COL6A4P1 collagen type VI alpha 4 pseudogene 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL6A4P1provided by HGNC
Official Full Name: collagen type VI alpha 4 pseudogene 1provided by HGNC
Primary source: HGNC:HGNC:33484
See related: Ensembl:ENSG00000291281 MIM:612397; AllianceGenome:HGNC:33484
Gene type: pseudo
RefSeq status: PROVISIONAL
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: DIVA; DVWA; VWA6; FAME3; COL6A4; COL6A4P
Summary: This transcribed pseudogene represents the 5' end of a presumed ortholog to a mouse gene which encodes a collagen VI alpha 4 chain protein (GeneID 68553). No complete ORF of comparable size to the mouse protein is found in this gene. The predicted protein lacks a signal peptide; however, this truncated collagen polypeptide may have achieved a different function as suggested by PubMed ID: 18622395. Evidence of in vivo translation is incomplete. A large chromosome break separates this pseudogene from the 3' end of the presumed ortholog (COL6A4P2, GeneID 646300) which is located downstream at chromosome 3q21.3. [provided by RefSeq, Jun 2009]
Annotation information: Note: The RefSeq record representing this transcribed pseudogene is shorter than its presumed genomic span as based on alignments of homologous mouse cDNA and human EST data. [26 Jun 2009]
Expression: Low expression observed in reference dataset See more
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Genomic context

Location:: 3p25.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (15165362..15205959, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (15167771..15208368, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (15206869..15247466, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

rs7639618 associated with a significantly increased risk of knee osteoarthritis in Asians [meta-analysis]
Title: Single Nucleotide Polymorphisms and Osteoarthritis: An Overview and a Meta-Analysis.
The DVWA SNPs rs11718863, rs7639618, rs7651842, rs7639807 and rs17040821 are probably able to induce protein functional changes leading to osteoarthritis.
Title: DVWA gene polymorphisms and osteoarthritis.
DVWA does not seem to be a risk factor for developmental dysplasia of the hip in the Chinese Han population.
Title: Lack of evidence for association between DVWA gene polymorphisms and developmental dysplasia of the hip in Chinese Han population.
The was no association of SNPs in DVWA with Kashin-Beck disease.
Title: [Association between polymorphism in DVWA and IL-1beta and Kashin-Beck disease].
DVWA is evolutionally very unique, which, together with its specific expression in articular cartilage, suggests its specific role in human cartilage metabolism.
Title: Cloning and characterization of the osteoarthritis-associated gene DVWA.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Prediction model for knee osteoarthritis based on genetic and clinical information.
Results suggest that there may be global relevance for the DVWA SNP rs7639618 among knee osteoarthritis cases.
Title: Large replication study and meta-analyses of DVWA as an osteoarthritis susceptibility locus in European and Asian populations.
Observational study of gene-disease association. (HuGE Navigator)
Title: [Association between polymorphism in DVWA and IL-1beta and Kashin-Beck disease].
data confirm that the GDF5 variant is consistently associated with the risk of knee osteoarthritis and ethnic variation in allele frequencies at the DVWA gene was found and no significant association was found in UK or by combining UK and Asian samples.
Title: Association of the DVWA and GDF5 polymorphisms with osteoarthritis in UK populations.
The discovery of three additional collagen VI chains doubles the collagen VI family and adds a layer of complexity to collagen VI assembly and function in the extracellular matrix.
Title: Three novel collagen VI chains, alpha4(VI), alpha5(VI), and alpha6(VI).

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See studies and variants in dbVar

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Other Names

collagen VI alpha 4 pseudogene 1
collagen, type VI, alpha 4, pseudogene
dual intracellular von Willebrand factor domain A
dual von Willebrand factor A domains
von Willebrand factor A domain containing 6

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.