The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000215.4(JAK3):c.307C>T (p.Arg103Cys)

CA9302208

384359 (ClinVar)

Gene: JAK3 (HGNC:3718)
Condition: T-B+ severe combined immunodeficiency due to JAK3 deficiency (MONDO:0010938)
Inheritance Mode: Autosomal recessive inheritance
UUID: c85a8c1d-d6af-48a6-a182-a644bdc1ba6c
Approved on: 2026-10-01
Published on: 2026-10-27

HGVS expressions

NM_000215.4(JAK3):c.307C>T (p.Arg103Cys)
NM_000215.4:c.307C>T
NC_000019.10:g.17843778G>A
CM000681.2:g.17843778G>A
NC_000019.9:g.17954587G>A
CM000681.1:g.17954587G>A
NC_000019.8:g.17815587G>A
NG_007273.1:g.9214C>T
ENST00000526008.6:c.307C>T
ENST00000458235.7:c.307C>T
ENST00000458235.5:c.307C>T
ENST00000526008.5:n.407C>T
ENST00000527031.5:n.397C>T
ENST00000527670.5:c.307C>T
ENST00000528293.1:n.324-287C>T
ENST00000534444.1:c.307C>T
NM_000215.3:c.307C>T
More

Likely Pathogenic

Met criteria codes 3
PM2_Supporting PP4 PM3_Strong
Not Met criteria codes 11
PP3 PP2 BA1 PM5 PM4 PM1 BS2 BS1 BP3 BP4 BP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Severe Combined Immunodeficiency Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for JAK3 Version 2.3

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Severe Combined Immunodeficiency Disease VCEP
The c.307C>T (p.Arg103Cys) variant in JAK3 gene, that encodes for Janus kinase 3, has been reported in in compound heterozygous status with Cys227Profs*49 which is classified as pathogenic by the VCEP, in 1 patient with T-B+NK- SCID (PMID: 34173127) [1 pt]. This variant has also been reported along with R445* (Phase unknown) which is classified as pathogenic by the VCEP, in 1 patient [P073] with T-B+ SCID [0.5 pt]. NK cell data not available (PMID: 28747913). In addition, this variant is reported in compound heterozygous status with c.421-6C>T which is a VUS, in 1 patient [P55] with SCID (PMID: 30778343) [0.25pt]. Also reported in compound heterozygous status with p.Arg117His which is a VUS, in a Patient with T-B+NkLow SCID [0.25pt]. Total 2pts so PM3 met. This variant was found in a patient with T-B+NK- lymphocyte subset profile (PMID: 34173127) [0.5pt], in a patient whose diagnosis of Leaky/Atypical SCID was established (PMID: 30778343) [0.5pt] and in one patient whose Targeted gene panel testing was conducted using NGS and no alternative genetic explanation was found (PMID: 30778343) [1pt]. Total 1.5pts so PP4 met. The GrpMax filtering allele frequency of the European (Non-Finnish) population is 0.00000124 which is less than the threshold <0.000115 so PM2_supporting is met. Therefore, the c.307C>T (p.Arg103Cys) variant in JAK3 gene is classified as likely pathogenic, as per the ClinGen Severe Combined Immunodeficiency Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for JAK3 Version 2.3. Evidence: PM3_Strong, PP4, PM2_Supporting
Met criteria codes
PM2_Supporting
The GrpMax filtering allele frequency of the European (Non-Finnish) population is 0.00000124 which is less than the threshold <0.000115 so PM2_supporting is met.
PP4
This variant was found in a patient whose diagnosis of Leaky/Atypical SCID was established [0.5pt] and Targeted gene panel testing was conducted using NGS and no alternative genetic explanation was found (PMID: 30778343) [1pt]. Total 1.5pts
PM3_Strong
Reported in compound heterozygous status with Cys227Profs*49 which is classified as pathogenic by the VCEP, in 1 patient with T-B+Nk- SCID (PMID: 34173127) [1 pt]. Reported along with R445* (Phase unknown) which is classified as pathogenic by the VCEP, in 1 patient [P073] with T-B+ SCID [0.5 pt]. NK cell data not available (PMID: 28747913). Reported in compound heterozygous status with c.421-6C>T which is a VUS, in 1 patient [P55] with SCID (PMID: 30778343) [0.25pt]. Reported in compound heterozygous status with p.Arg117His which is a VUS, in a Patient with T-B+NkLow SCID [0.25pt]. Total 2pts
Not Met criteria codes
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
ClinGen Terms of Use.
¤ Powered by BCM's Genboree.