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.1837C>T (p.Arg613Ter)

CA306130937

644288 (ClinVar)

Gene: JAK3 (HGNC:3718)
Condition: T-B+ severe combined immunodeficiency due to JAK3 deficiency (MONDO:0010938)
Inheritance Mode: Autosomal recessive inheritance
UUID: 6c260c2f-fbe4-45ba-8d5b-2c8e8d058744
Approved on: 2024-01-17
Published on: 2024-01-17

HGVS expressions

NM_000215.4:c.1837C>T
NM_000215.4(JAK3):c.1837C>T (p.Arg613Ter)
NC_000019.10:g.17836001G>A
CM000681.2:g.17836001G>A
NC_000019.9:g.17946810G>A
CM000681.1:g.17946810G>A
NC_000019.8:g.17807810G>A
NG_007273.1:g.16991C>T
ENST00000458235.7:c.1837C>T
ENST00000458235.5:c.1837C>T
ENST00000527031.5:n.2278+726C>T
ENST00000527670.5:c.1837C>T
ENST00000534444.1:c.1837C>T
NM_000215.3:c.1837C>T
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Pathogenic

Met criteria codes 4
PM3_Supporting PVS1 PP4_Moderate PM2_Supporting
Not Met criteria codes 4
BS2 PM1 PM5 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
The c.1837C>T (p.Arg613Ter) (NM_000215.4) variant in JAK3 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 14/24 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). The filtering allele frequency (the upper threshold of the 95% CI of 3/113712) of the c.1837C>T variant in JAK3 is 0.000007010 for European (non-Finnish) chromosomes by gnomAD 2.1.1, which is lower than the ClinGen SCID VCEP threshold (<0.000115) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). At least one patient with this variant displayed: * Diagnostic criteria for SCID/Leaky SCID/Omenn syndrome met (0.5pt), *T-B+NK- lymphocyte subset profile (0.5pt), and *SCID phenotype corrected by JAK3 gene therapy WITHOUT CNV testing performed (1pt), totalizing 2 points, which is highly specific for SCID (PP4_moderate. PMID: 26321643). This variant has been detected in at least one individual with SCID, which is homozygous for the variant (0.5 pt) (PM3_Supporting. PMID: 26321643). One additional patient was found on Clinvar; however, the affected status is unknown. In summary, this variant meets the criteria to be classified as Pathogenic for autosomal recessive SCID based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: PVS1, PP4_moderate, PM2_supporting and PM3_supporting. (VCEP specifications version 1).
Met criteria codes
PM3_Supporting
This variant has been detected in at least one individual with SCID, which is homozygous for the variant (0.5 pt) (PM3_Supporting. PMID: 26321643).
PVS1
The c.1837C>T (p.Arg613Ter) (NM_000215.4) variant in JAK3 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 14/24 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
PP4_Moderate
At least one patient with this variant displayed: * Diagnostic criteria for SCID/Leaky SCID/Omenn syndrome met (0.5pt), *T-B+NK- lymphocyte subset profile (0.5pt), and *SCID phenotype corrected by JAK3 gene therapy WITHOUT CNV testing performed (1pt), totalizing 2 points, which is highly specific for SCID (PP4_moderate. PMID: 26321643).
PM2_Supporting
The filtering allele frequency (the upper threshold of the 95% CI of 3/113712) of the c.1837C>T variant in JAK3 is 0.000007010 for European (non-Finnish) chromosomes by gnomAD 2.1.1, which is lower than the ClinGen SCID VCEP threshold (<0.000115) for PM2_Supporting, and therefore meets this criterion (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
PM1
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
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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