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NM_005419.4(STAT2):c.2507G>A (p.Arg836His) AND Primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 15, 2018
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000810155.2

Allele description [Variation Report for NM_005419.4(STAT2):c.2507G>A (p.Arg836His)]

NM_005419.4(STAT2):c.2507G>A (p.Arg836His)

Gene:
STAT2:signal transducer and activator of transcription 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q13.3
Genomic location:
Preferred name:
NM_005419.4(STAT2):c.2507G>A (p.Arg836His)
HGVS:
  • NC_000012.12:g.56343438C>T
  • NG_046314.1:g.21816G>A
  • NM_005419.4:c.2507G>AMANE SELECT
  • NM_198332.2:c.2495G>A
  • NP_005410.1:p.Arg836His
  • NP_938146.1:p.Arg832His
  • LRG_1329t1:c.2507G>A
  • LRG_1329:g.21816G>A
  • LRG_1329p1:p.Arg836His
  • NC_000012.11:g.56737222C>T
  • NM_005419.3:c.2507G>A
Protein change:
R832H
Links:
dbSNP: rs759254318
NCBI 1000 Genomes Browser:
rs759254318
Molecular consequence:
  • NM_005419.4:c.2507G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198332.2:c.2495G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection
Synonyms:
Immunodeficiency 44
Identifiers:
MONDO: MONDO:0014715; MedGen: C4225260; Orphanet: 431166; OMIM: 616636

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000950345Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 15, 2018) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000950345.1

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

Description

This sequence change replaces arginine with histidine at codon 836 of the STAT2 protein (p.Arg836His). The arginine residue is weakly conserved and there is a small physicochemical difference between arginine and histidine. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with STAT2-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The histidine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024