NM_006941.4(SOX10):c.1077_1078del (p.Glu359fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 22, 2023
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:: RCV002512880.10

Allele description [Variation Report for NM_006941.4(SOX10):c.1077_1078del (p.Glu359fs)]

NM_006941.4(SOX10):c.1077_1078del (p.Glu359fs)

Genes:

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

Variant type:

Microsatellite

Cytogenetic location:

22q13.1

Genomic location:

Preferred name:

NM_006941.4(SOX10):c.1077_1078del (p.Glu359fs)

HGVS:

NC_000022.11:g.37973819CT[1]
NG_007948.1:g.15712GA[1]
NM_001301130.2:c.293+6651_293+6652del
NM_001301131.2:c.293+6651_293+6652del
NM_001363825.1:c.*38+1511_*38+1512del
NM_006941.4:c.1077_1078delMANE SELECT
NP_008872.1:p.Glu359Aspfs
NP_008872.1:p.Glu359fs
LRG_271t1:c.1074_1075AG[1]
LRG_271:g.15712GA[1]
LRG_271p1:p.Glu359Aspfs
NC_000022.10:g.38369825_38369826del
NC_000022.10:g.38369826CT[1]
NM_006941.3:c.1074_1075AG[1]
NM_006941.3:c.1077_1078del

Protein change:

E359fs

Links:

OMIM: 602229.0004; dbSNP: rs397515367

NCBI 1000 Genomes Browser:

rs397515367

Molecular consequence:

NM_006941.4:c.1077_1078del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001301130.2:c.293+6651_293+6652del - intron variant - [Sequence Ontology: SO:0001627]
NM_001301131.2:c.293+6651_293+6652del - intron variant - [Sequence Ontology: SO:0001627]
NM_001363825.1:c.*38+1511_*38+1512del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Guillardia theta CCMP2712 unplaced genomic scaffold GUITHscaffold_17, whole geno...
Guillardia theta CCMP2712 unplaced genomic scaffold GUITHscaffold_17, whole genome shotgun sequence
gi|428180646|gnl|WGS:AEIE01|GUITHsc d_17|gb|JH992981.1|

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Homo sapiens RNA polymerase transcriptional regulation mediator (MED6) mRNA, com...
Homo sapiens RNA polymerase transcriptional regulation mediator (MED6) mRNA, complete cds
gi|3329505|gb|AF074723.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003444486	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 22, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23237859, 9462749, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003444486

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 22, 2023)

germline

clinical testing

PubMed (3)
[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

Spectrum of temporal bone abnormalities in patients with Waardenburg syndrome and SOX10 mutations.

Elmaleh-Bergès M, Baumann C, Noël-Pétroff N, Sekkal A, Couloigner V, Devriendt K, Wilson M, Marlin S, Sebag G, Pingault V.

AJNR Am J Neuroradiol. 2013 Jun-Jul;34(6):1257-63. doi: 10.3174/ajnr.A3367. Epub 2012 Dec 13.

PubMed [citation]

PMID:: 23237859
PMCID:: PMC7964579

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

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003444486.2

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

Description

This variant disrupts a region of the SOX10 protein in which other variant(s) (p.Gln399Valfs*2) have been determined to be pathogenic (PMID: 23237859). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 7396). This variant is also known as 1076delGA. This premature translational stop signal has been observed in individual(s) with Waardenburg syndrome (PMID: 9462749). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Glu359Aspfs*42) in the SOX10 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 108 amino acid(s) of the SOX10 protein. 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: Nov 3, 2024

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