VCV000007404.3 - ClinVar

NM_006941.4(SOX10):c.698-740_1085delinsCCT

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_006941.4(SOX10):c.698-740_1085delinsCCT

Variation ID: 7404 Accession: VCV000007404.3

Type and length

Indel, 1,128 bp

Location

Cytogenetic: 22q13.1 22: 37973811-37974938 (GRCh38) [ NCBI UCSC ] 22: 38369818-38370945 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Apr 4, 2013	Apr 4, 2013	Dec 1, 2007

HGVS

Nucleotide	Protein	Molecular consequence
NM_006941.4:c.698-740_1085delinsCCT MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice acceptor
NM_001301130.2:c.293+6641_293+7768delinsAGG		intron variant
NM_001301131.2:c.293+6641_293+7768delinsAGG		intron variant
NM_001363825.1:c.38+1501_38+2628delinsAGG		intron variant
NC_000022.11:g.37973811_37974938delinsAGG
NC_000022.10:g.38369818_38370945delinsAGG
NG_007948.1:g.14595_15722delinsCCT
LRG_271:g.14595_15722delinsCCT
LRG_271t1:c.698-740_1085delinsCCT

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA118775 dbVar: nssv3761608 dbVar: nsv1067867 OMIM: 602229.0012 VarSome

Comment on variant

NCBI staff used the Variation Reporter tool to convert the HGVS expression c.697-740_1085del ins CCT supplied in Table 1 of PubMed 17999358 to chromosome coordinates on GRCh37.

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
SOX10		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	-	438
POLR2F		-	-	GRCh38 GRCh37	5	444

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Waardenburg syndrome type 4C	Pathogenic (1)	no assertion criteria provided	Dec 1, 2007	RCV000007829.12

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Dec 01, 2007)	no assertion criteria provided Method: literature only	WAARDENBURG SYNDROME, TYPE 4C Affected status: not provided Allele origin: germline	OMIM Accession: SCV000028034.1 First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013	Publications: PubMed (1) PubMed: 17999358 Comment on evidence: In a 1-year-old boy with Waardenburg syndrome type 4C (613266), Bondurand et al. (2007) identified a heterozygous deletion that removed part of exon 5 of … (more) In a 1-year-old boy with Waardenburg syndrome type 4C (613266), Bondurand et al. (2007) identified a heterozygous deletion that removed part of exon 5 of the SOX10 gene. The mutation comprised a 1,128-bp deletion encompassing 740 bp of intron 4 and 388 bp of exon 5, and a 3-bp insertion (697-740_1085del ins CCT). The patient had short-segment Hirschsprung disease, bilateral sensorineural deafness, hair and skin hypopigmentation, and bilateral cryptorchidism. (less)

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Deletions at the SOX10 gene locus cause Waardenburg syndrome types 2 and 4.	Bondurand N	American journal of human genetics	2007	PMID: 17999358

Text-mined citations for this variant ...

Record last updated Nov 03, 2024

ClinVar Genomic variation as it relates to human health

NM_006941.4(SOX10):c.698-740_1085delinsCCT

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...