NM_006941.4(SOX10):c.481C>T (p.Arg161Cys) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 14, 2021
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:: RCV001909314.11

Allele description [Variation Report for NM_006941.4(SOX10):c.481C>T (p.Arg161Cys)]

NM_006941.4(SOX10):c.481C>T (p.Arg161Cys)

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.481C>T (p.Arg161Cys)

HGVS:

NC_000022.11:g.37978083G>A
NG_007948.1:g.11450C>T
NM_001301130.2:c.294-8071G>A
NM_001301131.2:c.293+10913G>A
NM_001363825.1:c.*38+5773G>A
NM_006941.4:c.481C>TMANE SELECT
NP_008872.1:p.Arg161Cys
NP_008872.1:p.Arg161Cys
LRG_271t1:c.481C>T
LRG_271:g.11450C>T
LRG_271p1:p.Arg161Cys
NC_000022.10:g.38374090G>A
NM_006941.3:c.481C>T

Protein change:

R161C

Links:

dbSNP: rs2145768544

NCBI 1000 Genomes Browser:

rs2145768544

Molecular consequence:

NM_001301130.2:c.294-8071G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001301131.2:c.293+10913G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001363825.1:c.*38+5773G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_006941.4:c.481C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002186454	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 14, 2021)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 25077900, 27562378, 29419413, 32908489, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002186454

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 14, 2021)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

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

The prevalence of CHD7 missense versus truncating mutations is higher in patients with Kallmann syndrome than in typical CHARGE patients.

Marcos S, Sarfati J, Leroy C, Fouveaut C, Parent P, Metz C, Wolczynski S, Gérard M, Bieth E, Kurtz F, Verier-Mine O, Perrin L, Archambeaud F, Cabrol S, Rodien P, Hove H, Prescott T, Lacombe D, Christin-Maitre S, Touraine P, Hieronimus S, Dewailly D, et al.

J Clin Endocrinol Metab. 2014 Oct;99(10):E2138-43. doi: 10.1210/jc.2014-2110. Epub 2014 Jul 31. Erratum in: J Clin Endocrinol Metab. 2015 Jan;100(1):317.

PubMed [citation]

PMID:: 25077900

Variations in Multiple Syndromic Deafness Genes Mimic Non-syndromic Hearing Loss.

Bademci G, Cengiz FB, Foster Ii J, Duman D, Sennaroglu L, Diaz-Horta O, Atik T, Kirazli T, Olgun L, Alper H, Menendez I, Loclar I, Sennaroglu G, Tokgoz-Yilmaz S, Guo S, Olgun Y, Mahdieh N, Bonyadi M, Bozan N, Ayral A, Ozkinay F, Yildirim-Baylan M, et al.

Sci Rep. 2016 Aug 26;6:31622. doi: 10.1038/srep31622.

PubMed [citation]

PMID:: 27562378
PMCID:: PMC4999867

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV002186454.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This missense change has been observed in individuals with SOX10-related conditions (PMID: 25077900, 27562378, 29419413, 32908489). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 161 of the SOX10 protein (p.Arg161Cys).

#	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 1, 2024

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