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JAK3
Final classification
VUS
PM2
JAK3
c.1531A>G
p.Met511Val
This variant

NM_000215.3:c.1531A>G (p.Met511Val) is a missense variant in exon 11 of JAK3 affecting the pseudokinase domain.

Transcript
NM_000215.3
HGVS · transcript:coding
NM_000215.3:c.1531A>G
GRCh38
chr19:17838301 T>C
GRCh37
chr19:17949110 T>C
Basis ClinGen Severe Combined Immunodeficiency Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for JAK3 Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
ClinGen Severe Combined Immunodeficiency Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for JAK3 Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2 VUS
JAK3 c.1531A>G

NM_000215.3:c.1531A>G (p.Met511Val) is a missense variant in exon 11 of JAK3 affecting the pseudokinase domain. This variant is extremely rare in population databases, with a popmax filtering allele frequency of 8.79e-06 in gnomAD v2.1 and 8.47e-06 in v4.1 (European non-Finnish), and zero homozygotes observed, meeting PM2_Supporting per SCID VCEP specifications (threshold <0.000115).1 The variant is absent from ClinVar, COSMIC, and gnomAD-Canada.2 No variant-specific functional evidence is available. The SCID VCEP-approved PS3_Supporting in vitro kinase assay (PMID:14615376) tested other JAK3 variants but not M511V. The related M511I variant has been characterized in a somatic T-ALL context (PMID:25193870) but these findings cannot be directly extrapolated to germline M511V in SCID.3 No de novo observations, segregation data, or patient phenotype information is available. PM1 does not apply because M511 is not one of the two specified JH2 domain residues (R651, C759).4 Based on SCID VCEP v2.3.0 criteria, the only applicable criterion met is PM2_Supporting. This is insufficient for classification as Likely Pathogenic or Pathogenic. The variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 VUS
Gene diagram · NM_000215.3 · variants mapped to exon structure
JAK3 NM_000215.3
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 12 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is extremely rare in gnomAD (popmax filtering allele frequency 8.79e-06 in European non-Finnish, v2.1; 8.47e-06 in v4.1), well below the SCID VCEP PM2_Supporting threshold of 0.000115, with zero homozygotes observed.
gnomAD v2.1: 1/251496 allelespopmax nfe AF=8.79e-06
Assessed · not applied · 11 not met · 1 not assessed
Pathogenic
PS1 No previously established pathogenic or likely pathogenic variant at the same nucleotide position (c.1531) in JAK3 classified by SCID VCEP specifications.
PS2 No de novo observation reported for this variant in any available source.
PS3 No variant-specific functional evidence available.
PM1 PM1 is defined by the SCID VCEP to include only missense alterations of two specific JH2 pseudokinase domain residues: R651W and C759R (PMID:11668610).
PM5 No previously established pathogenic missense variant at residue 511 classified by SCID VCEP specifications.
PM6 No de novo observation reported for this variant.
PP1 No co-segregation data available for this variant in any source.
PP4 No patient phenotype information is available to calculate the SCID VCEP PP4 patient score (requires diagnostic criteria, gene panel/sequencing results, phosphorylation data, gene therapy confirmation, or lymphocyte subset profile).
Benign
BA1 Popmax filtering allele frequency in gnomAD (8.79e-06) is well below the SCID VCEP BA1 Stand Alone threshold of >0.00447.
BS1 Popmax filtering allele frequency in gnomAD (8.79e-06) is below the SCID VCEP BS1 threshold of >0.00100.
BS2 No homozygotes have been observed in gnomAD (v2.1: 0 hom; v4.1: 0 hom).
BS4 No segregation data available to demonstrate lack of co-segregation with disease.
N/A · 13 PVS1 · PS4 · PP2 · PP3 · PP5 · BS3 · BP1 · BP2 · BP3 · BP4 · BP5 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.19572e-06; MAF= 0.00062%, 10/1614018 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47432e-06; MAF= 0.00085%, 10/1180036 alleles, homozygotes = 0); grpmax FAF= 4.29e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.97621e-06; MAF= 0.00040%, 1/251496 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.78966e-06; MAF= 0.00088%, 1/113770 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00062% · 10 / 1,614,018
0 hom · FAF 0.00043%
European (non-Finnish)
10 / 1,180,036
0.00085%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0004% · 1 / 251,496
0 hom
European (non-Finnish)
1 / 113,770
0.00088%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.25). REVEL score = 0.142. BayesDel score = -0.252601.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. JAK3, a non-receptor tyrosine kinase, is recurrently altered by mutation in hematologic malignancies.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 1 PMID not cited in assessment
25193870 ↗ JAK3 mutants transform hematopoietic cells through JAK1 activation, causing T-cell acute lymphoblastic leukemia in a mouse model. ONCOKB