Human Gene EVC2 (ENST00000344408.10) from GENCODE V43
  Description: Homo sapiens EvC ciliary complex subunit 2 (EVC2), transcript variant 1, mRNA. (from RefSeq NM_147127)
RefSeq Summary (NM_147127): 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].
Gencode Transcript: ENST00000344408.10
Gencode Gene: ENSG00000173040.13
Transcript (Including UTRs)
   Position: hg38 chr4:5,562,439-5,708,559 Size: 146,121 Total Exon Count: 22 Strand: -
Coding Region
   Position: hg38 chr4:5,562,848-5,708,513 Size: 145,666 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-02-17 13:02:02

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr4:5,562,439-5,708,559)mRNA (may differ from genome)Protein (1308 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSCGAPEnsemblEntrez GeneExonPrimerGencode

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Limbin; AltName: Full=Ellis-van Creveld syndrome protein 2; Short=EVC2; Flags: Precursor;
FUNCTION: Positive regulator of the hedgehog signaling pathway (By similarity). Plays a critical role in bone formation and skeletal development.
SUBUNIT: Interacts with EVC (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein (By similarity). Cytoplasm, cytoskeleton, cilium basal body (By similarity). Cell projection, cilium (By similarity). Cell projection, cilium membrane (By similarity). Nucleus (By similarity).
TISSUE SPECIFICITY: Found in the heart, placenta, lung, liver, skeletal muscle, kidney and pancreas.
DISEASE: Defects in EVC2 are a cause of Ellis-van Creveld syndrome (EVC) [MIM:225500]; also known as chondroectodermal dysplasia. EVC is an autosomal recessive disorder characterized by the clinical tetrad of chondrodystrophy, polydactyly, ectodermal dysplasia and cardiac anomalies. Patients manifest short-limb dwarfism, short ribs, postaxial polydactyly and dysplastic nails and teeth. Congenital heart defects, most commonly an atrioventricular septal defect, are observed in 60% of affected individuals.
DISEASE: Defects in EVC2 are a cause of acrofacial dysostosis Weyers type (WAD) [MIM:193530]; also known as Curry-Hall syndrome. Acrofacial dysostoses are a heterogeneous group of disorders combining limb defects with facial abnormalities. WAD is an autosomal dominant disorder characterized by dysplastic nails, postaxial polydactyly, acrofacial dysostosis, short limbs and short stature. The phenotype is milder than Ellis-van Creveld syndrome.
SEQUENCE CAUTION: Sequence=AAN86577.1; Type=Erroneous initiation; Sequence=AAN86578.1; Type=Erroneous initiation;

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: EVC2
Diseases sorted by gene-association score: ellis-van creveld syndrome* (1749), weyers acrofacial dysostosis* (968), evc2-related ellis-van creveld syndrome* (100), acrofacial dysostosis (26), dysostosis (14), polydactyly, postaxial, types a1 and b (12), phlebotomus fever (11), atrioventricular septal defect (9), biliary dyskinesia (6), compartment syndrome (5), mild pre-eclampsia (5), short-rib thoracic dysplasia 3 with or without polydactyly (5), ectodermal dysplasia 2, clouston type (4), hydrolethalus syndrome (4), cranioectodermal dysplasia 1 (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.59 RPKM in Ovary
Total median expression: 87.82 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -18.7046-0.407 Picture PostScript Text
3' UTR -106.50409-0.260 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR022076 - Limbin
IPR026501 - Limbin/Ellis-van_Creveld

Pfam Domains:
PF12297 - Ellis van Creveld protein 2 like protein

ModBase Predicted Comparative 3D Structure on Q86UK5
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007224 smoothened signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005929 cilium
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0042995 cell projection
GO:0060170 ciliary membrane
GO:0098797 plasma membrane protein complex

-  Descriptions from all associated GenBank mRNAs
  AY152403 - Homo sapiens EVC2 protein variant (EVC2) mRNA, complete cds.
AY152402 - Homo sapiens EVC2 protein (EVC2) mRNA, complete cds.
AY185210 - Homo sapiens EVC2 (EVC2) mRNA, complete cds.
BC143836 - Homo sapiens cDNA clone IMAGE:9052351.
AB083067 - Homo sapiens LBN mRNA for limbin, complete cds.
BC111455 - Synthetic construct Homo sapiens clone IMAGE:40080660, MGC:133448 EVC2 protein (EVC2) mRNA, encodes complete protein.
JD546124 - Sequence 527148 from Patent EP1572962.
JD151463 - Sequence 132487 from Patent EP1572962.
JD039766 - Sequence 20790 from Patent EP1572962.
JD300268 - Sequence 281292 from Patent EP1572962.
JD538201 - Sequence 519225 from Patent EP1572962.
JD558483 - Sequence 539507 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q86UK5 (Reactome details) participates in the following event(s):

R-HSA-5632679 EVC2:EVC binds p-SMO
R-HSA-5633051 EFCAB7:IQCE binds EVC2:EVC
R-HSA-5635838 Activation of SMO
R-HSA-5632684 Hedgehog 'on' state
R-HSA-5358351 Signaling by Hedgehog
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000344408.1, ENST00000344408.2, ENST00000344408.3, ENST00000344408.4, ENST00000344408.5, ENST00000344408.6, ENST00000344408.7, ENST00000344408.8, ENST00000344408.9, LBN, LBN_HUMAN, NM_147127, Q86UK5, Q86YT3, Q86YT4, Q8NG49, uc003gij.1, uc003gij.2, uc003gij.3, uc003gij.4, uc003gij.5
UCSC ID: ENST00000344408.10
RefSeq Accession: NM_147127
Protein: Q86UK5 (aka LBN_HUMAN)
CCDS: CCDS3382.2

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.