NM_153717.3(EVC):c.56_174+42del AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 25, 2022
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:
RCV003020449.3

Allele description [Variation Report for NM_153717.3(EVC):c.56_174+42del]

NM_153717.3(EVC):c.56_174+42del

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.56_174+42del
HGVS:
  • NC_000004.12:g.5711436_5711596del
  • NG_008843.1:g.5240_5400del
  • NG_008843.2:g.5237_5397del
  • NG_015821.1:g.2958_3118del
  • NG_015821.2:g.2957_3117del
  • NM_001306090.2:c.56_174+42del
  • NM_001306092.2:c.56_174+42del
  • NM_153717.3:c.56_174+42delMANE SELECT
  • NC_000004.11:g.5713158_5713318del
  • NC_000004.11:g.5713163_5713323del
Molecular consequence:
  • NM_001306090.2:c.56_174+42del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001306092.2:c.56_174+42del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_153717.3:c.56_174+42del - splice donor variant - [Sequence Ontology: SO:0001575]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003303983Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Jan 25, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

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
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003303983.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

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 has not been reported in the literature in individuals affected with EVC-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This variant results in the deletion of part of exon 1 (c.56_174+42del) of the EVC gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in EVC are known to be pathogenic (PMID: 23220543).

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

Last Updated: Sep 29, 2024