NM_198282.4(STING1):c.862G>A (p.Ala288Thr) AND STING-associated vasculopathy with onset in infancy

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 25, 2023
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:
RCV003749067.2

Allele description [Variation Report for NM_198282.4(STING1):c.862G>A (p.Ala288Thr)]

NM_198282.4(STING1):c.862G>A (p.Ala288Thr)

Gene:
STING1:stimulator of interferon response cGAMP interactor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q31.2
Genomic location:
Preferred name:
NM_198282.4(STING1):c.862G>A (p.Ala288Thr)
HGVS:
  • NC_000005.10:g.139477413C>T
  • NG_034249.1:g.10378G>A
  • NM_001301738.2:c.759+857G>A
  • NM_001367258.1:c.505G>A
  • NM_198282.4:c.862G>AMANE SELECT
  • NP_001354187.1:p.Ala169Thr
  • NP_938023.1:p.Ala288Thr
  • LRG_1308t1:c.862G>A
  • LRG_1308:g.10378G>A
  • LRG_1308p1:p.Ala288Thr
  • NC_000005.9:g.138856998C>T
Protein change:
A169T
Molecular consequence:
  • NM_001301738.2:c.759+857G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367258.1:c.505G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198282.4:c.862G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
STING-associated vasculopathy with onset in infancy
Synonyms:
Sting-associated vasculopathy, infantile-onset
Identifiers:
MONDO: MONDO:0014405; MedGen: C4014722; Orphanet: 425120; OMIM: 615934

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004539885Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 25, 2023) 		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, SCV004539885.1

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

Description

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 288 of the TMEM173 protein (p.Ala288Thr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TMEM173-related conditions. 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 TMEM173 protein function with a negative predictive value of 80%. 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