NM_005984.5(SLC25A1):c.539C>T (p.Thr180Met) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 21, 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:: RCV001931373.6

Allele description [Variation Report for NM_005984.5(SLC25A1):c.539C>T (p.Thr180Met)]

NM_005984.5(SLC25A1):c.539C>T (p.Thr180Met)

Gene:

SLC25A1:solute carrier family 25 member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_005984.5(SLC25A1):c.539C>T (p.Thr180Met)

HGVS:

NC_000022.11:g.19176938G>A
NG_033863.1:g.6926C>T
NM_001256534.2:c.560C>T
NM_001287387.2:c.230C>T
NM_005984.5:c.539C>TMANE SELECT
NP_001243463.1:p.Thr187Met
NP_001274316.1:p.Thr77Met
NP_005975.1:p.Thr180Met
NC_000022.10:g.19164451G>A
NR_046298.3:n.463C>T

Protein change:

T180M

Links:

dbSNP: rs147446778

NCBI 1000 Genomes Browser:

rs147446778

Molecular consequence:

NM_001256534.2:c.560C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001287387.2:c.230C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_005984.5:c.539C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_046298.3:n.463C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Chromosome neighbors for GEO Profiles (Select 33897841) (20)
GEO Profiles
SH2D1A SH2 domain containing 1A [Homo sapiens]
SH2D1A SH2 domain containing 1A [Homo sapiens]
Gene ID:4068

Gene
Gene Links for GEO Profiles (Select 33870172) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002198077	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 21, 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

SCV002198077

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 21, 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, SCV002198077.3

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

Description

ClinVar contains an entry for this variant (Variation ID: 1430172). 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with SLC25A1-related conditions. This variant is present in population databases (rs147446778, gnomAD 0.009%). This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 180 of the SLC25A1 protein (p.Thr180Met).

#	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

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