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Variant: NM_000215.4(JAK3):c.2317G>A (p.Val773Ile)

CA9301626

933853 (ClinVar)

Gene: JAK3
Condition: T-B+ severe combined immunodeficiency due to JAK3 deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 1982c3f0-03dd-461d-b050-aef6aceadcde
Approved on: 2024-02-21
Published on: 2024-02-21

HGVS expressions

NM_000215.4:c.2317G>A
NM_000215.4(JAK3):c.2317G>A (p.Val773Ile)
NC_000019.10:g.17834604C>T
CM000681.2:g.17834604C>T
NC_000019.9:g.17945413C>T
CM000681.1:g.17945413C>T
NC_000019.8:g.17806413C>T
NG_007273.1:g.18388G>A
ENST00000526008.6:c.*874G>A
ENST00000696967.1:n.1494G>A
ENST00000696970.1:n.972G>A
ENST00000458235.7:c.2317G>A
ENST00000458235.5:c.2317G>A
ENST00000527031.5:n.2278+2123G>A
ENST00000527670.5:c.2317G>A
ENST00000534444.1:c.2317G>A
NM_000215.3:c.2317G>A

Uncertain Significance

Met criteria codes 1
PM2_Supporting
Not Met criteria codes 6
BA1 PM1 PM5 BS2 BS1 PS1

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
NM_000215.4(JAK3):c.2317G>A variant in JAK3 is a missense variant predicted to cause substitution of valine by isoleucine at amino acid 773 (p.Val773Ile). The total Grpmax Filtering allele frequency (the upper threshold of the 95% confidence) is 0.00004416 for East Asian chromosomes by gnomeAD v 4.0.0, which is lower than the ClinGen SCID JAK3 VCEP threshold [(<0,000115)] for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). This variant has been found in ClinVar; however, the affected status of the patient is unknown (VCV000933853.6) This variant does not meet the criteria to be classified as pathogenic, likely pathogenic, 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 0.00004416 in gnomeAD v 4.0.0, which is lower than the ClinGen SCID JAK3 VCEP threshold [(<0,000115)] for PM2_Supporting, and therefore meets this criterion (PM2_Supporting)
Not Met criteria codes
BA1
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
PM5
No other reported variants in this location
BS2
Not observed in homozygous
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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