Table 4.
Clinical implication of genes-associated with novel TASVs in the KPGP9 genome.
| Gene symbol | Genes | Types of TASV (density of the given TE) | Disease (# OMIM. Phenotype) | Inheritance | UMLS ID | Source | No. of SNPs | No. of publications |
|---|---|---|---|---|---|---|---|---|
| Insertion | ||||||||
| PRPH2a | Peripherin 2 | AluYa5 insertion (33.54%) | Retinitis Pigmentosa 7 (#608133) | Autosomal dominant inheritance | umls:C1842475 | CLINVAR, CTD_human, MGD, UNIPROT | 9 | 6 |
| Patterned dystrophy of retinal pigment epithelium (#169150, #608161) | Autosomal dominant inheritance | umls:C1868569 | CLINVAR, CTD_human, UNIPROT | 7 | 4 | |||
| CHOROIDAL DYSTROPHY, CENTRAL AREOLAR 2 (#613105) | Autosomal dominant inheritance | umls:C2751290 | BeFree, CLINVAR, CTD_human, UNIPROT | 4 | 2 | |||
| DMDa | Dystrophin |
AluYa5 insertion (6.24%) |
Muscular Dystrophy, Duchenne (# 310200) | X-linked recessive inheritance | umls:C0013264 | BeFree, CLINVAR, CTD_human, GAD, LHGDN, MGD, ORPHANET, UNIPROT | 175 | 535 |
| Becker Muscular Dystrophy (# 300376) | X-linked recessive inheritance | umls:C0917713 | BeFree, CLINVAR, GAD, MGD, ORPHANET, UNIPROT | 136 | 205 | |||
| DMD-associated dilated cardiomyopathy | X-linked recessive inheritance | umls:C3668940 | BeFree, CLINVAR, CTD_human, GAD, UNIPROT | 213 | 35 | |||
| EPB41 | Erythrocyte membrane protein band 4.1 |
Two AluYa5 insertion (31.54%) |
Hereditary Elliptocytosis 1 | Autosomal dominant inheritance | umls:C2678497 | CLINVAR, CTD_human, MGD | 1 | 29 |
| MTPAPa | Mitochondrial poly(A) polymerase |
AluYa5 insertion (31.51%) |
SPASTIC ATAXIA 4, AUTOSOMAL RECESSIVE (#613672) | Autosomal recessive inheritance | umls:C3150925 | CLINVAR, CTD_human, ORPHANET, UNIPROT | 1 | 1 |
| XDH | Xanthine dehydrogenase |
AluYa5 insertion (4.74%) |
Xanthinuria, Type I | Autosomal recessive inheritance | umls:C0268118 | BeFree, CLINVAR, CTD_human, ORPHANET, UNIPROT | 2 | 8 |
| PDE8Ba | Phosphodiesterase 8B |
AluYa5 insertion (7.07%) |
Striatal Degeneration, Autosomal Dominant (#609161) | Autosomal dominant inheritance | umls:C1836694 | BeFree, CLINVAR, CTD_human, ORPHANET | 0 | 1 |
| CASKa | Calcium/calmodulin-dependent serine protein kinase |
AluYb8 insertion (13.84%) |
Mental Retardation and Microcephaly With Pontine And Cerebellar Hypoplasia (#300749) | X-linked dominant inheritance | umls:C2677903 | CLINVAR, CTD_human, ORPHANET, UNIPROT | 20 | 1 |
| FTOa | Fat mass and obesity associated |
AluYb8 insertion (10.15%) |
Diabetes Mellitus, Non-Insulin-Dependent | Autosomal dominant inheritance | umls:C0011860 | BeFree, CTD_human, GAD, GWASCAT | 61 | 116 |
| Obesity/BODY MASS INDEX QUANTITATIVE TRAIT (# 612460) | Polygenic inheritance | umls:C0028754 | BeFree, CTD_human, GAD, GWASCAT | 36 | 345 | |||
| Growth Retardation, Developmental Delay, Coarse Facies, And Early Death (#612938) | Autosomal recessive multiple congenital | umls:C2752001 | CLINVAR, CTD_human, ORPHANET, UNIPROT | 2 | 1 | |||
| KCNJ6a | Potassium channel, inwardly rectifying subfamily J, member 6 |
AluYb8 insertion (4.7%) |
KEPPEN-LUBINSKY SYNDROME (#614098) | Undefined | umls:C3279800 | BeFree, CLINVAR, ORPHANET, UNIPROT | 2 | 1 |
| RAF1a | Raf-1 proto-oncogene, serine/threonine kinase |
SVA_F insertion (0%) |
Noonan Syndrome/CARDIOMYOPATHY, DILATED (#615916) | Autosomal dominant inheritance | umls:C0028326 | BeFree, CLINVAR, CTD_human, GAD, LHGDN, ORPHANET | 5 | 25 |
| Deletion | ||||||||
| FA2Ha | Fatty acid 2-hydroxylase |
NAHR-ARMDs (22.04%) |
Leukodystrophy, Dysmyelinating, And Spastic Paraparesis With Or Without Dystonia (#612319) | Autosomal recessive inheritance | umls:C3496228 | CTD_human, MGD, ORPHANET, UNIPROT | 0 | 3 |
| EHMT1a | Euchromatic histone-lysine N-methyltransferase 1 |
NAHR-ARMDs (20.66%) |
Kleefstra Syndrome (#610253) | Autosomal dominant inheritance | umls:C0795833 | BeFree, CLINVAR, CTD_human, MGD, UNIPROT | 16 | 8 |
| INSRa | Insulin receptor |
NAHR-ARMDs (40.47%) |
Diabetes Mellitus, Non-Insulin-Dependent | Autosomal dominant inheritance | umls:C0011860 | BeFree, CLINVAR, GAD, RGD, UNIPROT | 11 | 114 |
| Insulin Resistance (#262190) | Autosomal dominant inheritance | umls:C0021655 | CLINVAR, CTD_human, GAD, RGD | 3 | 8 | |||
| Donohue Syndrome (#246200) | Autosomal dominant inheritance | umls:C0265344 | BeFree, CLINVAR, CTD_human, GAD, ORPHANET, UNIPROT | 17 | 46 | |||
| Rabson-Mendenhall Syndrome | Autosomal recessive inheritance | umls:C0271695 | BeFree, CLINVAR, ORPHANET, UNIPROT | 4 | 19 | |||
| Hyperinsulinemic Hypoglycemia, Familial, 5 (#609968) | Autosomal dominant inheritance | umls:C1864952 | CLINVAR, CTD_human, ORPHANET, UNIPROT | 3 | 1 | |||
| SERPINF2 | Serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2 |
NHEJ-ARMDs (38.39%) |
ALPHA-2-PLASMIN INHIBITOR DEFICIENCY | Autosomal recessive inheritance | umls:C2752081 | CLINVAR, MGD, ORPHANET, UNIPROT | 2 | 1 |
| PCCBa | Propionyl CoA carboxylase, beta polypeptide |
NHEJ-L1RMDs (40.53%) |
Propionic acidemia (#606054) | Autosomal recessive inheritance | umls:C0268579 | BeFree, CLINVAR, CTD_human, ORPHANET, UNIPROT | 24 | 23 |
aThe genes annotated in OMIM phenotype data.