EVC2 EvC ciliary complex subunit 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EVC2provided by HGNC
Official Full Name: EvC ciliary complex subunit 2provided by HGNC
Primary source: HGNC:HGNC:19747
See related: Ensembl:ENSG00000173040 MIM:607261; AllianceGenome:HGNC:19747
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LBN; WAD
Summary: 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]
Expression: Ubiquitous expression in ovary (RPKM 2.2), endometrium (RPKM 1.3) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4p16.2

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (5529011..5709548, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (5498451..5681203, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (5564166..5711275, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of Compound Heterozygous EVC2 Gene Variants in Two Mexican Families with Ellis-van Creveld Syndrome.
Title: Identification of Compound Heterozygous EVC2 Gene Variants in Two Mexican Families with Ellis-van Creveld Syndrome.
Dental Anomalies in Ciliopathies: Lessons from Patients with BBS2, BBS7, and EVC2 Mutations.
Title: Dental Anomalies in Ciliopathies: Lessons from Patients with BBS2, BBS7, and EVC2 Mutations.
Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution.
Title: Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution.
Novel mutation in EFCAB7 alters expression and interaction with EVC2 protein.
Title: Novel mutation in EFCAB7 alters expression and interaction of Ellis-van Creveld ciliary proteins.
Novel Wnt10A mutations (c.521T>C and c.653T>G) and EVC2 mutation (c.1472C>T) were identified in families with selective tooth agenesis. The Wnt10A c.521T>C mutation and the EVC2 c.1472C>T mutation were considered as pathogenic for affecting highly conserved amino acids, co-segregated with phenotype and predicted to be disease-causing by SIFT and PolyPhen2.
Title: Novel mutations identified in patients with tooth agenesis by whole-exome sequencing.
he whole exome sequencing (WES) in this family revealed two homozygous variants in EVC2 (c.30dupC; p.Thr11Hisfs*45) and TMC1 (c.1696-1G>A) genes. In family B, WES revealed novel compound heterozygous variants (p.Ser307Pro, c.2894+3A>G) in the EVC gene.
Title: Ellis-van Creveld syndrome and profound deafness resulted by sequence variants in the EVC/EVC2 and TMC1 genes.
we detected two novel nonsense mutations and a partial deletion of EVC/EVC2 in two Vietnamese families with EvC. Moreover, we found in one family a missense mutation of EFCAB7, a possible modifier gene in EvC and its related disorders.
Title: Truncation and microdeletion of EVC/EVC2 with missense mutation of EFCAB7 in Ellis-van Creveld syndrome.
sequence analysis identified a novel nonsense mutation (p.Trp234*) in exon 8 of the EVC2 gene and 15 bp duplication in exon 14 of the EVC gene in the two families..
Title: Novel homozygous mutations in the EVC and EVC2 genes in two consanguineous families segregating autosomal recessive Ellis-van Creveld syndrome.
Sequencing of both EVC and EVC2 identified two novel heterozygous splice site mutations c.384+5G>C in intron 3 and c.1465-1G>A in intron 10 in EVC, which were inherited from mother and father, respectively.
Title: Novel mutations in EVC cause aberrant splicing in Ellis-van Creveld syndrome.
Exome sequencing revealed a likely pathogenic mutation in three novel candidate MKS disease genes-C5orf42, EVC2 and SEC8 (also known as EXOC4), which encodes an exocyst protein with an established role in ciliogenesis
Title: Genomic analysis of Meckel-Gruber syndrome in Arabs reveals marked genetic heterogeneity and novel candidate genes.

Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Curry-Hall syndrome MedGen: C0457013 OMIM: 193530 GeneReviews: Not available	Compare labs
Ellis-van Creveld syndrome MedGen: C0013903 OMIM: 225500 GeneReviews: Ellis-van Creveld Syndrome	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D4S2354 (e-PCR)
- UniSTS:45169

G16701 (e-PCR)
- UniSTS:62927

G33508 (e-PCR)
- UniSTS:74987

EVC2__7605 (e-PCR)
- UniSTS:466158

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in smoothened signaling pathway	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in ciliary membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary membrane	TAS Traceable Author Statement more info
located_in cilium	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in nucleus	HDA more info	PubMed
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of plasma membrane protein complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: limbin

Names: Ellis van Creveld syndrome 2; ellis-van Creveld syndrome protein 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_015821.2 RefSeqGene

Range

5989..152109

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001166136.2 → NP_001159608.1 limbin isoform 2

See identical proteins and their annotated locations for NP_001159608.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream translational start codon, compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 1.

Source sequence(s)

AC114738, AC116613, AW137166, AY152402, BG755658

Consensus CDS

CCDS54718.1

UniProtKB/TrEMBL

A0A0A0RAS4

Related

ENSP00000311683.2, ENST00000310917.6

Conserved Domains (1) summary

pfam12297
Location:157 → 580

EVC2_like; Ellis van Creveld protein 2 like protein
NM_147127.5 → NP_667338.3 limbin isoform 1

See identical proteins and their annotated locations for NP_667338.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the shorter transcript but encodes the longer isoform (1).

Source sequence(s)

AW137166, AY185210, BG755658

Consensus CDS

CCDS3382.2

UniProtKB/Swiss-Prot

Q86UK5, Q86YT3, Q86YT4, Q8NG49

UniProtKB/TrEMBL

A0A0A0RAS4

Related

ENSP00000342144.5, ENST00000344408.10

Conserved Domains (1) summary

pfam12297
Location:237 → 660

EVC2_like; Ellis van Creveld protein 2 like protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

5529011..5709548 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047449611.1 → XP_047305567.1 limbin isoform X2

UniProtKB/TrEMBL

A0A0C4DGE7
XM_017007736.2 → XP_016863225.1 limbin isoform X1

UniProtKB/TrEMBL

A0A0A0RAS4

Conserved Domains (1) summary

pfam12297
Location:157 → 580

EVC2_like; Ellis van Creveld protein 2 like protein
XM_047449610.1 → XP_047305566.1 limbin isoform X1

UniProtKB/TrEMBL

A0A0A0RAS4
XM_047449612.1 → XP_047305568.1 limbin isoform X3

UniProtKB/TrEMBL

A0A0C4DGE7
XM_017007738.2 → XP_016863227.1 limbin isoform X4

UniProtKB/TrEMBL

A0A0A0RAS4