Table 2.
Overview of variants reported to the medical specialist from both samples by clinical laboratory geneticists from participating centers with classification per center in parentheses. Gene names, diseases, MIM numbers, and variants are mentioned in separate columns, followed by columns indicating whether the variant was identified and reported to a medical specialist in the specific centers. Plus signs in bold indicate the original sample site. Variants are described according to HGVS nomenclature.
| Gene name | Disease, form of inheritance | MIM number | Variant (HGVS genomic, cDNA, and protein level) | Analyzing center | ||||
|---|---|---|---|---|---|---|---|---|
| Site 1 | Site 2 | Site 3 | Site 4 | |||||
| Sample site 1A* | PSTPIP1 | PAPA (pyogenic sterile arthiritis, pyoderma gangrenosum, and acne) syndrome, AD | 604416 |
NC_000015.9:g.77323533C > T heterozygote NM_003978.3:c.655C > T NP_003969.2:p.(Gln219*) |
+(VUS)** | +(LP) | +(VUS) | +(VUS) |
| MEFV | Familial mediterranean fever, AD/AR | 134610; 249100 |
NC_000016.9:g.(?_3293841)_(3296472_?)’ dup heterozygote NM_000243.2:c.(?_1610 + 53)_(1792 + 19_?)dup NP_000234.1: p.(?) |
+(VUS) | − | – | – | |
| RFXANK | MHC class II deficiency complementation group B, AR | 209920 |
NC_000019.9:g.19304942 G > A heterozygote NM_003721.2:c.187G > A NP_003712.1:p.(Ala63Thr) |
− | +(LP) | – | – | |
| Sample site 1B | IFIH1 | Aicardi–Goutieres syndrome 7, AD | 615846 |
NC_000002.11:g.163124688 G > A heterozygote NM_022168.3:c.2716 C > T NP_071451.2: p.(Leu906Phe) |
− | +(VUS) | +(VUS) | – |
| Sample site 2A | STX11 | Hemophagocytic lymphohistiocytosis, familial, 4, AR | 603552 |
NC_000006.11:g.144508133_144508140delinsTGG homozygote NM_003764.3:c.369_376delinsTGG NP_003755.2: p.(Val124Glyfs*60) |
+(P) | +(P) | + (P) | +(P) |
| Sample site 2B | – | – | – | − | − | – | – | |
| Sample site 3A | BTK | Agammaglobulinemia, X-linked 1; isolated growth hormone deficiency, type III, with agammaglobulinemia, XLR | 300755; 307200 |
NC_000023.10:g.100609676 G > A hemizygote NM_000061.2:c.1573 C > T NP_000052.1:p.(Arg525*) |
+(P) | +(LP) | +(P) | +(P) |
| NFKB2 | Common variable immunodeficiency, 10, AD | 615577 |
NC_000010.10:g.104161009 C > T heterozygote NM_001288724.1:c.2144 C > T NP_001275653.1:p.(Ser715Leu) |
− | +(VUS) | +(VUS) | – | |
| Sample site 3B | – | – | – | – | − | − | – | – |
| Sample site 4A | UNC13D | Hemophagocytic lymphohistiocytosis, familial, 3, AR | 608898 |
NC_000017.10:g.73827397_73827400delGTGA homozygote NM_199242.2:c.2477_2480delTCAC NP_954712.1:p.(Leu826Glnfs*20) |
+(P) | +(P) | +(P) | +(P) |
| ADAR | Aicardi–Goutieres syndrome 6, AR; dyschromatosis symmetrica hereditaria, AD | 615010; 127400 |
NC_000001.10:g.154557340T > C heterozygote NM_001111.4:c.3623A > G NP_001102.2:p.(Tyr1208Cys) |
− | +(VUS) | +(VUS) | – | |
| LTBP3 | Dental anomalies and short stature, AR; geleophysic dysplasia 3, AD | 601216; 617809 |
NC_000011.9:g.65307562A > C heterozygote NM_001130144.2:c.3307T > G NP_001123616.1:p.(Ser1103Ala) |
− | +(VUS) | +(VUS) | – | |
| GINS1 | Immunodeficiency 55, AR | 617827 |
NC_000020.10:g.25394425G > A NC_000020.10(NM_021067.4):c.76-1G > A NP_066545.3: p.(?) |
− | − | +(LP) | – | |
| Sample site 4B | PLEKHM1 | Osteopetrosis, autosomal recessive 6, AR; osteopetrosis, autosomal dominant 3, AD | 611497; 618107 |
NC_000017.10:g.43528096C > G NM_014798.2:c.2531G > C NP_055613.1:p.(Arg844Pro) |
− | +(VUS) | – | – |
*The description of A and B indicates the samples with confirmed genetic diagnosis and unknown genetic diagnosis, respectively.
**Variant was initially classified as pathogenic in its own center (Site 1).
AD autosomal dominant, AR autosomal recessive, XLR X-linked recessive.