The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000215.4(JAK3):c.1333C>T (p.Arg445Ter)

CA120306

9364 (ClinVar)

Gene: JAK3
Condition: T-B+ severe combined immunodeficiency due to JAK3 deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 5df6ef2d-fd3f-47e1-97ae-fd5a465806ea
Approved on: 2024-06-13
Published on: 2024-06-13

HGVS expressions

NM_000215.4:c.1333C>T
NM_000215.4(JAK3):c.1333C>T (p.Arg445Ter)
NC_000019.10:g.17839585G>A
CM000681.2:g.17839585G>A
NC_000019.9:g.17950394G>A
CM000681.1:g.17950394G>A
NC_000019.8:g.17811394G>A
NG_007273.1:g.13407C>T
ENST00000526008.6:c.1333C>T
ENST00000696967.1:n.510C>T
ENST00000458235.7:c.1333C>T
ENST00000458235.5:c.1333C>T
ENST00000526008.5:n.1433C>T
ENST00000527031.5:n.1423C>T
ENST00000527670.5:c.1333C>T
ENST00000528705.1:n.682C>T
ENST00000534444.1:c.1333C>T
NM_000215.3:c.1333C>T

Pathogenic

Met criteria codes 3
PVS1 PP4_Moderate PM2_Supporting
Not Met criteria codes 1
PP3

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.1333C>T (p.Arg445Ter) (NM_000215.4) variant in JAK3 is a nonsense variant observed to cause a premature stop codon in a gene in which loss-of-function is an established disease mechanism (PVS1). The filtering allele frequency in gnomAD v4.1.0 is 0.0000002800 (2/1179170 alleles) in European (non-Finnish) population, which is lower than the ClinGen SCID VCEP threshold (<0.000115) for PM2_Supporting. Additionally, no homozygotes have been observed in gnomAD. (PM2_Supporting). At least one patient in the literature, LP1, presents JAk3 expression and phosphorylation absent; STAT5a phosphorylation is absent, and STAT6 phosphorylation is reduced. Thus: *Reduced or constitutive cytokine-induced tyrosine phosphorylation in patient cells (1pt) + *Reduced cytokine-induced phosphorylation of STAT5 in patient-derived T or B cells (1pt). Total 2 points, PP4_Moderate (PMID 9618765). In summary, this variant meets the criteria to be classified as Pathogenic 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: PVS1, PM2_Supporting, and PP4_Moderate (VCEP specifications version 1).
Met criteria codes
PVS1
The c.1333C>T (p.Arg445Ter) (NM_000215.4) variant in JAK3 is a nonsense variant predicted to cause a premature stop codon in a gene in which loss-of-function is an established disease mechanism (PVS1). PMID 10900158
PP4_Moderate
At least one patient in the literature, LP1, presents JAk3 expression and phosphorylation absent; STAT5a phosphorylation is absent and STAT6 phosphorylation is reduced. Thus: *Reduced or constitutive cytokine-induced tyrosine phosphorylation in patient cells (1pt) + Reduced cytokine-induced phosphorylation of STAT5 in patient-derived T or B cells (1pt). Total 2 points, PP4_Moderate (PMID 9618765).
PM2_Supporting
The filtering allele frequency in gnomAD v4.1.0 is 0.0000002800 (2/1179170 alleles) in European (non-Finnish) population, which is lower than the ClinGen SCID VCEP threshold (<0.000115) for PM2_Supporting. Additionally, no homozygotes have been observed in gnomAD. (PM2_Supporting).
Not Met criteria codes
PP3
LRT and FATHM-MKL predict neutral impact; MutationTaster is disease causing Automatic. No consistent and clear pathogenic prediction, Not met
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