NM_006941.4(SOX10):c.1081G>A (p.Ala361Thr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 29, 2024
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:: RCV002537632.10

Allele description [Variation Report for NM_006941.4(SOX10):c.1081G>A (p.Ala361Thr)]

NM_006941.4(SOX10):c.1081G>A (p.Ala361Thr)

Genes:

POLR2F:RNA polymerase II, I and III subunit F [Gene - OMIM - HGNC]
SOX10:SRY-box transcription factor 10 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.1

Genomic location:

Preferred name:

NM_006941.4(SOX10):c.1081G>A (p.Ala361Thr)

HGVS:

NC_000022.11:g.37973815C>T
NG_007948.1:g.15718G>A
NM_001301130.2:c.293+6645C>T
NM_001301131.2:c.293+6645C>T
NM_001363825.1:c.*38+1505C>T
NM_006941.4:c.1081G>AMANE SELECT
NP_008872.1:p.Ala361Thr
NP_008872.1:p.Ala361Thr
LRG_271t1:c.1081G>A
LRG_271:g.15718G>A
LRG_271p1:p.Ala361Thr
NC_000022.10:g.38369822C>T
NM_006941.3:c.1081G>A

Protein change:

A361T

Links:

dbSNP: rs770105416

NCBI 1000 Genomes Browser:

rs770105416

Molecular consequence:

NM_001301130.2:c.293+6645C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001301131.2:c.293+6645C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001363825.1:c.*38+1505C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_006941.4:c.1081G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

MAG: Candidatus Omnitrophica bacterium ADurb.Bin277 BWY42_contig000142, whole ge...
MAG: Candidatus Omnitrophica bacterium ADurb.Bin277 BWY42_contig000142, whole genome shotgun sequence
gi|1167222907|gb|MWBP01000142.1||gn :MWBP01|BWY42_contig000142

Nucleotide
PREDICTED: Mus musculus bridging integrator 1 (Bin1), transcript variant X8, mRN...
PREDICTED: Mus musculus bridging integrator 1 (Bin1), transcript variant X8, mRNA
gi|1907130104|ref|XM_006525984.5|

Nucleotide

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
SCV003456719	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 29, 2024)	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

SCV003456719

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 29, 2024)

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, SCV003456719.2

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

Description

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 361 of the SOX10 protein (p.Ala361Thr). This variant is present in population databases (rs770105416, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with SOX10-related conditions. ClinVar contains an entry for this variant (Variation ID: 982663). 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 SOX10 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.

#	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: Nov 3, 2024

ClinVar

Relating variation to medicine