NM_153717.3(EVC):c.2562-3_2584del AND multiple conditions

Clinical significance:Likely pathogenic (Last evaluated: Dec 14, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000824617.1

Allele description [Variation Report for NM_153717.3(EVC):c.2562-3_2584del]

NM_153717.3(EVC):c.2562-3_2584del

Gene:
EVC:EvC ciliary complex subunit 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
4p16.2
Genomic location:
Preferred name:
NM_153717.3(EVC):c.2562-3_2584del
HGVS:
  • NC_000004.12:g.5808198_5808223del
  • NG_008843.1:g.102002_102027del
  • NM_001306090.2:c.2562-3_2584del
  • NM_153717.3:c.2562-3_2584delMANE SELECT
  • NC_000004.11:g.5809925_5809950del
  • NM_153717.2:c.2562-3_2584del
Links:
dbSNP: rs1577663625
NCBI 1000 Genomes Browser:
rs1577663625
Molecular consequence:
  • NM_001306090.2:c.2562-3_2584del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_153717.3:c.2562-3_2584del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Ellis-van Creveld syndrome (EVC)
Synonyms:
Chondroectodermal dysplasia; Mesoectodermal dysplasia
Identifiers:
MONDO: MONDO:0009162; MedGen: C0013903; Orphanet: 289; OMIM: 225500
Name:
Curry-Hall syndrome (WAD)
Synonyms:
Acrofacial dysostosis of Weyers; WEYERS ACRODENTAL DYSOSTOSIS
Identifiers:
MONDO: MONDO:0008673; MedGen: C0457013; Orphanet: 952; OMIM: 193530

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000965522Invitaecriteria provided, single submitter
Likely pathogenic
(Dec 14, 2018)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Novel and recurrent EVC and EVC2 mutations in Ellis-van Creveld syndrome and Weyers acrofacial dyostosis.

D'Asdia MC, Torrente I, Consoli F, Ferese R, Magliozzi M, Bernardini L, Guida V, Digilio MC, Marino B, Dallapiccola B, De Luca A.

Eur J Med Genet. 2013 Feb;56(2):80-7. doi: 10.1016/j.ejmg.2012.11.005. Epub 2012 Dec 7.

PubMed [citation]
PMID:
23220543

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000965522.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change affects an acceptor splice site in intron 17 of the EVC gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with EVC-related conditions. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in EVC are known to be pathogenic (PMID: 23220543). 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.

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

Last Updated: Nov 27, 2021

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