The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000215.4(JAK3):c.187A>G (p.Ile63Val)

CA9302225

252471 (ClinVar)

Gene: JAK3
Condition: T-B+ severe combined immunodeficiency due to JAK3 deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 641ea27c-92d8-4753-b95d-a6ae575c37d6
Approved on: 2024-01-23
Published on: 2024-01-23

HGVS expressions

NM_000215.4:c.187A>G
NM_000215.4(JAK3):c.187A>G (p.Ile63Val)
NC_000019.10:g.17843898T>C
CM000681.2:g.17843898T>C
NC_000019.9:g.17954707T>C
CM000681.1:g.17954707T>C
NC_000019.8:g.17815707T>C
NG_007273.1:g.9094A>G
ENST00000458235.7:c.187A>G
ENST00000458235.5:c.187A>G
ENST00000526008.5:n.287A>G
ENST00000527031.5:n.277A>G
ENST00000527670.5:c.187A>G
ENST00000528293.1:n.323+336A>G
ENST00000534444.1:c.187A>G
NM_000215.3:c.187A>G
More

Likely Benign

Met criteria codes 2
BS1 BS2_Supporting

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 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Severe Combined Immunodeficiency Disease VCEP
The c.187A>G (NM_000215.4) variant in JAK3 is a missense variant predicted to cause the substitution of Isoleucine by Valine at amino acid 63 (p.Ile63Val). The popmax filtering allele frequency (the upper threshold of the 95% CI) of this variant is 0.00007135 (105/1179936 alleles) for European (non-Finnish) chromosomes by gnomAD v.4, which is lower than the ClinGen SCID VCEP threshold (<0.000115) for PM2_Supporting; However, the highest MAF in the Ashkenazi Jewish population is 0.007061 (209/29600 alleles), which is above the SCID VCEP established threshold of >0.00100 for BS1. As this population is not known to have a higher prevalence, this is considered to meet BS1. One homozygote is described in gnomAD v.4 in the Ashkenazi Jewish population (BS2_Supporting). To our knowledge, this variant has not been reported in the literature in individuals affected with JAk3-SCID/related conditions or in functional studies. In summary, this variant meets the criteria to be classified as Likely Benign for autosomal recessive T-B+ severe combined immunodeficiency due to JAK3 deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: BS1 and BS2_Supporting (VCEP specifications version 1.0).
Met criteria codes
BS1
The popmax filtering allele frequency (the upper threshold of the 95% CI) of this variant is 0.00007135 (105/1179936 alleles) for European (non-Finnish) chromosomes by gnomAD v.4, which is lower than the ClinGen SCID VCEP threshold (<0.000115) for PM2_Supporting; However, the highest MAF in the Ashkenazi Jewish population is 0.007061 (209/29600 alleles), which is above the SCID VCEP established threshold of >0.00100 for BS1. As this population is not known to have a higher prevalence, this is considered to meet BS1.
BS2_Supporting
One homozygote is described in gnomAD v.4, in the Ashkenazi Jewish population; (BS2_Supporting).
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.
¤ Powered by BCM's Genboree.