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NM_022336.4(EDAR):c.1213G>C (p.Gly405Arg) AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 18, 2021
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:
RCV001337468.4

Allele description [Variation Report for NM_022336.4(EDAR):c.1213G>C (p.Gly405Arg)]

NM_022336.4(EDAR):c.1213G>C (p.Gly405Arg)

Genes:
RANBP2:RAN binding protein 2 [Gene - OMIM - HGNC]
EDAR:ectodysplasin A receptor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q13
Genomic location:
Preferred name:
NM_022336.4(EDAR):c.1213G>C (p.Gly405Arg)
HGVS:
  • NC_000002.12:g.108897041C>G
  • NG_008257.1:g.97332G>C
  • NM_022336.4:c.1213G>CMANE SELECT
  • NP_071731.1:p.Gly405Arg
  • NC_000002.11:g.109513497C>G
Protein change:
G405R
Links:
dbSNP: rs1696610650
NCBI 1000 Genomes Browser:
rs1696610650
Molecular consequence:
  • NM_022336.4:c.1213G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Ectodermal dysplasia 10A, hypohidrotic/hair/nail type, autosomal dominant (ECTD10A)
Synonyms:
Ectodermal Dysplasia 3, Anhidrotic
Identifiers:
MONDO: MONDO:0007509; MedGen: C3888065; Orphanet: 1810; Orphanet: 238468; OMIM: 129490
Name:
Autosomal recessive hypohidrotic ectodermal dysplasia syndrome
Synonyms:
Autosomal recessive hypohidrotic ectodermal dysplasia
Identifiers:
MONDO: MONDO:0016619; MedGen: C0406702

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001531071Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Oct 18, 2021)
germlineclinical testing

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

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, SCV001531071.4

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

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Gly405 amino acid residue in EDAR. Other variant(s) that disrupt this residue have been determined to be pathogenic (Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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 EDAR protein function. ClinVar contains an entry for this variant (Variation ID: 1034708). This variant has not been reported in the literature in individuals affected with EDAR-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glycine with arginine at codon 405 of the EDAR protein (p.Gly405Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine.

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

Last Updated: Feb 28, 2024