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NM_025216.3(WNT10A):c.321C>A (p.Cys107Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
11 (Most recent: Mar 28, 2019)
Last evaluated:
Dec 21, 2018
Accession:
VCV000004461.5
Variation ID:
4461
Description:
single nucleotide variant
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NM_025216.3(WNT10A):c.321C>A (p.Cys107Ter)

Allele ID
19500
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q35
Genomic location
2: 218882368 (GRCh38) GRCh38 UCSC
2: 219747090 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.219747090C>A
NC_000002.12:g.218882368C>A
NM_025216.3:c.321C>A NP_079492.2:p.Cys107Ter nonsense
NG_012179.1:g.6836C>A
Protein change
C107*
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00059
The Genome Aggregation Database (gnomAD) 0.00080
The Genome Aggregation Database (gnomAD), exomes 0.00062
Trans-Omics for Precision Medicine (TOPMed) 0.00091
Links
OMIM: 606268.0002
dbSNP: rs121908119
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, multiple submitters, no conflicts Jul 10, 2018 RCV000255732.5
Pathogenic 1 criteria provided, single submitter Sep 7, 2014 RCV000190800.3
Pathogenic 2 criteria provided, single submitter Oct 31, 2018 RCV000477935.2
Pathogenic 1 criteria provided, single submitter Dec 21, 2018 RCV000536747.4
WNT10A-Related Disorders
Pathogenic 1 criteria provided, single submitter Oct 31, 2018 RCV000779308.1
Pathogenic 1 no assertion criteria provided May 1, 2012 RCV000004715.4
Pathogenic 1 no assertion criteria provided May 1, 2012 RCV000004716.4
Pathogenic 1 no assertion criteria provided May 1, 2012 RCV000030650.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
WNT10A - - GRCh38
GRCh37
101 122

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Sep 07, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary disease
Allele origin: germline
Ambry Genetics
Accession: SCV000244241.5
Submitted: (Feb 08, 2018)
Evidence details
Publications
PubMed (6)
Comment:
Lines of evidence used in support of classification: POSITIVE: Relevant Alteration(s) Detected
Pathogenic
(Jul 10, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000322007.7
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The C107X pathogenic variant in the WNT10A gene is one of the most common pathogenic variants reported in the WNT10A gene, and has been reported ... (more)
Pathogenic
(Dec 21, 2018)
criteria provided, single submitter
Method: clinical testing
Tooth agenesis, selective, 4
Odontoonychodermal dysplasia
Allele origin: germline
Invitae
Accession: SCV000638465.4
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (6)
Comment:
This sequence change creates a premature translational stop signal (p.Cys107*) in the WNT10A gene. It is expected to result in an absent or disrupted protein ... (more)
Pathogenic
(Aug 17, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics
Accession: SCV000331436.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/em...
Pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Tooth agenesis, selective, 4
Schopf-Schulz-Passarge syndrome
Odontoonychodermal dysplasia
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000893580.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
WNT10A-Related Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000915891.1
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (8)
Comment:
The WNT10A c.321C>A (p.Cys107Ter) variant is a stop-gained variant that is predicted to result in a premature termination of the protein. Across a selection of ... (more)
Pathogenic
(May 01, 2012)
no assertion criteria provided
Method: literature only
ODONTOONYCHODERMAL DYSPLASIA
Allele origin: germline
OMIM
Accession: SCV000024890.3
Submitted: (Aug 16, 2016)
Evidence details
Publications
PubMed (3)
Pathogenic
(May 01, 2012)
no assertion criteria provided
Method: literature only
SCHOPF-SCHULZ-PASSARGE SYNDROME
Allele origin: germline
OMIM
Accession: SCV000024891.3
Submitted: (Aug 16, 2016)
Evidence details
Publications
PubMed (3)
Pathogenic
(May 01, 2012)
no assertion criteria provided
Method: literature only
TOOTH AGENESIS, SELECTIVE 4
Allele origin: germline
OMIM
Accession: SCV000053328.3
Submitted: (Aug 09, 2012)
Evidence details
Publications
PubMed (3)
Pathogenic
(Aug 13, 2016)
no assertion criteria provided
Method: research
Tooth agenesis, selective, 4
Odontoonychodermal dysplasia
Schopf-Schulz-Passarge syndrome
Allele origin: germline
Division of Human Genetics,Children's Hospital of Philadelphia
Study: CSER-PediSeq
Accession: SCV000536908.1
Submitted: (Jan 23, 2017)
Evidence details
Publications
PubMed (6)
Pathogenic
(Jun 25, 2018)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: de novo
Molecular Genetics Laboratory,BC Children's and BC Women's Hospitals
Accession: SCV000898154.1
Submitted: (Jan 22, 2019)
Evidence details

Citations for this variant

Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Dental and extra-oral clinical features in 41 patients with WNT10A gene mutations: A multicentric genotype-phenotype study. Tardieu C Clinical genetics 2017 PMID: 28105635
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 Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
Taurodontism, variations in tooth number, and misshapened crowns in Wnt10a null mice and human kindreds. Yang J Molecular genetics & genomic medicine 2015 PMID: 25629078
WNT10A coding variants and maxillary lateral incisor agenesis with associated dental anomalies. Mostowska A European journal of oral sciences 2015 PMID: 25545742
Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions. Farwell KD Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25356970
Clinical features and WNT10A mutations in seven unrelated cases of Schöpf-Schulz-Passarge syndrome. Tziotzios C The British journal of dermatology 2014 PMID: 24902757
Dento-maxillo-facial phenotype and implants-based oral rehabilitation in Ectodermal Dysplasia with WNT10A gene mutation: report of a case and literature review. Clauss F Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery 2014 PMID: 24702986
The WNT10A gene in ectodermal dysplasias and selective tooth agenesis. Mues G American journal of medical genetics. Part A 2014 PMID: 24700731
WNT10A mutations account for ¼ of population-based isolated oligodontia and show phenotypic correlations. Arzoo PS American journal of medical genetics. Part A 2014 PMID: 24449199
Variability in dentofacial phenotypes in four families with WNT10A mutations. Vink CP European journal of human genetics : EJHG 2014 PMID: 24398796
WNT10A variants are associated with non-syndromic tooth agenesis in the general population. Song S Human genetics 2014 PMID: 24043634
Mutations in WNT10A are frequently involved in oligodontia associated with minor signs of ectodermal dysplasia. Plaisancié J American journal of medical genetics. Part A 2013 PMID: 23401279
Nucleotide variants of genes encoding components of the Wnt signalling pathway and the risk of non-syndromic tooth agenesis. Mostowska A Clinical genetics 2013 PMID: 23167694
Mutations in WNT10A are present in more than half of isolated hypodontia cases. van den Boogaard MJ Journal of medical genetics 2012 PMID: 22581971
Schöpf-Schulz-Passarge syndrome resulting from a homozygous nonsense mutation, p.Cys107X, in WNT10A. Petrof G The Australasian journal of dermatology 2011 PMID: 21834823
WNT10A mutations are a frequent cause of a broad spectrum of ectodermal dysplasias with sex-biased manifestation pattern in heterozygotes. Bohring A American journal of human genetics 2009 PMID: 19559398
Mutation in WNT10A is associated with an autosomal recessive ectodermal dysplasia: the odonto-onycho-dermal dysplasia. Adaimy L American journal of human genetics 2007 PMID: 17847007
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=WNT10A - - - -

Record last updated Aug 30, 2019