NM_025216.3(WNT10A):c.216G>T (p.Met72Ile) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 25, 2022
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:
RCV000558141.5

Allele description [Variation Report for NM_025216.3(WNT10A):c.216G>T (p.Met72Ile)]

NM_025216.3(WNT10A):c.216G>T (p.Met72Ile)

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.216G>T (p.Met72Ile)
HGVS:
  • NC_000002.12:g.218882263G>T
  • NG_012179.1:g.6731G>T
  • NM_025216.3:c.216G>TMANE SELECT
  • NP_079492.2:p.Met72Ile
  • NC_000002.11:g.219746985G>T
  • NM_025216.2:c.216G>T
Protein change:
M72I
Links:
dbSNP: rs373607885
NCBI 1000 Genomes Browser:
rs373607885
Molecular consequence:
  • NM_025216.3:c.216G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Odonto-onycho-dermal dysplasia
Synonyms:
Odontoonychodermal dysplasia
Identifiers:
MONDO: MONDO:0009773; MedGen: C0796093; Orphanet: 2721; OMIM: 257980
Name:
Tooth agenesis, selective, 4 (STHAG4)
Synonyms:
LATERAL INCISORS, ABSENCE OF; LATERAL INCISORS, PEGGED OR MISSING; TOOTH AGENESIS, SELECTIVE, 4, WITH OR WITHOUT ECTODERMAL DYSPLASIA
Identifiers:
MONDO: MONDO:0007881; MedGen: C1835492; Orphanet: 99798; OMIM: 150400

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000638464Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 25, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000638464.4

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

Description

This sequence change replaces methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 72 of the WNT10A protein (p.Met72Ile). This variant is present in population databases (rs373607885, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with WNT10A-related conditions. ClinVar contains an entry for this variant (Variation ID: 464180). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Nov 11, 2023