NM_006941.4(SOX10):c.1205_1209del (p.Asp401_Tyr402insTer) AND Waardenburg syndrome type 4C

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 22, 2017
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:: RCV000681523.12

Allele description [Variation Report for NM_006941.4(SOX10):c.1205_1209del (p.Asp401_Tyr402insTer)]

NM_006941.4(SOX10):c.1205_1209del (p.Asp401_Tyr402insTer)

Genes:

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

Variant type:

Deletion

Cytogenetic location:

22q13.1

Genomic location:

Preferred name:

NM_006941.4(SOX10):c.1205_1209del (p.Asp401_Tyr402insTer)

HGVS:

NC_000022.11:g.37973689_37973693del
NG_007948.1:g.15842_15846del
NM_001301130.2:c.293+6519_293+6523del
NM_001301131.2:c.293+6519_293+6523del
NM_001363825.1:c.*38+1379_*38+1383del
NM_006941.4:c.1205_1209delMANE SELECT
NP_008872.1:p.(Tyr402*)
NP_008872.1:p.Asp401_Tyr402insTer
NP_008872.1:p.Tyr402Terfs
LRG_271t1:c.1205_1209del
LRG_271:g.15842_15846del
NC_000022.10:g.38369696_38369700del
NM_006941.3:c.1203_1207delCTACT
NM_006941.3:c.1205_1209del

Links:

dbSNP: rs1569167586

NCBI 1000 Genomes Browser:

rs1569167586

Molecular consequence:

NM_001301130.2:c.293+6519_293+6523del - intron variant - [Sequence Ontology: SO:0001627]
NM_001301131.2:c.293+6519_293+6523del - intron variant - [Sequence Ontology: SO:0001627]
NM_001363825.1:c.*38+1379_*38+1383del - intron variant - [Sequence Ontology: SO:0001627]
NM_006941.4:c.1205_1209del - nonsense - [Sequence Ontology: SO:0001587]

Functional consequence:

protein truncation [Variation Ontology: 0015]

Observations:

Condition(s)

Name:: Waardenburg syndrome type 4C (WS4C)
Synonyms:: WAARDENBURG SYNDROME WITH HIRSCHSPRUNG DISEASE, TYPE 4C
Identifiers:: MONDO: MONDO:0013202; MedGen: C2750452; Orphanet: 897; OMIM: 613266

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000700087	Area of Clinical and Molecular Genetics, Hospital Universitario Vall de Hebron	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 22, 2017)	maternal, de novo	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

SCV000700087

Area of Clinical and Molecular Genetics, Hospital Universitario Vall de Hebron

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Aug 22, 2017)

maternal, de novo

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	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	maternal	yes	1	not provided	not provided	not provided	not provided	clinical testing
Caucasian	maternal	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Area of Clinical and Molecular Genetics, Hospital Universitario Vall de Hebron, SCV000700087.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	not provided	not provided	clinical testing	PubMed (1)
2		1	not provided	not provided	clinical testing	PubMed (1)
3	Caucasian	1	not provided	not provided	clinical testing	PubMed (1)

Description

This variant results in the deletion of 5 nucleotids and the creation of a termination codon at position 402 of the protein, which predicts a truncated protein 66 aminoacid shorter than the wild type.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	yes	not provided	not provided	not provided		1	not provided	not provided	not provided
2	de novo	yes	not provided	not provided	not provided		1	not provided	not provided	not provided
3	maternal	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Apr 20, 2024

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