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VWC2L von Willebrand factor C domain containing 2 like [ Homo sapiens (human) ]

Gene ID: 402117, updated on 7-Apr-2024

Summary

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Official Symbol
VWC2Lprovided by HGNC
Official Full Name
von Willebrand factor C domain containing 2 likeprovided by HGNC
Primary source
HGNC:HGNC:37203
See related
Ensembl:ENSG00000174453 MIM:619794; AllianceGenome:HGNC:37203
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to be involved in negative regulation of BMP signaling pathway. Predicted to act upstream of or within positive regulation of neuron differentiation. Predicted to be located in extracellular region and synapse. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward brain (RPKM 1.2) See more
Orthologs
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Genomic context

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See VWC2L in Genome Data Viewer
Location:
2q34-q35
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (214411054..214578976)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (214895548..215063486)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (215275778..215443700)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene sperm associated antigen 16 Neighboring gene uncharacterized LOC124907973 Neighboring gene ribosomal protein L5 pseudogene 8 Neighboring gene VWC2L intronic transcript 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:215458325-215458965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17071 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:215667579-215668122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17073 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12296 Neighboring gene endosulfine alpha pseudogene 3 Neighboring gene BRCA1 associated RING domain 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. Modulation of matrix mineralization by Vwc2-like protein and its novel splicing isoforms. Ohyama Y, et al. Biochem Biophys Res Commun, 2012 Feb 3. PMID 22209847, Free PMC Article
  2. Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans. Jeff JM, et al. Ann Hum Genet, 2013 Jul. PMID 23534349, Free PMC Article
  3. Evidence for genes on chromosome 2 contributing to alcohol dependence with conduct disorder and suicide attempts. Dick DM, et al. Am J Med Genet B Neuropsychiatr Genet, 2010 Sep. PMID 20468071, Free PMC Article
  4. Identification of host proteins required for HIV infection through a functional genomic screen. Brass AL, et al. Science, 2008 Feb 15. PMID 18187620
  5. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Yachie N, et al. Mol Syst Biol, 2016 Apr 22. PMID 27107012, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Vwc2l is a novel secreted protein that promotes matrix mineralization by modulating Osterix expression likely through TGF-beta superfamily growth factor signaling pathway.
    Title: Modulation of matrix mineralization by Vwc2-like protein and its novel splicing isoforms.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Evidence for genes on chromosome 2 contributing to alcohol dependence with conduct disorder and suicide attempts.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans.
EBI GWAS Catalog

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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of von Willebrand factor C domain containing protein 2-like (VWC2L; LOC402117) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

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

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of BMP signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of AMPA glutamate receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in synapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
von Willebrand factor C domain-containing protein 2-like
Names
VWC2-like protein
brorin-like
von Willebrand factor C domain containing protein 2 like

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.

mRNA and Protein(s)

  1. NM_001080500.4 → NP_001073969.1  von Willebrand factor C domain-containing protein 2-like isoform 1 precursor

    See identical proteins and their annotated locations for NP_001073969.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC068051, AC107218, BC146903
    Consensus CDS
    CCDS46509.1
    UniProtKB/Swiss-Prot
    A6NC69, B2RUW7, B2RUY7, B7X8X1
    Related
    ENSP00000308976.5, ENST00000312504.10
    Conserved Domains (1) summary
    cl17735
    Location:116 → 171
    VWC; von Willebrand factor type C domain

  2. NM_001345929.2 → NP_001332858.1  von Willebrand factor C domain-containing protein 2-like isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC068051, AC107218, BC171841
    Consensus CDS
    CCDS86917.1
    UniProtKB/TrEMBL
    B7ZW27, E6Y2G6
    Related
    ENSP00000403779.1, ENST00000427124.1

RNA

  1. NR_159945.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC068051, AC107218

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    214411054..214578976
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    214895548..215063486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
B2RUY7.1 GenPept UniProtKB/Swiss-Prot:B2RUY7

Gene LinkOut

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