rs886039394
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PP3_StrongPP5_Very_Strong
The NM_000215.4(JAK3):c.1765G>A(p.Gly589Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000355 in 1,407,352 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. G589G) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000215.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAK3 | NM_000215.4 | c.1765G>A | p.Gly589Ser | missense_variant | Exon 13 of 24 | ENST00000458235.7 | NP_000206.2 | |
JAK3 | XM_047438786.1 | c.1765G>A | p.Gly589Ser | missense_variant | Exon 13 of 24 | XP_047294742.1 | ||
JAK3 | XM_011527991.3 | c.1765G>A | p.Gly589Ser | missense_variant | Exon 13 of 14 | XP_011526293.2 | ||
JAK3 | XR_007066796.1 | n.1815G>A | non_coding_transcript_exon_variant | Exon 13 of 20 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000355 AC: 5AN: 1407352Hom.: 0 Cov.: 32 AF XY: 0.00000288 AC XY: 2AN XY: 695120
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
T-B+ severe combined immunodeficiency due to JAK3 deficiency Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 25, 2023 | This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 589 of the JAK3 protein (p.Gly589Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with severe combined immunodeficiency (PMID: 14615376, 33040328). ClinVar contains an entry for this variant (Variation ID: 265205). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt JAK3 protein function. Experimental studies have shown that this missense change affects JAK3 function (PMID: 14615376). For these reasons, this variant has been classified as Pathogenic. - |
Severe combined immunodeficiency disease Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Sep 20, 2024 | Variant summary: JAK3 c.1765G>A (p.Gly589Ser) results in a non-conservative amino acid change located in the Protein kinase domain (IPR000719) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The frequency data for this variant in gnomAD is considered unreliable, as metrics indicate poor data quality at this position. c.1765G>A has been reported in the literature in homozygous and compound heterozygous individuals affected with Severe Combined Immunodeficiency (El Hawary_2021, El Hawary_2022). These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in abrogation of JAK3 kinase activity (Roberts_2004). The following publications have been ascertained in the context of this evaluation (PMID: 33040328, 35482138, 14615376). ClinVar contains an entry for this variant (Variation ID: 265205). Based on the evidence outlined above, the variant was classified as likely pathogenic. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Feb 01, 2016 | The G589S pathogenic variant in the JAK3 gene has been reported previously in the homozygous state in association with Severe Combined Immunodeficiency (SCID) (Roberts et al., 2004; Pasic et al., 2014). The G589S variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. G589S is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This variant is located in the conserved JH2 domain of the JAK3 protein, and in vitro functional studies showed that this variant disrupts the normal catalytic functions of the protein (Roberts et al., 2004). - |
Adenoid cystic carcinoma Other:1
-, no assertion criteria provided | research | Genome Sciences Centre, British Columbia Cancer Agency | Nov 13, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at