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.362G>A (p.Arg121His)

CA9302185

532747 (ClinVar)

Gene: JAK3
Condition: T-B+ severe combined immunodeficiency due to JAK3 deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 28829ecb-6faa-4ed5-b4df-26d6b78b5a20
Approved on: 2024-01-23
Published on: 2024-01-23

HGVS expressions

NM_000215.4:c.362G>A
NM_000215.4(JAK3):c.362G>A (p.Arg121His)
NC_000019.10:g.17843438C>T
CM000681.2:g.17843438C>T
NC_000019.9:g.17954247C>T
CM000681.1:g.17954247C>T
NC_000019.8:g.17815247C>T
NG_007273.1:g.9554G>A
ENST00000458235.7:c.362G>A
ENST00000458235.5:c.362G>A
ENST00000526008.5:n.462G>A
ENST00000527031.5:n.452G>A
ENST00000527670.5:c.362G>A
ENST00000528293.1:n.377G>A
ENST00000534444.1:c.362G>A
NM_000215.3:c.362G>A

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.362G>A (NM_000215.4) variant in JAK3 is a missense variant predicted to cause the substitution of Arginine by Histidine at amino acid 121 (p.Arg121His). The popmax filtering allele frequency in gnomAD v.4 is 0.0001262 (based on 11/58232 alleles in the Admixed American population), which is higher than the SCID VCEP established threshold of <0.000115 for PM2_Supporting and lower than >0.00447 (BA1 threshold) and 0.001 (BS1 threshold); However, the highest MAF in the Ashkenazi Jewish population is 0.001469 (43/29280 alleles), which is above the SCID VCEP established threshold of >0.00100. As this population is not known to have a higher prevalence of SCID, this is considered to meet BS1. There is a homozygote in gnomAD v.4 in the Ashkenazi Jewish population (43/29280 alleles), BS2_Supporting. To our knowledge, this variant has not been reported in the literature in individuals affected with JAK3-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 in gnomAD v.4 is 0.0001262 (based on 11/58232 alleles in the Admixed American population), which is higher than the SCID VCEP established threshold of <0.000115 for PM2_Supporting and lower than >0.00447 (BA1 threshold) and 0.001 (BS1 threshold); However, the highest MAF in the Ashkenazi Jewish population is 0.001469 (43/29280 alleles), which is above the SCID VCEP established threshold of >0.00100. As this population is not known to have a higher prevalence of SCID, this is considered to meet BS1.
BS2_Supporting
There is a homozygote in gnomAD v.4 in the Ashkenazi Jewish population (43/29280 alleles), BS2_Supporting. https://gnomad.broadinstitute.org/variant/19-17843438-C-T?dataset=gnomad_r4 w
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.