NC_000004.11:g.(?_2200251)_(5710240_?)del AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 17, 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:: RCV001386270.3

Allele description [Variation Report for NC_000004.11:g.(?_2200251)_(5710240_?)del]

NC_000004.11:g.(?_2200251)_(5710240_?)del

Genes:

POLN:DNA polymerase nu [Gene - OMIM - HGNC]
EVC2:EvC ciliary complex subunit 2 [Gene - OMIM - HGNC]
GRK4:G protein-coupled receptor kinase 4 [Gene - OMIM - HGNC]
HAUS3:HAUS augmin like complex subunit 3 [Gene - OMIM - HGNC]
HGFAC:HGF activator [Gene - OMIM - HGNC]
LRPAP1:LDL receptor related protein associated protein 1 [Gene - OMIM - HGNC]
LYAR:Ly1 antibody reactive [Gene - OMIM - HGNC]
MXD4:MAX dimerization protein 4 [Gene - OMIM - HGNC]
MSANTD1:Myb/SANT DNA binding domain containing 1 [Gene - HGNC]
NOP14:NOP14 nucleolar protein [Gene - OMIM - HGNC]
SH3BP2:SH3 domain binding protein 2 [Gene - OMIM - HGNC]
TNIP2:TNFAIP3 interacting protein 2 [Gene - OMIM - HGNC]
ADD1:adducin 1 [Gene - OMIM - HGNC]
ADRA2C:adrenoceptor alpha 2C [Gene - OMIM - HGNC]
CYTL1:cytokine like 1 [Gene - OMIM - HGNC]
DOK7:docking protein 7 [Gene - OMIM - HGNC]
FAM193A:family with sequence similarity 193 member A [Gene - OMIM - HGNC]
HTT:huntingtin [Gene - OMIM - HGNC]
LINC01587:long intergenic non-protein coding RNA 1587 [Gene - HGNC]
MFSD10:major facilitator superfamily domain containing 10 [Gene - OMIM - HGNC]
MSX1:msh homeobox 1 [Gene - OMIM - HGNC]
NSG1:neuronal vesicle trafficking associated 1 [Gene - OMIM - HGNC]
OTOP1:otopetrin 1 [Gene - OMIM - HGNC]
RGS12:regulator of G protein signaling 12 [Gene - OMIM - HGNC]
RNF4:ring finger protein 4 [Gene - OMIM - HGNC]
STK32B:serine/threonine kinase 32B [Gene - HGNC]
STX18:syntaxin 18 [Gene - OMIM - HGNC]
TMEM128:transmembrane protein 128 [Gene - HGNC]
ZFYVE28:zinc finger FYVE-type containing 28 [Gene - OMIM - HGNC]
ZBTB49:zinc finger and BTB domain containing 49 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

4p16.3-16.2

Genomic location:

Chr4: 2200251 - 5710240 (on Assembly GRCh37)

Preferred name:

NC_000004.11:g.(?_2200251)_(5710240_?)del

HGVS:

NC_000004.11:g.(?_2200251)_(5710240_?)del

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001586434	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 17, 2020)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 25174843, 18454448, 17024374, 19810119, 19876929, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001586434

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 17, 2020)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Role of CGH array in the diagnosis of autosomal recessive disease: a case of Ellis-van Creveld syndrome.

D'Ambrosio V, Votino C, Cos T, Boulanger S, Dheedene A, Jani J, Keymolen K.

Prenat Diagn. 2015 Jan;35(1):97-9. doi: 10.1002/pd.4490. Epub 2014 Oct 2. No abstract available.

PubMed [citation]

PMID:: 25174843

Long interspersed nuclear element-1 (LINE1)-mediated deletion of EVC, EVC2, C4orf6, and STK32B in Ellis-van Creveld syndrome with borderline intelligence.

Temtamy SA, Aglan MS, Valencia M, Cocchi G, Pacheco M, Ashour AM, Amr KS, Helmy SM, El-Gammal MA, Wright M, Lapunzina P, Goodship JA, Ruiz-Perez VL.

Hum Mutat. 2008 Jul;29(7):931-8. doi: 10.1002/humu.20778.

PubMed [citation]

PMID:: 18454448

See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001586434.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the EVC2 gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. Isolated whole-gene deletions of EVC2 have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 25174843, 18454448). Loss-of-function variants in EVC2 are known to be pathogenic (PMID: 17024374, 19810119, 19876929). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Jan 13, 2025

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