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JAK3
Final classification
VUS
JAK3 c.1531A>G · p.Met511Val
JAK3

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

Gene
JAK3
Transcript
NM_000215.3
HGVS · transcript:coding
NM_000215.3:c.1531A>G
Consequence
N/A
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 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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