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NM_025216.3(WNT10A):c.321C>A (p.Cys107Ter) AND Odonto-onycho-dermal dysplasia

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Mar 12, 2024
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:
RCV000004715.8

Allele description [Variation Report for NM_025216.3(WNT10A):c.321C>A (p.Cys107Ter)]

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

Gene:
WNT10A:Wnt family member 10A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q35
Genomic location:
Preferred name:
NM_025216.3(WNT10A):c.321C>A (p.Cys107Ter)
HGVS:
  • NC_000002.12:g.218882368C>A
  • NG_012179.1:g.6836C>A
  • NM_025216.3:c.321C>AMANE SELECT
  • NP_079492.2:p.Cys107Ter
  • NC_000002.11:g.219747090C>A
  • NM_025216.2:c.321C>A
Protein change:
C107*; CYS107TER
Links:
OMIM: 606268.0002; dbSNP: rs121908119
NCBI 1000 Genomes Browser:
rs121908119
Molecular consequence:
  • NM_025216.3:c.321C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Odonto-onycho-dermal dysplasia
Synonyms:
Odontoonychodermal dysplasia
Identifiers:
MONDO: MONDO:0009773; MedGen: C0796093; Orphanet: 2721; OMIM: 257980

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000024890OMIM
no assertion criteria provided
Pathogenic
(May 1, 2012)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV005039405Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Mar 12, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations in WNT10A are present in more than half of isolated hypodontia cases.

van den Boogaard MJ, Créton M, Bronkhorst Y, van der Hout A, Hennekam E, Lindhout D, Cune M, Ploos van Amstel HK.

J Med Genet. 2012 May;49(5):327-31. doi: 10.1136/jmedgenet-2012-100750.

PubMed [citation]
PMID:
22581971

Mutations in WNT10A are frequently involved in oligodontia associated with minor signs of ectodermal dysplasia.

Plaisancié J, Bailleul-Forestier I, Gaston V, Vaysse F, Lacombe D, Holder-Espinasse M, Abramowicz M, Coubes C, Plessis G, Faivre L, Demeer B, Vincent-Delorme C, Dollfus H, Sigaudy S, Guillén-Navarro E, Verloes A, Jonveaux P, Martin-Coignard D, Colin E, Bieth E, Calvas P, Chassaing N.

Am J Med Genet A. 2013 Apr;161A(4):671-8. doi: 10.1002/ajmg.a.35747. Epub 2013 Feb 7.

PubMed [citation]
PMID:
23401279
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000024890.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In affected members of 3 families with odontoonychodermal dysplasia (OODD; 257980) and 1 proband of a family with Schopf-Schulz-Passarge syndrome (SPSS; 224750), Bohring et al. (2009) identified homozygosity for a 321C-A transversion in the WNT10A gene, resulting in a cys107-to-ter (C107X) substitution that was not found in 200 control chromosomes. In 2 additional probands with OODD, the C107X mutation was found in compound heterozygosity with a phe228-to-ile (F228I; 606268.0003) mutation, and in a brother and sister who had oligodontia and sparse body hair and eyebrows as their only manifestations, the C107X mutation was found in compound heterozygosity with an arg128-to-gln (R128Q; 606268.0004) mutation. Of 18 heterozygous carriers of the C107X mutation, 10 exhibited some phenotypic manifestation, including anomalies of teeth, skin, and nails.

In 2 unrelated patients with nonsyndromic tooth agenesis (STHAG4; 150400), van den Boogaard et al. (2012) identified heterozygosity for the C107X mutation in the WNT10A gene; in 3 other patients, the mutation was present in compound heterozygosity with the F228I mutation. In addition, van den Boogaard et al. (2012) identified mutations in the C107X mutation in 6 patients with tooth agenesis who had mild features of ectodermal dysplasia, but who did not exhibit the characteristic features of OODD; 2 were heterozygous, 1 was homozygous, and 3 were compound heterozygous for C207X and F228I.

In 4 probands with tooth agenesis and features of ectodermal dysplasia, Plaisancie et al. (2013) identified the C107X mutation in the WNT10A gene, present in homozygosity in 1 patient and in compound heterozygosity in 3 patients, including with the F228I mutation in 1 proband. In the latter family, the proband's unaffected father and mother were each heterozygous for 1 of the mutations.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005039405.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: WNT10A c.321C>A (p.Cys107X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 0.00062 in 251318 control chromosomes (gnomAD). c.321C>A has been reported in the literature in multiple individuals affected with ectodermal dysplasia (example: Bohring_2009). These data indicate that the variant is very likely to be associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 19559398). ClinVar contains an entry for this variant (Variation ID: 4461). Based on the evidence outlined above, the variant was classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024