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

Gene ID: 132884, updated on 3-Apr-2024

Summary

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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
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Genomic context

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See EVC2 in Genome Data Viewer
Location:
4p16.2
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (5529011..5709548, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (5498451..5681203, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (5564166..5711275, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene serine/threonine kinase 32B Neighboring gene RN7SK pseudogene 275 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:5526681-5527880 Neighboring gene uncharacterized LOC124900166 Neighboring gene long intergenic non-protein coding RNA 1587 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:5593995-5594527 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5595317-5595818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5595819-5596318 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:5610365-5610542 Neighboring gene NANOG hESC enhancer GRCh37_chr4:5613379-5613880 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:5641443-5642642 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:5666069-5667268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21241 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5710226-5710845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21242 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15223 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:5754671-5755626 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:5760129-5761328 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:5774235-5774978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:5774979-5775720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21246 Neighboring gene EvC ciliary complex subunit 1 Neighboring gene NANOG hESC enhancer GRCh37_chr4:5876470-5876991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5888332-5888859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5888860-5889386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5891930-5892674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5892675-5893418 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:5914348-5914973 Neighboring gene collapsin response mediator protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:5923869-5924368 Neighboring gene chromosome 4 open reading frame 50 Neighboring gene microRNA 378d-1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Identification of Compound Heterozygous EVC2 Gene Variants in Two Mexican Families with Ellis-van Creveld Syndrome. Negrete-Torres N, et al. Genes (Basel), 2023 Apr 9. PMID 37107645, Free PMC Article
  2. Novel and recurrent EVC and EVC2 mutations in Ellis-van Creveld syndrome and Weyers acrofacial dyostosis. D'Asdia MC, et al. Eur J Med Genet, 2013 Feb. PMID 23220543
  3. Identification of one novel mutation in the EVC2 gene in a Chinese family with Ellis-van Creveld syndrome. Zhang Z, et al. Gene, 2012 Dec 15. PMID 23026208
  4. Two novel heterozygous mutations of EVC2 cause a mild phenotype of Ellis-van Creveld syndrome in a Chinese family. Shen W, et al. Am J Med Genet A, 2011 Sep. PMID 21815252
  5. Ellis-van Creveld syndrome and congenital heart defects: presentation of an additional 32 cases. Hills CB, et al. Pediatr Cardiol, 2011 Oct. PMID 21533779

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution.
    Title: Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 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

  1. NG_015821.2 RefSeqGene

    Range
    5989..152109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    5529011..5709548 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449611.1 → XP_047305567.1  limbin isoform X2

  2. 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

  3. XM_047449610.1 → XP_047305566.1  limbin isoform X1

  4. XM_047449612.1 → XP_047305568.1  limbin isoform X3

  5. XM_017007738.2 → XP_016863227.1  limbin isoform X4

    UniProtKB/TrEMBL
    A0A0A0RAS4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    5498451..5681203 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348934.1 → XP_054204909.1  limbin isoform X2

  2. XM_054348933.1 → XP_054204908.1  limbin isoform X1

  3. XM_054348932.1 → XP_054204907.1  limbin isoform X1

  4. XM_054348935.1 → XP_054204910.1  limbin isoform X3

  5. XM_054348936.1 → XP_054204911.1  limbin isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86UK5.1 GenPept UniProtKB/Swiss-Prot:Q86UK5

Gene LinkOut

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