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.349C>T (p.Arg117Cys)

CA16608977

381576 (ClinVar)

Gene: JAK3
Condition: T-B+ severe combined immunodeficiency due to JAK3 deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 5d9a8a9d-57c7-428f-9d6e-75cffc66d758

HGVS expressions

NM_000215.4:c.349C>T
NM_000215.4(JAK3):c.349C>T (p.Arg117Cys)
NC_000019.10:g.17843451G>A
CM000681.2:g.17843451G>A
NC_000019.9:g.17954260G>A
CM000681.1:g.17954260G>A
NC_000019.8:g.17815260G>A
NG_007273.1:g.9541C>T
ENST00000458235.7:c.349C>T
ENST00000458235.5:c.349C>T
ENST00000526008.5:n.449C>T
ENST00000527031.5:n.439C>T
ENST00000527670.5:c.349C>T
ENST00000528293.1:n.364C>T
ENST00000534444.1:c.349C>T
NM_000215.3:c.349C>T

Uncertain Significance

Met criteria codes 3
PM3_Supporting PP4 PM2_Supporting
Not Met criteria codes 4
BS2 BS3 PS3 PM1

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.349C>T (NM_000215.4) variant in JAK3 is a missense variant predicted to cause the substitution of Arginine by Cysteine at amino acid 117 (p.Arg117Cys). The highest population minor allele frequency in gnomAD v2.1.1 is 0.0001755 (1/5698 alleles) in the "Other" population; this frequency will not be considered here as the "Other" population is characterized on gnomAD as a bottleneck population. The second highest MAF is 0.00003543 (1/28224 alleles) in the South Asia population, which is lower than the ClinGen SCID VCEP threshold (<0.000115) for PM2_Supporting, meeting this criterion (PM2_Supporting). No homozygotes have been observed in gnomAD (BS2 is not met). This variant has been described in at least two patients in the literature (PMIDs: 32215810 and 23069490). At least one patient with this variant displayed: *Diagnostic criteria for Leaky SCID 0.5 pts + *Reduced or constitutive cytokine-induced JAK3 tyrosine phosphorylation in patient cells 1 pt + *T-B+NK- lymphocyte subset profile not applied because only IL7R was sequenced, so we can not rule out alternative cause. Total is 1.5 points, PP4_Supporting (PMID: 23069490). The patient is homozygous for this variant (0.5 pts, PM3_Supporting, PMID: 23069490) In summary, this variant meets the criteria to be classified as a variant of uncertain significance 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. Criteria applied: PM2_Supporting, PM3_Supporting, and PP4_Supporting (VCEP specifications version 1.0).
Met criteria codes
PM3_Supporting
one homozygous patient, 0.5pts, PM3_Supporting (PMID: 23069490).
PP4
This variant has been described in ate least two patients in the literature (PMIDs: 32215810 and 23069490). At least one patient with this variant displayed: *Diagnostic criteria for Leaky SCID 0.5 pts + *Reduced or constitutive cytokine-induced JAK3 tyrosine phosphorylation in patient cells 1 pt + *T-B+NK- lymphocyte subset profile not applied because only IL7R was sequenced, so we can not rule out alternative cause. Total is 1.5 points, PP4_Supporting (PMID: 23069490).
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1 is 0.0001755 (1/5698 alleles) in the "Other" population; this frequency will not be considered here as the "Other" population is characterized on gnomAD as a bottleneck population. The second highest MAF is 0.00003543 (1/28224 alleles) in the South Asia population, which is lower than the ClinGen SCID VCEP threshold (<0.000115) for PM2_Supporting, meeting this criterion (PM2_Supporting).
Not Met criteria codes
BS2
No homozygotes have been observed in gnomAD (BS2 is not met).
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
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
Approved on: 2024-01-23
Published on: 2024-01-23
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.