NM_000215.4(JAK3):c.394C>A (p.Pro132Thr) AND Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-negative

Clinical significance:Benign/Likely benign (Last evaluated: Nov 23, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000550265.4

Allele description [Variation Report for NM_000215.4(JAK3):c.394C>A (p.Pro132Thr)]

NM_000215.4(JAK3):c.394C>A (p.Pro132Thr)

Gene:
JAK3:Janus kinase 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.11
Genomic location:
Preferred name:
NM_000215.4(JAK3):c.394C>A (p.Pro132Thr)
Other names:
p.P132T:CCA>ACA
HGVS:
  • NC_000019.10:g.17843406G>T
  • NG_007273.1:g.9586C>A
  • NM_000215.3:c.394C>A
  • NM_000215.4:c.394C>AMANE SELECT
  • NP_000206.2:p.Pro132Thr
  • NP_000206.2:p.Pro132Thr
  • LRG_77t1:c.394C>A
  • LRG_77:g.9586C>A
  • LRG_77p1:p.Pro132Thr
  • NC_000019.9:g.17954215G>T
  • NC_000019.9:g.17954215G>T
  • P52333:p.Pro132Thr
Protein change:
P132T
Links:
UniProtKB: P52333#VAR_019336; dbSNP: rs3212723
NCBI 1000 Genomes Browser:
rs3212723
Molecular consequence:
  • NM_000215.3:c.394C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_000215.4:c.394C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-negative
Synonyms:
SCID, T CELL-NEGATIVE, B CELL-POSITIVE, NK CELL-NEGATIVE; Severe Combined Immune Deficiency, Autosomal Recessive, T Cell-Negative, B Cell -Positive, NK Cell-Negative, JAK3-Related
Identifiers:
MONDO: MONDO:0010938; MedGen: C1833275; Orphanet: 35078; OMIM: 600802

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000411124Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Apr 27, 2017)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link,

SCV000638326Invitaecriteria provided, single submitter
Benign
(Nov 23, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing.

Bodian DL, McCutcheon JN, Kothiyal P, Huddleston KC, Iyer RK, Vockley JG, Niederhuber JE.

PLoS One. 2014;9(4):e94554. doi: 10.1371/journal.pone.0094554.

PubMed [citation]
PMID:
24728327
PMCID:
PMC3984285

Description of a novel Janus kinase 3 P132A mutation in acute megakaryoblastic leukemia and demonstration of previously reported Janus kinase 3 mutations in normal subjects.

Riera L, Lasorsa E, Bonello L, Sismondi F, Tondat F, Di Bello C, Di Celle PF, Chiarle R, Godio L, Pich A, Facchetti F, Ponzoni M, Marmont F, Zanon C, Bardelli A, Inghirami G.

Leuk Lymphoma. 2011 Sep;52(9):1742-50. doi: 10.3109/10428194.2011.574757. Epub 2011 May 23.

PubMed [citation]
PMID:
21599579
See all PubMed Citations (6)

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000411124.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000638326.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 25, 2021

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