NM_006941.4(SOX10):c.378C>A (p.Tyr126Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 20, 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:: RCV002570664.10

Allele description [Variation Report for NM_006941.4(SOX10):c.378C>A (p.Tyr126Ter)]

NM_006941.4(SOX10):c.378C>A (p.Tyr126Ter)

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.378C>A (p.Tyr126Ter)

HGVS:

NC_000022.11:g.37983407G>T
NG_007948.1:g.6126C>A
NG_148296.1:g.684G>T
NM_001301130.2:c.294-2747G>T
NM_001301131.2:c.293+16237G>T
NM_001363825.1:c.*38+11097G>T
NM_006941.4:c.378C>AMANE SELECT
NP_008872.1:p.Tyr126Ter
NP_008872.1:p.Tyr126Ter
LRG_271t1:c.378C>A
LRG_271:g.6126C>A
LRG_271p1:p.Tyr126Ter
NC_000022.10:g.38379414G>T
NM_006941.3:c.378C>A

Protein change:

Y126*

Links:

dbSNP: rs2145776981

NCBI 1000 Genomes Browser:

rs2145776981

Molecular consequence:

NM_001301130.2:c.294-2747G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001301131.2:c.293+16237G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001363825.1:c.*38+11097G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_006941.4:c.378C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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maltase-glucoamylase, intestinal isoform X3 [Delphinapterus leucas]
maltase-glucoamylase, intestinal isoform X3 [Delphinapterus leucas]
gi|1246147653|ref|XP_022435021.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003315238	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 20, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 9462749, 15004559, 21965087, 33442024, 33724713, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003315238

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 20, 2022)

germline

clinical testing

PubMed (6)
[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

SOX10 mutations in patients with Waardenburg-Hirschsprung disease.

Pingault V, Bondurand N, Kuhlbrodt K, Goerich DE, Préhu MO, Puliti A, Herbarth B, Hermans-Borgmeyer I, Legius E, Matthijs G, Amiel J, Lyonnet S, Ceccherini I, Romeo G, Smith JC, Read AP, Wegner M, Goossens M.

Nat Genet. 1998 Feb;18(2):171-3.

PubMed [citation]

PMID:: 9462749

Molecular mechanism for distinct neurological phenotypes conveyed by allelic truncating mutations.

Inoue K, Khajavi M, Ohyama T, Hirabayashi S, Wilson J, Reggin JD, Mancias P, Butler IJ, Wilkinson MF, Wegner M, Lupski JR.

Nat Genet. 2004 Apr;36(4):361-9. Epub 2004 Mar 7.

PubMed [citation]

PMID:: 15004559

See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003315238.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This sequence change creates a premature translational stop signal (p.Tyr126*) in the SOX10 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SOX10 are known to be pathogenic (PMID: 9462749, 15004559, 21965087, 33442024). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with deafness (PMID: 33724713). ClinVar contains an entry for this variant (Variation ID: 1185066). For these reasons, this variant has been classified as Pathogenic.

#	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: Oct 26, 2024

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