COL3A1 collagen type III alpha 1 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL3A1provided by HGNC
Official Full Name: collagen type III alpha 1 chainprovided by HGNC
Primary source: HGNC:HGNC:2201
See related: Ensembl:ENSG00000168542 MIM:120180; AllianceGenome:HGNC:2201
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: EDS4A; EDSVASC; PMGEDSV
Summary: This gene encodes the pro-alpha1 chains of type III collagen, a fibrillar collagen that is found in extensible connective tissues such as skin, lung, uterus, intestine and the vascular system, frequently in association with type I collagen. Mutations in this gene are associated with Ehlers-Danlos syndrome type IV, and with aortic and arterial aneurysms. [provided by R. Dalgleish, Feb 2008]
Expression: Biased expression in gall bladder (RPKM 1491.0), placenta (RPKM 1173.3) and 12 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q32.2

Exon count:: 51

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (188974373..189012746)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (189463283..189501589)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (189839099..189877472)

Chromosome 2 - NC_000002.12 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?

COL3A1-positive endothelial cells influence LUAD prognosis and regulate LUAD carcinogenesis by NCL-PI3K-AKT axis.
Title: COL3A1-positive endothelial cells influence LUAD prognosis and regulate LUAD carcinogenesis by NCL-PI3K-AKT axis.
COL3A1 is a potential diagnostic biomarker for synovial chondromatosis and affects the cell cycle and migration of chondrocytes.
Title: COL3A1 is a potential diagnostic biomarker for synovial chondromatosis and affects the cell cycle and migration of chondrocytes.
Identification of two novel COL3A1 variants in patients with vascular Ehlers-Danlos syndrome.
Title: Identification of two novel COL3A1 variants in patients with vascular Ehlers-Danlos syndrome.
Features of Vascular Ehlers-Danlos Syndrome Among Biobank Participants Harboring Predicted High-Risk COL3A1 Genotypes.
Title: Features of Vascular Ehlers-Danlos Syndrome Among Biobank Participants Harboring Predicted High-Risk COL3A1 Genotypes.
COL3A1, CXCL8, VCAN, THBS2, and COL1A2 are correlated with the onset of biliary atresia.
Title: COL3A1, CXCL8, VCAN, THBS2, and COL1A2 are correlated with the onset of biliary atresia.
COL3A1 Overexpression Associates with Poor Prognosis and Cisplatin Resistance in Lung Cancer
Title: COL3A1 Overexpression Associates with Poor Prognosis and Cisplatin Resistance in Lung Cancer.
Phenotype of COL3A1/COL5A2 deletion patients.
Title: Phenotype of COL3A1/COL5A2 deletion patients.
Carriers of COL3A1 pathogenic variants in Denmark: Interfamilial variability in severity and outcome of elective surgical procedures.
Title: Carriers of COL3A1 pathogenic variants in Denmark: Interfamilial variability in severity and outcome of elective surgical procedures.
Atypical variants in COL1A1 and COL3A1 associated with classical and vascular Ehlers-Danlos syndrome overlap phenotypes: expanding the clinical phenotype based on additional case reports.
Title: Atypical variants in COL1A1 and COL3A1 associated with classical and vascular Ehlers-Danlos syndrome overlap phenotypes: expanding the clinical phenotype based on additional case reports.
Overexpressed COL3A1 has prognostic value in human esophageal squamous cell carcinoma and promotes the aggressiveness of esophageal squamous cell carcinoma by activating the NF-kappaB pathway.
Title: Overexpressed COL3A1 has prognostic value in human esophageal squamous cell carcinoma and promotes the aggressiveness of esophageal squamous cell carcinoma by activating the NF-κB pathway.

Submit: New GeneRIF Correction See all GeneRIFs (167)

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

Professional guidelines

Description
Professional guideline ACMG 2013 The ACMG recommends that laboratories performing clinical sequencing seek and report mutations in COL3A1 that are pathogenic or expected to be pathogenic. GuidelinePubMed

Associated conditions

Description	Tests
Ehlers-Danlos syndrome, type 4 MedGen: C0268338 OMIM: 130050 GeneReviews: Vascular Ehlers-Danlos Syndrome	Compare labs
Polymicrogyria with or without vascular-type Ehlers-Danlos syndrome MedGen: C5193040 OMIM: 618343 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2017-01-12) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2017-01-12) ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat upregulates the steady-state RNA levels for fibronectin and types I and III collagen in glioblastoma cells and salivary gland cell lines	PubMed

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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

COL3A1 (e-PCR)
- UniSTS:480020

GDB:180981 (e-PCR)
- UniSTS:155156

RH99230 (e-PCR)
- UniSTS:86818

GDB:181238 (e-PCR)
- UniSTS:155206

D2S2587 (e-PCR)
- UniSTS:30538

RH134399 (e-PCR)
- UniSTS:217681

GDB:178182 (e-PCR)
- UniSTS:154983

GDB:178183 (e-PCR)
- UniSTS:154984

X57983 (e-PCR)
- UniSTS:125805

COL3A1-379 (e-PCR), detects polymorphism
- UniSTS:251510

COL3A1_428 (e-PCR)
- UniSTS:277115

GDB:178411 (e-PCR)
- UniSTS:155007

GDB:178412 (e-PCR)
- UniSTS:155008

COL3A1-95 (e-PCR), detects polymorphism
- UniSTS:519063

RH69964 (e-PCR)
- UniSTS:67759

MARC_23660-23661:1029504961:1 (e-PCR)
- UniSTS:268738

WI-16343 (e-PCR)
- UniSTS:68589

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables SMAD binding	IEA Inferred from Electronic Annotation more info
enables extracellular matrix structural constituent	IMP Inferred from Mutant Phenotype more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	HDA more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables integrin binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables integrin binding	NAS Non-traceable Author Statement more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables platelet-derived growth factor binding	IDA Inferred from Direct Assay more info	PubMed
enables protease binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in aorta smooth muscle tissue morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in basement membrane organization	IEA Inferred from Electronic Annotation more info
involved_in cell-matrix adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to amino acid stimulus	IEA Inferred from Electronic Annotation more info
involved_in cerebral cortex development	ISS Inferred from Sequence or Structural Similarity more info
involved_in chondrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in collagen fibril organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in collagen fibril organization	NAS Non-traceable Author Statement more info	PubMed
involved_in digestive tract development	IEA Inferred from Electronic Annotation more info
involved_in elastic fiber assembly	IEA Inferred from Electronic Annotation more info
involved_in endochondral bone morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in fibroblast proliferation	IEA Inferred from Electronic Annotation more info
involved_in heart development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in integrin-mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in layer formation in cerebral cortex	IEA Inferred from Electronic Annotation more info
involved_in limb joint morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in lung development	IEA Inferred from Electronic Annotation more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of neuron migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron migration	IEA Inferred from Electronic Annotation more info
involved_in peptide cross-linking	IDA Inferred from Direct Assay more info	PubMed
involved_in platelet activation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of Rho protein signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to angiotensin	IEA Inferred from Electronic Annotation more info
involved_in response to cytokine	IDA Inferred from Direct Assay more info	PubMed
involved_in response to radiation	IDA Inferred from Direct Assay more info	PubMed
involved_in skin development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in supramolecular fiber organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tissue homeostasis	IEA Inferred from Electronic Annotation more info
involved_in transforming growth factor beta receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in transforming growth factor beta1 production	IEA Inferred from Electronic Annotation more info
involved_in wound healing	IDA Inferred from Direct Assay more info	PubMed
involved_in wound healing	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of collagen type III trimer	IDA Inferred from Direct Assay more info	PubMed
part_of collagen type III trimer	IMP Inferred from Mutant Phenotype more info	PubMed
part_of collagen type III trimer	IPI Inferred from Physical Interaction more info	PubMed
part_of collagen type III trimer	NAS Non-traceable Author Statement more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in collagen-containing extracellular matrix	IMP Inferred from Mutant Phenotype more info	PubMed
colocalizes_with collagen-containing extracellular matrix	TAS Traceable Author Statement more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular region	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: collagen alpha-1(III) chain

Names: Ehlers-Danlos syndrome type IV, autosomal dominant; alpha-1 type III collagen; alpha1 (III) collagen; collagen, fetal; collagen, type III, alpha 1

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_007404.1 RefSeqGene

Range

5001..43374

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_3

mRNA and Protein(s)

NM_000090.4 → NP_000081.2 collagen alpha-1(III) chain preproprotein

Status: REVIEWED

Source sequence(s)

AC066694

Consensus CDS

CCDS2297.1

UniProtKB/Swiss-Prot

D2JYH5, D3DPH4, P02461, P78429, Q15112, Q16403, Q53S91, Q541P8, Q6LDB3, Q6LDJ2, Q6LDJ3, Q7KZ56, Q8N6U4, Q9UC88, Q9UC89, Q9UC90, Q9UC91, R4N3C5, V9GZI1

Related

ENSP00000304408.4, ENST00000304636.9

Conserved Domains (4) summary

pfam01391
Location:414 → 473

Collagen; Collagen triple helix repeat (20 copies)

PRK07764
Location:245 → 452

PRK07764; DNA polymerase III subunits gamma and tau; Validated

pfam00093
Location:32 → 88

VWC; von Willebrand factor type C domain

pfam01410
Location:1233 → 1465

COLFI; Fibrillar collagen C-terminal domain