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NM_182758.4(WDR72):c.88C>T (p.Arg30Ter) AND Amelogenesis imperfecta

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 24, 2018
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:
RCV000604368.4

Allele description [Variation Report for NM_182758.4(WDR72):c.88C>T (p.Arg30Ter)]

NM_182758.4(WDR72):c.88C>T (p.Arg30Ter)

Gene:
WDR72:WD repeat domain 72 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q21.3
Genomic location:
Preferred name:
NM_182758.4(WDR72):c.88C>T (p.Arg30Ter)
HGVS:
  • NC_000015.10:g.53733062G>A
  • NG_017034.2:g.31601C>T
  • NM_182758.4:c.88C>TMANE SELECT
  • NP_877435.3:p.Arg30Ter
  • NC_000015.9:g.54025259G>A
  • NM_182758.2:c.88C>T
  • NR_102334.2:n.328C>T
  • p.Arg30X
Protein change:
R30*
Links:
dbSNP: rs770804941
NCBI 1000 Genomes Browser:
rs770804941
Molecular consequence:
  • NR_102334.2:n.328C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_182758.4:c.88C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Amelogenesis imperfecta (AI)
Synonyms:
Congenital enamel hypoplasia
Identifiers:
MONDO: MONDO:0019507; MedGen: C0002452; OMIM: PS104500; Human Phenotype Ontology: HP:0000705

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000731982Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)		Likely pathogenic
(Jan 24, 2018) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000731982.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The p.Arg30X variant (NM_182758.2 c.88C>T) in WDR72 has not been previously repo rted in the literature, but has been identified in 2/34392 of Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; d bSNP rs770804941). Although this variant has been seen in the general population , its frequency is low enough to be consistent with a recessive carrier frequenc y. This nonsense variant leads to a premature termination codon at position 30, which is predicted to lead to a truncated or absent protein. Biallelic loss of f unction of the WDR72 gene has been associated with amelogenesis imperfecta. In s ummary, although additional studies are required to fully establish its clinical significance, the p.Arg30X variant is likely pathogenic based on a predicted nu ll effect. ACMG/AMP Criteria applied: PVS1; PM2 (Richards 2015).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

Last Updated: Dec 31, 2022