NM_001399.5(EDA):c.866G>A (p.Arg289His) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 1, 2020
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:: RCV001248822.1

Allele description [Variation Report for NM_001399.5(EDA):c.866G>A (p.Arg289His)]

NM_001399.5(EDA):c.866G>A (p.Arg289His)

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.866G>A (p.Arg289His)

HGVS:

NC_000023.11:g.70033470G>A
NG_009809.2:g.422404G>A
NM_001005609.2:c.866G>A
NM_001005612.3:c.857G>A
NM_001399.5:c.866G>AMANE SELECT
NP_001005609.1:p.Arg289His
NP_001005612.2:p.Arg286His
NP_001390.1:p.Arg289His
NC_000023.10:g.69253320G>A
NM_001399.4:c.866G>A

Protein change:

R286H

Links:

dbSNP: rs876657641

NCBI 1000 Genomes Browser:

rs876657641

Molecular consequence:

NM_001005609.2:c.866G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001005612.3:c.857G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001399.5:c.866G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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

Name:: Tooth agenesis, selective, X-linked, 1 (STHAGX1)
Synonyms:: HYPODONTIA/OLIGODONTIA, X-LINKED, 1
Identifiers:: MONDO: MONDO:0010741; MedGen: C1970757; Orphanet: 99798; OMIM: 313500

Recent activity

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mitogen-activated protein kinase 6 isoform X1 [Homo sapiens]
mitogen-activated protein kinase 6 isoform X1 [Homo sapiens]
gi|530406172|ref|XP_005254594.1|

Protein
ankyrin repeat domain-containing protein 6 isoform X32 [Homo sapiens]
ankyrin repeat domain-containing protein 6 isoform X32 [Homo sapiens]
gi|2462606991|ref|XP_054210694.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001366090	Biotechnology Lab, Dept of Biomolecular Sciences, University of Urbino See additional submitters Coordinamento Interdipartimentale Malattie Rare, Azienda Ospedaliero Universitaria Ospedali Riuniti di Ancona	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 1, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001366090

Biotechnology Lab, Dept of Biomolecular Sciences, University of Urbino

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 1, 2020)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Biotechnology Lab, Dept of Biomolecular Sciences, University of Urbino, SCV001366090.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	not provided	not provided	clinical testing	PubMed (1)

Description

The Arg289His variant in EDA has been reported in one Italian family with X-linked dominant tooth agenesis, segregated with the disease in affected relatives (present study), and was absent from large population studies. Additionally, the same variant causes X-linked recessive hypohidrotic ectodermal dysplasia in hemizygous males within the same family. Furthermore, this variant has been described to segregate with non-syndromic oligodontia and ectodermal dysplasia in families (PMID: 26753551, Invitae). Two other missense variants affecting the same amino acidic residue Arg289 (c.865C>T p.Arg289Cys, c.866G>T p.Arg289Leu), but causing different amino acid substitutions, has been reported to be pathogenic and associated to non-syndromic oligodontia (PMID: 19278982, 24487376). In summary, the Arg289His variant meets our criteria to be classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: May 12, 2024

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