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NM_147127.5(EVC2):c.3057+1del AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 15, 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:
RCV001944964.7

Allele description [Variation Report for NM_147127.5(EVC2):c.3057+1del]

NM_147127.5(EVC2):c.3057+1del

Gene:
EVC2:EvC ciliary complex subunit 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
4p16.2
Genomic location:
Preferred name:
NM_147127.5(EVC2):c.3057+1del
HGVS:
  • NC_000004.12:g.5584624del
  • NG_015821.1:g.129927del
  • NG_015821.2:g.129926del
  • NM_001166136.2:c.2817+1del
  • NM_147127.5:c.3057+1delMANE SELECT
  • NC_000004.11:g.5586349del
  • NC_000004.11:g.5586351del
Links:
dbSNP: rs772639262
NCBI 1000 Genomes Browser:
rs772639262
Molecular consequence:
  • NM_001166136.2:c.2817+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_147127.5:c.3057+1del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Ellis-van Creveld syndrome (EVC)
Synonyms:
MESOECTODERMAL DYSPLASIA; Chondroectodermal 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
SCV002131334Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Feb 15, 2021)
germlineclinical testing

PubMed (4)
[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

Sequencing EVC and EVC2 identifies mutations in two-thirds of Ellis-van Creveld syndrome patients.

Tompson SW, Ruiz-Perez VL, Blair HJ, Barton S, Navarro V, Robson JL, Wright MJ, Goodship JA.

Hum Genet. 2007 Jan;120(5):663-70. Epub 2006 Sep 21.

PubMed [citation]
PMID:
17024374

Widening the mutation spectrum of EVC and EVC2: ectopic expression of Weyer variants in NIH 3T3 fibroblasts disrupts Hedgehog signaling.

Valencia M, Lapunzina P, Lim D, Zannolli R, Bartholdi D, Wollnik B, Al-Ajlouni O, Eid SS, Cox H, Buoni S, Hayek J, Martinez-Frias ML, Antonio PA, Temtamy S, Aglan M, Goodship JA, Ruiz-Perez VL.

Hum Mutat. 2009 Dec;30(12):1667-75. doi: 10.1002/humu.21117.

PubMed [citation]
PMID:
19810119
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002131334.3

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

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with EVC2-related conditions. This variant is also known as c.3057+1del. This variant is present in population databases (rs772639262, ExAC 0.008%). This sequence change creates a premature translational stop signal (p.Glu1020Serfs*39) in the EVC2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in EVC2 are known to be pathogenic (PMID: 17024374, 19810119, 19876929).

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

Last Updated: Jan 13, 2025