rs1553812417

chr4-5565282-AG-ATC

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_Strong PM2 PP5_Moderate

The NM_147127.5(EVC2):c.3634delinsGA(p.Leu1212AspfsTer53) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. L1212L) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: EVC2 NM_147127.5 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 3.54

Genes affected

EVC2 (HGNC:19747): (EvC ciliary complex subunit 2) This gene encodes a protein that functions in bone formation and skeletal development. Mutations in this gene, as well as in a neighboring gene that lies in a head-to-head configuration, cause Ellis-van Creveld syndrome, an autosomal recessive skeletal dysplasia that is also known as chondroectodermal dysplasia. Mutations in this gene also cause acrofacial dysostosis Weyers type, also referred to as Curry-Hall syndrome, a disease that combines limb and facial abnormalities. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 13 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 4-5565283-G-TC is Pathogenic according to our data. Variant chr4-5565283-G-TC is described in ClinVar as [Pathogenic]. Clinvar id is 455997.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EVC2	NM_147127.5	c.3634delinsGA	p.Leu1212AspfsTer53	frameshift_variant	21/22	ENST00000344408.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EVC2	ENST00000344408.10	c.3634delinsGA	p.Leu1212AspfsTer53	frameshift_variant	21/22	1	NM_147127.5	P2
EVC2	ENST00000310917.6	c.3394delinsGA	p.Leu1132AspfsTer53	frameshift_variant	21/22	1		A2
EVC2	ENST00000475313.5	c.3394delinsGA	p.Leu1132AspfsTer30	frameshift_variant, NMD_transcript_variant	21/23	1
EVC2	ENST00000509670.1	c.*2027delinsGA		3_prime_UTR_variant, NMD_transcript_variant	22/23	1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Ellis-van Creveld syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

May 03, 2017

This sequence change deletes 1 nucleotide and inserts 2 nucleotides in exon 21 of the EVC2 mRNA (c.3634delinsGA), causing a frameshift at codon 1212. This creates a premature translational stop signal in the last exon of the EVC2 mRNA (p.Leu1212Aspfs*53). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 97 amino acids of the EVC2 protein. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a EVC2-related disease. A different truncation downstream of this variant (p.Ser1220Argfs*3) has been determined to be pathogenic (PMID: 12571802, 19810119). This suggests that deletion of this region of the EVC2 protein is causative of disease. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1553812417; hg19: chr4-5567010;