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NM_001399.5(EDA):c.865C>T (p.Arg289Cys) AND Hypohidrotic X-linked ectodermal dysplasia

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Jun 17, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000692210.8

Allele description [Variation Report for NM_001399.5(EDA):c.865C>T (p.Arg289Cys)]

NM_001399.5(EDA):c.865C>T (p.Arg289Cys)

Gene:
EDA:ectodysplasin A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq13.1
Genomic location:
Preferred name:
NM_001399.5(EDA):c.865C>T (p.Arg289Cys)
HGVS:
  • NC_000023.11:g.70033469C>T
  • NG_009809.2:g.422403C>T
  • NM_001005609.2:c.865C>T
  • NM_001005612.3:c.856C>T
  • NM_001399.5:c.865C>TMANE SELECT
  • NP_001005609.1:p.Arg289Cys
  • NP_001005612.2:p.Arg286Cys
  • NP_001390.1:p.Arg289Cys
  • NC_000023.10:g.69253319C>T
  • NM_001399.4:c.865C>T
  • Q92838:p.Arg289Cys
Protein change:
R286C; ARG289CYS
Links:
UniProtKB: Q92838#VAR_071456; OMIM: 300451.0021; dbSNP: rs879255551
NCBI 1000 Genomes Browser:
rs879255551
Molecular consequence:
  • NM_001005609.2:c.865C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005612.3:c.856C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001399.5:c.865C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hypohidrotic X-linked ectodermal dysplasia (XHED)
Synonyms:
ECTODERMAL DYSPLASIA, HYPOHIDROTIC, 1; Anhidrotic ectodermal dysplasia X-linked; Christ Siemens Touraine syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010585; MedGen: C0162359; Orphanet: 181; Orphanet: 238468; OMIM: 305100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000820022Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 17, 2022) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV001480047Medical Molecular Genetics Department, National Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Feb 13, 2021) 		maternalresearch

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
not providedmaternalyesnot providednot providednot providednot providednot providedresearch

Citations

PubMed

Functional Study of Ectodysplasin-A Mutations Causing Non-Syndromic Tooth Agenesis.

Shen W, Wang Y, Liu Y, Liu H, Zhao H, Zhang G, Snead ML, Han D, Feng H.

PLoS One. 2016;11(5):e0154884. doi: 10.1371/journal.pone.0154884.

PubMed [citation]
PMID:
27144394
PMCID:
PMC4856323

EDA gene mutations underlie non-syndromic oligodontia.

Song S, Han D, Qu H, Gong Y, Wu H, Zhang X, Zhong N, Feng H.

J Dent Res. 2009 Feb;88(2):126-31. doi: 10.1177/0022034508328627.

PubMed [citation]
PMID:
19278982
PMCID:
PMC3317984
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000820022.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

Experimental studies have shown that this missense change affects EDA function (PMID: 27144394). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt EDA protein function. ClinVar contains an entry for this variant (Variation ID: 253054). This missense change has been observed in individuals with non-syndromic oligodontia (PMID: 19278982; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 289 of the EDA protein (p.Arg289Cys). This variant disrupts the p.Arg289 amino acid residue in EDA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 26753551; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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

From Medical Molecular Genetics Department, National Research Center, SCV001480047.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 14, 2024