NM_005419.4(STAT2):c.2539A>G (p.Met847Val) AND Primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 23, 2022
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:: RCV001918583.6

Allele description [Variation Report for NM_005419.4(STAT2):c.2539A>G (p.Met847Val)]

NM_005419.4(STAT2):c.2539A>G (p.Met847Val)

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.2539A>G (p.Met847Val)

HGVS:

NC_000012.12:g.56343406T>C
NG_046314.1:g.21848A>G
NM_001385110.1:c.2506A>G
NM_001385111.1:c.2440A>G
NM_001385113.1:c.*108A>G
NM_001385114.1:c.2518A>G
NM_001385115.1:c.2497A>G
NM_005419.4:c.2539A>GMANE SELECT
NM_198332.2:c.2527A>G
NP_001372039.1:p.Met836Val
NP_001372040.1:p.Met814Val
NP_001372043.1:p.Met840Val
NP_001372044.1:p.Met833Val
NP_005410.1:p.Met847Val
NP_938146.1:p.Met843Val
LRG_1329t1:c.2539A>G
LRG_1329:g.21848A>G
LRG_1329p1:p.Met847Val
NC_000012.11:g.56737190T>C

Protein change:

M814V

Links:

dbSNP: rs772907846

NCBI 1000 Genomes Browser:

rs772907846

Molecular consequence:

NM_001385113.1:c.*108A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001385110.1:c.2506A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001385111.1:c.2440A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001385114.1:c.2518A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001385115.1:c.2497A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_005419.4:c.2539A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_198332.2:c.2527A>G - 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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002177784	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 23, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002177784

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 23, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV002177784.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

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. 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 not expected to disrupt STAT2 protein function. ClinVar contains an entry for this variant (Variation ID: 1407723). This variant has not been reported in the literature in individuals affected with STAT2-related conditions. This variant is present in population databases (rs772907846, gnomAD 0.007%). This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 847 of the STAT2 protein (p.Met847Val).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine