BA | Definitive (14.5) | platelet-type von Willebrand disease (AD) | MONDO:0008332 | von Willebrand disease, platelet-type (#177820) | This was curated as a distinct disease due to differences in molecular mechanism (gain of function versus loss of function), inheritance pattern (autosomal dominant vs. predominantly autosomal recessive), and phenotypic variability. |
| GP1BB | Definitive (18) | Bernard-Soulier syndrome (AR) | MONDO:0009276 | Bernard-Soulier syndrome, type B (#231200) Giant platelet disorder, isolated (#231200) |
Giant platelets are part of the phenotypic spectrum of Bernard-Soulier syndrome. |
| GP6 | Definitive (13) | platelet-type bleeding disorder 11 (AR) | MONDO:0013623 | Bleeding disorder, platelet-type, 11 (#614201) | − |
| GP9 | Definitive (14.5) | Bernard-Soulier syndrome (AR) | MONDO:0009276 | Bernard-Soulier syndrome, type C (#231200) | − |
| HOXA11 | Limited (6) | radioulnar synostosis with amegakaryocytic thrombocytopenia 1 (AD) | MONDO:0024558 | Radioulnar synostosis with amegakaryocytic thrombocytopenia 1 (#605432) | − |
| HPS1 | Definitive (17.5) | Hermansky-Pudlak syndrome 1 (AR) | MONDO:0008748 | Hermansky-Pudlak syndrome 1 (#203300) | − |
| HPS3 | Definitive (17) | Hermansky-Pudlak syndrome 3 (AR) | MONDO:0013555 | Hermansky-Pudlak syndrome 3 (#614072) | − |
| HPS4 | Definitive (15.5) | Hermansky-Pudlak syndrome 4 (AR) | MONDO:0013556 | Hermansky-Pudlak syndrome 4 (#614073) | − |
| HPS5 | Definitive (18) | Hermansky-Pudlak syndrome 5 (AR) | MONDO:0013557 | Hermansky-Pudlak syndrome 5 (#614074) | − |
| HPS6 | Definitive (18) | Hermansky-Pudlak syndrome 6 (AR) | MONDO:0013558 | Hermansky-Pudlak syndrome 6 (#614075) | − |
| HRG | Moderate (6.6) | hereditary thrombophilia due to congenital histidine-rich (poly-L) glycoprotein deficiency (AD) | MONDO:0013143 | Thrombophilia due to HRG deficiency (#613116) | − |
| IKZF5 | Moderate (9.2) | thrombocytopenia 7 (AD) | MONDO:0030867 | Thrombocytopenia, autosomal dominant, 7 (#619130) | − |
| ITGA2B | Definitive (15.5) | Glanzmann thrombasthenia (AR) | MONDO:0100326 | Glanzmann thrombasthenia 1 (#273800) | Given differences in the phenotype, inheritance pattern, and molecular mechanism (loss of function versus gain of function) underlying the two disease entities, these were curated separately. |
| ITGA2B | Moderate (9.5) | platelet-type bleeding disorder 16 (AD) | MONDO:0008552 | Bleeding disorder, platelet-type, 16, autosomal dominant (#187800) | |
| ITGB3 | Definitive (17) | Glanzmann thrombasthenia (AR) | MONDO:0100326 | Glanzmann thrombasthenia 2 (#619267) | Given differences in the phenotype, inheritance pattern, and molecular |
| ITGB3 | Moderate (9.1) | platelet-type bleeding disorder 16 (AD) | MONDO:0008552 | Bleeding disorder, platelet-type, 24, autosomal dominant (#619271) | mechanism (loss of function versus gain of function) underlying the two disease entities, these were curated separately. |
| KDSR | Definitive (12.25) | erythrokeratodermia variabilis et progressiva 4 (AR) | MONDO:0033014 | Erythrokeratodermia variabilis et progressiva 4 (#617526) | − |
| KNG1 | Definitive (14) | congenital high-molecular-weight kininogen deficiency (AR) | MONDO:0009234 | High molecular weight kininogen deficiency (#228960) Kininogen deficiency (#228960) |
This curation is considered a gene-deficiency curation, due to the lack of evidence supporting this gene being involved in any disease or disorder beyond a prolonged partial thromboplastin time. Autosomal dominant angioedema was not considered in this curation. |
| LMAN1 | Definitive (14.5) | factor V and factor VIII, combined deficiency of, type 1 (AR) | MONDO:0009206 | Combined factor V and VIII deficiency (#227300) | − |
| LYST | Definitive (16.5) | Chediak-Higashi syndrome (AR) | MONDO:0008963 | Chediak-Higashi syndrome (#214500) | − |
| MCFD2 | Definitive (14.5) | factor V and factor VIII, combined deficiency of, 2 (AR) | MONDO:0013331 | Factor V and factor VIII, combined deficiency of (#613625) | − |
| MECOM | Definitive (15.5) | MECOM-associated syndrome (AD) | MONDO:0100458 | Radioulnar synostosis with amegakaryocytic thrombocytopenia 2 (#616738) | − |
| MPIG6B | Definitive (13.5) | thrombocytopenia, anemia, and myelofibrosis (AR) | MONDO:0044316 | Thrombocytopenia, anemia, and myelofibrosis (#617441) | − |
| MPL | Definitive (18) | congenital amegakaryocytic thrombocytopenia (AR) | MONDO:0011469 | Thrombocytopenia, congenital amegakaryocytic (#604498) | Given differences in the phenotype, inheritance pattern, and molecular mechanism (loss of function versus gain of function) underlying the two disease entities, these were curated separately. |
| MPL | Definitive (12.7) | thrombocythemia 2 (AD) | MONDO:0011173 | Thrombocythemia 2 (#601977) | |
| MYH9 * | Definitive (18) | MYH-9 related disease (AD) | MONDO:0015912 | Deafness, autosomal dominant 17 (#603622) Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss (#155100) |
MYH9 was curated by the ClinGen Hearing Loss GCEP (https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_d6801442-c490-44a0-9a60-84ab5b20f7ac-2018-07-17T191819.148Z) for MYH9-Related Disorders, a class of autosomal dominant disorders characterized by congenital macrothrombocytopenia and variable leucocyte inclusion bodies, renal abnormalities, cataracts, and progressive sensorineural hearing loss. |
| NBEA * | Definitive (16) | complex neurodevelopmental disorder (AD) | MONDO:0100038 | Neurodevelopmental disorder with or without early-onset generalized epilepsy (#619157) | NBEA was curated by the ClinGen Intellectual Disability and Autism GCEP (https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_f40357db-6cc2-4240-8771-1206cd27298a-2020-12-02T170000.000Z), including the patient with dense granules in platelets. [51] |
| NBEAL2 | Definitive (17.5) | gray platelet syndrome (AR) | MONDO:0007686 | Gray platelet syndrome (#139090) | − |
| P2RY12 | Moderate (7) | platelet-type bleeding disorder 8 (AD) | MONDO:0012354 | − | Due to differences in molecular mechanism, (purportive) dominant negative versus inactivating variants, autosomal dominant and recessive cases were considered separately. |
| P2RY12 | Moderate (7.5) | platelet-type bleeding disorder 8 (AR) | MONDO:0012354 | Bleeding disorder, platelet-type, 8 (#609821) | |
| PLA2G4A | Moderate (6.5) | cytosolic phospholipase-A2 alpha deficiency associated bleeding disorder (AR) | MONDO:0018794 | Gastrointestinal ulceration, recurrent, with dysfunctional platelets (#618372) | − |
| PLAU | Moderate (7) | Quebec platelet disorder (AD) | MONDO:0011136 | Quebec platelet disorder (#601709) | − |
| PLG | Definitive (16.5) | hypoplasminogenemia (AR) | MONDO:0009009 | Dysplasminogenemia (#217090) Plasminogen deficiency, type I (#217090) |
Due to differences in phenotype and inheritance pattern, autosomal dominant angioedema was not considered in this curation. |
| PROC | Definitive (17) | hereditary thrombophilia due to congenital protein C deficiency (SD) | MONDO:0019145 | Thrombophilia due to protein C deficiency, autosomal dominant (#176860) Thrombophilia due to protein C deficiency, autosomal recessive (#612304) |
Both monoallelic and biallelic cases with inactivating mutations representative of a continuum of disease were curated as a single disease entity. |
| PROS1 | Definitive (15.5) | hereditary thrombophilia due to congenital protein S deficiency (SD) | MONDO:0019144 | Thrombophilia due to protein S deficiency, autosomal dominant (#612336) Thrombophilia due to protein S deficiency, autosomal recessive (#614514) |
Both monoallelic and biallelic cases with inactivating mutations representative of a continuum of disease were curated as a single disease entity. |
| PTGS1 | Limited (5.9) | platelet-type bleeding disorder 12 (SD) | MONDO:0011588 | − | Given similarity in phenotype and the fact that the mode of inheritance remains to be fully elucidated monoallelic and biallelic cases were considered in a single curation. |
| RAP1B | Limited (3) | syndromic constitutional thrombocytopenia (AD) | MONDO:0018795 | − | − |
| RASGRP2 | Definitive (18) | platelet-type bleeding disorder 18 (AR) | MONDO:0014386 | Bleeding disorder, platelet-type, 18 (#615888) | − |
| RBM8A | Definitive (15.25) | thrombocytopenia-absent radius syndrome (AR) | MONDO:0010121 | Thrombocytopenia-absent radius syndrome (#274000) | − |
| RNU4ATAC * | − | − | − | − | The ClinGen SCID-CID GCEP will curate RNU4ATAC, including Roifman syndrome (with the thrombocytopenia phenotype). |
| RUNX1 * | Definitive (17.5) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome (AD) | MONDO:0011071 | Platelet disorder, familial, with associated myeloid malignancy (#601399) | Curation was completed by the ClinGen Hereditary Cancer GCEP (https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_06aed341-58db- 459b-a750-7142e29b420b-2018-06-04T194655.831Z). |
| SERPINC1 | Definitive (16.5) | hereditary antithrombin deficiency (SD) | MONDO:0013144 | Thrombophilia due to antithrombin III deficiency (#613118) | Both monoallelic and biallelic cases with inactivating mutations representative of a continuum of disease were curated as a single disease entity. |
| SERPIND1 | Definitive (12.9) | heparin cofactor 2 deficiency (AD) | MONDO:0012876 | Thrombophilia due to heparin cofactor II deficiency (#612356) | − |
| SERPINE1 | Moderate (10.5) | congenital plasminogen activator inhibitor type 1 deficiency (AR) | MONDO:0013227 | Plasminogen activator inhibitor- 1 deficiency (#613329) | − |
| SERPINF2 | Definitive (16) | alpha-2-plasmin inhibitor deficiency (AR) | MONDO:0009883 | Alpha-2-plasmin inhibitor deficiency (#262850) | − |
| SLFN14 | Moderate (7.7) | platelet-type bleeding disorder 20 (AD) | MONDO:0014830 | Bleeding disorder, platelet-type, 20 (#616913) | − |
| SMAD4 | Definitive (16) | Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome (AD) | MONDO:0008278 | Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome (#175050) Polyposis, juvenile intestinal (#174900) | Of note, this gene has also been implicated in Myhre syndrome (MIM#139210), which was not considered in this curation due to the distinct phenotypes and molecular mechanisms (Myhre syndrome is associated with variation at Ile500 and nearby amino acids only). |
| SRC | Moderate (8) | Hereditary thrombocytopenia with early-onset myelofibrosis (AD) | MONDO:0014837 | Thrombocytopenia 6 (#616937) | − |
| STIM1 * | Definitive (17) | tubular aggregate myopathy (AD) | MONDO:0008051 | Myopathy, tubular aggregate, 1 (#160565) Stormorken syndrome (#185070) |
Stormorken syndrome (including the thrombocytopenia phenotype) was found to form a clinical continuum of phenotypic severity with Tubular Aggregate Myopathy and so these were curated jointly by the ClinGen Congenital Myopathies GCEP (https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_9419adda-b3fb-4c2d-8562-6a0318260bbd-2021-04-01T160000.000Z). Of note STIM1 is also implicated in Immunodeficiency type 10 (MIM3#612783), however due to differences in molecular mechanism, inheritance pattern and phenotypic variability it was not considered in this curation or within the purview of the HT GCEP. |
| STXBP2 * | Definitive (15.5) | familial hemophagocytic lymphohistiocytosis 5 | MONDO:0013135 | Hemophagocytic lymphohistiocytosis, familial, 5, with or without microvillus inclusion disease (#613101) | Curation was completed by the ClinGen Primary Immune Regulatory Disorders GCEP (https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_0b5c9256-89e0-4f97-a7ca-dd07bdd237f9-2023-09-19T160000.000Z) |
| TBXA2R | Moderate (9.5) | qualitative platelet defect (AD) | MONDO:0001197 | − | − |
| TBXAS1 | Moderate (7.5) | ghosal hematodiaphyseal dysplasia (AR) | MONDO:0009274 | Ghosal hematodiaphyseal syndrome (#231095) | − |
| THBD | Moderate (9) | thrombomodulin-related bleeding disorder (AD) | MONDO:0013775 | − | Differences in inheritance pattern correspond to differences in variant type (truncating dominant variants and missense recessive variants) that result in either |
| THBD | Limited (8) | thrombomodulin-related bleeding disorder (AR) | MONDO:0013775 | − | increased or decreased plasma thrombomodulin, respectively. As such these were considered distinct disease entities. |
| THPO | Moderate (7.9) | Congenital amegakaryocytic thrombocytopenia (AR) | MONDO:0011469 | − | Given differences in the phenotype, inheritance pattern, and molecular mechanism (loss of function versus gain of function) underlying the two disease entities, these were curated separately. |
| THPO | Moderate (9.1) | thrombocythemia 1 (AD) | MONDO:0008554 | Thrombocythemia 1 (#187950) | |
| TPM4 | Moderate (7) | autosomal dominant macrothrombocytopenia (AD) | MONDO:0015372 | − | − |
| TUBB1 | Definitive (18) | macrothrombocytopenia, isolated, 1, autosomal dominant (AD) | MONDO:0800047 | Macrothrombocytopenia, autosomal dominant, TUBB1-related (#613112) | − |
| VIPAS39 | Definitive (15.5) | arthrogryposis, renal dysfunction, and cholestasis 2 (AR) | MONDO:0013255 | Arthrogryposis, renal dysfunction, and cholestasis 2 (#613404) | − |
| VKORC1 | Moderate (7) | vitamin K-dependent clotting factors, combined deficiency of, type 2 (AR) | MONDO:0011837 | Vitamin K-dependent clotting factors, combined deficiency of, 2 (#607473) | − |
| VPS33B | Definitive (17.5) | arthrogryposis, renal dysfunction, and cholestasis 1 (AR) | MONDO:0008822 | Arthrogryposis, renal dysfunction, and cholestasis 1 (#208085) | − |
| VWF | Definitive (18) | hereditary von Willebrand disease (AD/AR-LOF) | MONDO:0019565 | von Willebrand disease, type 1 (#193400) von Willebrand disease, type 3 (#277480) von Willebrand disease, types 2A, 2M, and 2N (#613554) |
Differences in molecular mechanisms (gain of function in type 2B versus inactivating and loss of function in types 1, 2A, 2M, 2N, and 3) and phenotypic variability (type 2B having the unique phenotypes of thrombocytopenia, increased platelet |
| VWF | Definitive (18) | von Willebrand disease type 2B (AD-GOF | MONDO:0015629 | von Willebrand disease, type 2B (#613554) | volume, and enhanced ristocetin-induced platelet aggregation) were considered to separate curations for the disease entities hereditary von Willebrand disease (curated for the predominant autosomal dominant form, though recessive type 2N and type 3 were also included) and von Willebrand disease type 2B. |
| WAS * | Definitive (18) | Wiskott-Aldrich syndrome (XL) | MONDO:0010518 | Thrombocytopenia, X-linked (#313900) Thrombocytopenia, X-linked, intermittent (#313900) Wiskott-Aldrich syndrome (#301000) |
WAS was curated by the ClinGen Hereditary Cancer GCEP (https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_a936b3ba-f1d0-4f14-bd56-14f64ad4de3a-2018-10-12T205425.459Z) for Wiskott-Aldrich syndrome (including the thrombocytopenia phenotype). Of note WAS is also implicated in Neutropenia, severe congenital, X-linked (MIM#300299), which was not considered within this curation due to differences in phenotype and molecular mechanism and is outside the purview of the HT GCEP. |
Genes curated by alternate ClinGen Gene Curation Expert Panel
Abbreviations: AD, autosomal dominant, AR, autosomal recessive, GOF, gain of function, LOF, loss of function, SD, semi-dominant, XL, X-linked
FIGURE 1.
(A) Distribution of gene-disease classifications with percentages of gene-disease relationships at each clinical validity cassification. A total of 101 gene-disease relationships were assessed. (B) Distribution of scores for genetic (black) and experimental (orange) evidence within each gene-disease cassification. Dashed lines indicate the maximum score for each category of evidence, and Xs indicate the mean scores.
FIGURE 2.
Hemostasis and thrombosis Definitive gene-disease classifications with genetic and experimental scores. Genetic and experimental points are depicted by black and orange bars, respectively. Total points for each classification are as follows: Limited (0.1–6 points; light blue), Moderate (7–11 points; medium blue), and Definitive (12–18 points; dark blue). The Strong classification is not depicted because there were no gene-disease relationships in this category.
The non-Definitive classifications earned 1–12 points and lacked evidence in either or both of the genetic or experimental categories (Figure 3). Twenty-six gene-disease pairs received a Moderate classification; a Moderate classification typically means that there is emerging but insufficient evidence for the validity of the gene-disease relationship at the time to classify as Strong, although it is likely to reach Strong/Definitive in time.[7] In the Moderate classification all genes had both genetic (4.7 +/− 1.7 points) and experimental (3.7 +/− 1.4 points) evidence. Seven gene-disease pairs reached only the Limited classification with genetic evidence of 2.8 +/− 1.8 points and experimental evidence of 2.8 +/− 2.2 points (Figure 1B).
FIGURE 3.
Hemostasis and thrombosis non-Definitive gcne-disease classifications with genetic and experimental scores. Genetic and experimental points are depicted by black and orange bars, respectively. Total points for each classification are as follows: Limited (0.1–6 points; light blue). Moderate (7–11 points; medium blue), and Definitive (12–18 points; dark blue). The Strong classification is not depicted because there were no genc-disease relationships in this category. Classifications modified for either insufficient genetic or experimental evidence are indicated to the right of the bars (M, moderate; L, limited).
DISCUSSION
The mission of ClinGen is to curate the clinical genome in order to improve patient care. The HT GCEP has furthered this mission through the aggregation of structured evidence regarding genetic conditions of BTPDs and the genes that cause them. One hundred one gene-disease relationships were curated and assigned a clinical validity classification. The majority of the genes investigated are well established, and as expected, resulted in a Definitive classification within our validation. In addition to the 67% Definitive another 26% were Moderate classifications which are expected to increase to Definitive with time and additional evidence; these curations will be re-evaluated every two years to maintain current gene-disease validity classifications. The latest information is regularly updated on the ClinGen website (www.clinicalgenome.org).
The majority, 85%, of gene disease relationships scored clearly within an appropriate validity classification and were approved as such by the HT GCEP. However, scores at the boundary of a classification and/or lacking significant evidence in either the genetic or experimental categories, were further scrutinized for potential classification modifications. Two gene disease relationships had curation scores at the lower boundary of the Strong/Definitive classification (12 points). One curation, for FYB1 related thrombocytopenia, received 6 points in both experimental and genetic evidence. Robust evidence was included across the experimental evidence categories; the gene disease relationship was supported by its restricted expression in hematopoietic cells, [8] its function as an adaptor protein involved in integrin activation, [9] the resulting defect in platelet spreading when this function is disrupted, [10,11] and both conventional and conditional knockout mouse models that recapitulate disease. [10,12] For genetic evidence, two probands have been reported, [11,13] and because each proband was homozygous for a null variant 2 points were awarded for each and an additional 2 points were scored for segregation of the variants in affected family members. Thus, the curation score reached the lower boundary of the Strong classification, however expert opinion was that with only two families reported, both consanguineous, a Moderate classification is appropriate until a third proband is identified for this gene disease relationship. On the other hand BLOC1S6 related Hermansky-Pudlak syndrome (HPS) also scored 12 points, at the lower boundary of the Strong/Definitive classification, but maintained a Definitive classification due to more robust genetic evidence from five probands. A modest 3 points were awarded for experimental evidence, based on protein interactions with other known HPS related genes, [14] and a mouse model that recapitulates HPS. [15] The BLOC1S6 curation originally received a Moderate classification in 2020, with 7 points of genetic evidence, from four probands, [16–19] adding to the 3 points of experimental evidence for 10 points in total. However, an additional proband was reported in 2021, [20] adding 2 points to bring the total to 12 points, and a classification of Definitive was approved by the HT GCEP in 2022. The importance of re-evaluation and additional case reports is exemplified by the curation of BLOC1S6, which was reclassified from Moderate to Definitive with the addition of a newly published case during the course of the GCEP’s three year working period.
Similarly, several genes (CYCS, HRG, PLAU, PLA2G4A, P2RY12-AD, TPM4, and VKORC1) scored at the lower boundary of the Moderate classification (6.5–7 points). Each of these genes, except CYCS, had at least a modest experimental evidence score (≥3) and all, except PLAU, also had genetic evidence from ≥3 unrelated probands, thus P2RY12-AD, TPM4, VKORC1, HRG, PLA2G4A each received a Moderate clinical validity classification, while CYCS and PLAU were considered for downgrading to Limited. CYCS was first reported in relation to autosomal dominant thrombocytopenia in 2008, [21] and received a score between the Limited and Moderate thresholds (6.8 points). At least 15 probands have been reported, all of whom harbor heterozygous missense variants in CYCS. [21–26] Most of these variants have not been functionally characterized, resulting in the minimum score of 0.1 points each, totaling 6.3 points. Despite 6.3 points of genetic evidence, expert opinion was that a Limited classification was appropriate due to the lack of experimental evidence (0.5 points) tying the gene to a disease mechanism. While functional alteration of platelet formation was shown in patient cells, [27] the normal function of CYCS in relation to platelet formation remains unclear. Until additional evidence, such as a model organism, is produced, these types of curations will remain Limited. On the other hand, the PLAU-Quebec platelet disorder curation has only one scored proband, but it was identified in a large family from the Canadian province of Quebec and has been described in at least 3 dozen members of this single family.[28,29] Alongside substantial exerpimental evidence (4 points),cosegregation within this large pedigree was sufficient genetic evidence (3 points), without additional probands, to maintain the Moderate classification. Indeed, it only lacks a Definitive classification because all reported cases are within one family, constraining the genetic evidence total.
Two additional curations did receive modified classifications due to the lack of reported probands. Both AP3D1 and THBD-AR had point totals of 8 (with 4 or 6 points of experimental evidence, respectively), which reached the threshold for a Moderate classification, however with just two probands reported for each gene-disease relationship, expert opinion was that the genetic evidence, of 2 to 4 points, was insufficient for a Moderate classification. As with the FYB1 curation, the lack of probands for genetic evidence resulted in the classification being downgraded one level, to a final classification of Limited for AP3D1 and THBD-AR.
The remaining four genes (HOXA11, PTGS1, RAP1B and F9-GoF) with their respective disease relationships scored in the Limited classification. Data have shown that most genes in the Limited category, particularly those that remain Limited for more than 5 years, do not accumulate evidence in the future to move to a higher classification. [7] Four of the Limited curations are for recent disease gene discoveries (AP3D1, PTGS1, RAP1B and THBD-AR), between 2016 and 2020, and although more genetic and/or experimental evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. Another recently identified disease gene, GNE [30] was originally curated, in 2020, with four probands (scoring 4.6 points), and while its role in autosomal recessive isolated macrothrombocytopenia is supported by its function in the sialylation pathway, which is known to affect platelet lifespan,[31,32] there was insufficient experimental evidence (0.5 points) to score above the Limited classification. Subsequent publications [33–37] resulted in a significant amount of additional genetic evidence, with five probands added to the curation in 2022, totaling 7.6 points genetic evidence and reclassifying this gene-disease relationship as Moderate.
The two additional Limited classifications for HOXA11 and F9-GoF, with their respective disease entities, each have just one proband publication, greater than five years old, from 2000 or 2009, respectively.[38,39] HOXA11, related to radioulnar synostosis with amegakaryocytic thrombocytopenia, one frameshift variant has been reported in two probands in a single publication, segregating in four additional affected family members.[38] This gene-disease relationship is supported by its expression during limb development and a mouse model with skeletal malformations in the limbs,[40] as well as its expression and function in early hematopoietic development.[41] F9 and thrombophilia due to increased factor IX plasma clotting activity, an X-linked disorder, was first reported based on one missense variant with a suspected gain of function mechanism, identified in two siblings.[39] This is the only family and only variant considered in the curation, while a few other polymorphisms, including F9 Malmo, have been reported in association with risk of deep vein thrombosis,[42] these variants have not been included in the curation which only considered monogenic disease. Of note, F9-LoF has been evaluated in relation to hemophilia B, reaching a Definitive classification. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts these two Limited gene-disease relationships. Replication of the gene-disease relationships is necessary to confirm more than a Limited classification. These Limited curations will be re-evaluated every three years to maintain current gene-disease validity classifications. In this regard, the ClinGen HT GCEP recommends clinicians/investigators publish new cases of rare variants, even if the gene-disease relation has already been reported, and journal editors to allow these publications, in order to reach a Definitive classification. Clinicians/investigators can consult clinicalgenome.org, or access gene curation results through The Gene Curation Coalition (thegencc.org) database, [43] to determine if their gene of interest has reached the Definitive threshold.
While most genes were evaluated for a single gene-disease relationship, the ClinGen Lumping and Splitting process identified 12 genes (F2, F5, F9, F12, GP1BA, ITGA2B, ITGB3, MPL, P2RY12, THBD, THPO, VWF) each related to two distinct diseases within the purview of the HT GCEP (Table 1). The hemostatic system is a balance between pro- and anti-hemostatic forces and disruption of this balance can cause either thrombosis or bleeding, depending on how the scale is tipped. For this reason inactivating versus activating mutations in the same gene (i.e., F2, F5, F9, MPL, THPO) can cause either a bleeding/coagulation disorder or a thrombotic disorder respectively, generally correlated with differences in recessive versus dominant inheritance patterns. Other genes (i.e., GP1BA, ITGA2B, ITGB3, P2RY12, THBD, VWF) involved in platelet function were also split due to differences in inactivating versus activating molecular mechanisms with recessive versus dominant inheritance, although diseases of both mechanisms may result in bleeding phenotypes. Seven additional gene-disease relationships (i.e., FGA, FGB, FGG, F11, PROC, PROS1, SERPINC1) were associated with both monoallelic and biallelic cases but for these cases all were inactivating mutations (except F11 which had both biallelic loss of function and dominant negative variants related to congenital factor XI deficiency); here the difference in the inheritance patterns was representative of a continuum of disease in a single disease entity and was curated using the inheritance pattern descriptor of semidominant.
Based on the previous work of SSC-GinTH, each of these 89 genes are considered a TIER1 gene on the ThromboGenomics high-throughput sequencing panel, given their relationship to at least one BTPD. [23] Here these genes were put through the rigor of the ClinGen clinical validity curation process, resulting in an agreement that all genes are categorized in levels of supportive evidence, however, the TIER1 genes spanned the Definitive, Moderate, and Limited classifications. Moving forward the HT GCEP will continue to evaluate novel genes put forward by the SSC-GinTH, as their gene list is re-assessed at the yearly International Society on Thrombosis and Haemostasis (ISTH) meeting, including those currently considered TIER2 with only a single small pedigree and little to no functional studies. The main goal of ClinGen is to generate a public resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This work will inform gene panel recommendations for clinical testing, highlighting the importance of assessing gene-disease clinical validity in order to facilitate variant interpretation and diagnosis for patients with BTPDs.
ACKNOWLEDGMENTS
The ClinGen Hemostasis/Thrombosis Gene Curation Expert Panel would like to thank Rutendo Mapeta for her contribution to some curations, as well as Marie-Christine Morel-Kopp and the ClinGen Gene Curation Working Group for review of the manuscript. Research reported in this publication was supported by the National Human Genome Research Institute (NHGRI) under award number U41HG009650.
Footnotes
CONFLICTS OF INTEREST
The following authors are an employee, trainee, or consultant for a commercial laboratory offering genetic testing related to disorders of hemostasis/thrombosis: L.B., K.F., P.G., C.K., J.P.B., M.S., J.Z. The following authors have made substantial contributions to the literature on gene-disease relationships relevant to this work: L.B., K.D., K.F., P.G., C.K., M.L., K.M., P.M., N.M., J.P.B., N.S., K.Z. Additionally, K.F. chairs the SSC genomics in thrombosis and hemostasis of the ISTH. The other authors declare no conflicts of interest.
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