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Variant: NM_000215.4(JAK3):c.2291C>T (p.Pro764Leu)

CA9301631

863482 (ClinVar)

Gene: JAK3
Condition: T-B+ severe combined immunodeficiency due to JAK3 deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: bfaa4a3a-7ea8-4d5b-8db9-c022851f5cd1
Approved on: 2024-02-21
Published on: 2024-02-21

HGVS expressions

NM_000215.4:c.2291C>T
NM_000215.4(JAK3):c.2291C>T (p.Pro764Leu)
NC_000019.10:g.17834630G>A
CM000681.2:g.17834630G>A
NC_000019.9:g.17945439G>A
CM000681.1:g.17945439G>A
NC_000019.8:g.17806439G>A
NG_007273.1:g.18362C>T
ENST00000526008.6:c.*848C>T
ENST00000696967.1:n.1468C>T
ENST00000696970.1:n.946C>T
ENST00000458235.7:c.2291C>T
ENST00000458235.5:c.2291C>T
ENST00000527031.5:n.2278+2097C>T
ENST00000527670.5:c.2291C>T
ENST00000534444.1:c.2291C>T
NM_000215.3:c.2291C>T

Uncertain Significance

Met criteria codes 1
PM2_Supporting
Not Met criteria codes 5
BS2 BS1 PM5 PS1 BA1

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 NM_000215.4(JAK3):c.2291C>T variant in JAK3 is a missense variant predicted to cause substitution of proline by leucine at amino acid 764 (p.Pro764Leu). The filtering allele frequency (the upper threshold of the 95% CI of 3/33008) of the c.2291C>T variant is 0.00002408 for African/African American subpopulation chromosomes by gnomAD v.4.0.0, which is lower than the threshold (<0.000115) defined by the ClinGen Severe Combined immunodeficiency Disease Variant Curation Expert Panel (SCID VCEP) for JAK3 variants (PM2_supporting). One patient was found reported on Clinvar; however, the affected status is unknown (VCV000863482.6). This variant does not meet the criteria to be classified as pathogenic, likely pahogenic, benign or likely benign for T-B+ severe combined immunodeficiency due to JAK3 deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID JAK3 VCEP (PM2_supporting) ; therefore is classified as a variant of unknown significance (VUS) for this disease. (VCEP specifications version 1).
Met criteria codes
PM2_Supporting
The total Grpmax Filtering AF (the upper threshold of the 95% confidence) is 0.00002408 in gnomAD v 4.0.0), which is a lower than the threshold ([<0.000115]) defined by the ClinGen Severe Combined Immunodeficiency Disease Variant Curation Expert Panel (SCID VCEP) for JAK3 variants (PM2_supporting).
Not Met criteria codes
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
PM5
Not other P/LP variant reported in this position
PS1
Not reported
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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