COL1A1 collagen type I alpha 1 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL1A1provided by HGNC
Official Full Name: collagen type I alpha 1 chainprovided by HGNC
Primary source: HGNC:HGNC:2197
See related: Ensembl:ENSG00000108821 MIM:120150
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: OI1; OI2; OI3; OI4; EDSC; CAFYD; EDSARTH1
Summary: This gene encodes the pro-alpha1 chains of type I collagen whose triple helix comprises two alpha1 chains and one alpha2 chain. Type I is a fibril-forming collagen found in most connective tissues and is abundant in bone, cornea, dermis and tendon. Mutations in this gene are associated with osteogenesis imperfecta types I-IV, Ehlers-Danlos syndrome type VIIA, Ehlers-Danlos syndrome Classical type, Caffey Disease and idiopathic osteoporosis. Reciprocal translocations between chromosomes 17 and 22, where this gene and the gene for platelet-derived growth factor beta are located, are associated with a particular type of skin tumor called dermatofibrosarcoma protuberans, resulting from unregulated expression of the growth factor. Two transcripts, resulting from the use of alternate polyadenylation signals, have been identified for this gene. [provided by R. Dalgleish, Feb 2008]
Expression: Biased expression in gall bladder (RPKM 850.7), urinary bladder (RPKM 497.1) and 11 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q21.33

Exon count:: 51

Annotation release	Status	Assembly	Chr	Location
109.20210514	current	GRCh38.p13 (GCF_000001405.39)	17	NC_000017.11 (50184096..50201649, complement)
105.20201022	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (48261462..48278992, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Inter- and Intrafamilial Phenotypic Variability in Individuals with Collagen-Related Osteogenesis Imperfecta.
Title: Inter- and Intrafamilial Phenotypic Variability in Individuals with Collagen-Related Osteogenesis Imperfecta.
Autophagy facilitates type I collagen synthesis in periodontal ligament cells.
Title: Autophagy facilitates type I collagen synthesis in periodontal ligament cells.
Assessment of COL1A1 and MMP9 expression in patients with dermatochalasis.
Title: Assessment of COL1A1 and MMP9 expression in patients with dermatochalasis.
Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta.
Title: Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta.
The impact of COL1A1 and COL6A1 expression on hypospadias and penile curvature severity.
Title: The impact of COL1A1 and COL6A1 expression on hypospadias and penile curvature severity.
Myositis ossificans-like soft tissue aneurysmal bone cyst: a clinical, radiological, and pathological study of seven cases with COL1A1-USP6 fusion and a novel ANGPTL2-USP6 fusion.
Title: Myositis ossificans-like soft tissue aneurysmal bone cyst: a clinical, radiological, and pathological study of seven cases with COL1A1-USP6 fusion and a novel ANGPTL2-USP6 fusion.
Targeting lncRNA H19/miR-29b/COL1A1 Axis Impedes Myofibroblast Activities of Precancerous Oral Submucous Fibrosis.
Title: Targeting lncRNA H19/miR-29b/COL1A1 Axis Impedes Myofibroblast Activities of Precancerous Oral Submucous Fibrosis.
Differential Protein Expression between Cystic and Solid Vestibular Schwannoma Using Tandem Mass Tag-Based Quantitative Proteomic Analysis.
Title: Differential Protein Expression between Cystic and Solid Vestibular Schwannoma Using Tandem Mass Tag-Based Quantitative Proteomic Analysis.
COL1A1 Is a Potential Prognostic Biomarker and Correlated with Immune Infiltration in Mesothelioma.
Title: COL1A1 Is a Potential Prognostic Biomarker and Correlated with Immune Infiltration in Mesothelioma.
A novel splicing pathogenic variant in COL1A1 causing osteogenesis imperfecta (OI) type I in a Chinese family.
Title: A novel splicing pathogenic variant in COL1A1 causing osteogenesis imperfecta (OI) type I in a Chinese family.

Submit: New GeneRIF Correction See all GeneRIFs (517)

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
A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study. GeneReviews: Not available
Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 1 MedGen: C5436842 OMIM: 619115 GeneReviews: Not available	Compare labs
Ehlers-Danlos syndrome, arthrochalasia type, 1 MedGen: C4551623 OMIM: 130060 GeneReviews: Not available	Compare labs
Genetic association with overall survival of taxane-treated lung cancer patients - A genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study. GeneReviews: Not available
Infantile cortical hyperostosis MedGen: C0020497 OMIM: 114000 GeneReviews: Caffey Disease	Compare labs
Osteogenesis imperfecta MedGen: C0029434 GeneReviews: COL1A1/2 Osteogenesis Imperfecta	Compare labs
Osteogenesis imperfecta type I MedGen: C0023931 OMIM: 166200 GeneReviews: COL1A1/2 Osteogenesis Imperfecta	Compare labs
Osteogenesis imperfecta type III MedGen: C0268362 OMIM: 259420 GeneReviews: COL1A1/2 Osteogenesis Imperfecta	Compare labs
Osteogenesis imperfecta with normal sclerae, dominant form MedGen: C0268363 OMIM: 166220 GeneReviews: COL1A1/2 Osteogenesis Imperfecta	Compare labs
Osteogenesis imperfecta, recessive perinatal lethal MedGen: C0268358 OMIM: 166210 GeneReviews: COL1A1/2 Osteogenesis Imperfecta	Compare labs
Postmenopausal osteoporosis MedGen: C0029458 OMIM: 166710 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2012-08-23) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2012-08-23) 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
Envelope surface glycoprotein gp120	env	HIV-1 X4-tropic gp120 upregulates alpha-SMA (ACTA2) and collagen I alpha 1 expression via the ERK1/2 pathway in a CXCR4-dependent manner in activated human hepatic stellate cells	PubMed
Tat	tat	HIV-1 Tat, through its basic domain (amino acids 46-60), inhibits the adhesion of collagen I to the neuroblastoma cell line GI-CA-N, suggesting a role for Tat in the neurologic dysfunction and destruction of the CNS observed in infants infected with HIV-1	PubMed
	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
Vpu	vpu	HIV-1 Vpu-expressing U937 monocytes coculture with LX2 stellate cells to upregulate expression of profibrogenic markers COL-1, PCT, SMA-1, VEGF, and MMP2, which is inhibited by MIF treatment	PubMed
matrix	gag	Treatment of human stellate cells with HIV-1 MA upregulates the expression of CXCR2, syndecan-2, collagen-I, alpha-SMA, vimentin, and endothelin-1	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

COL1A1 (e-PCR)
- UniSTS:262913

MARC_5785-5786:991939715:3 (e-PCR)
- UniSTS:231169

MARC_5785-5786:997299286:1 (e-PCR)
- UniSTS:231169

GDB:180975 (e-PCR)
- UniSTS:155152

Col1a1 (e-PCR), detects polymorphism
- UniSTS:141374

PMC34669P1 (e-PCR)
- UniSTS:273227

GDB:177792 (e-PCR)
- UniSTS:154961

COL1A1_1682 (e-PCR)
- UniSTS:277113

MARC_5219-5220:996690145:1 (e-PCR)
- UniSTS:269465

fj67h06.x1 (e-PCR)
- UniSTS:199838

WI-18942 (e-PCR)
- UniSTS:30883

RH77855 (e-PCR)
- UniSTS:68277

GDB:180347 (e-PCR)
- UniSTS:155079

SGC32927 (e-PCR)
- UniSTS:73934

RH45119 (e-PCR)
- UniSTS:58326

GDB:177260 (e-PCR)
- UniSTS:154850

Homology

Homologs of the COL1A1 gene: The COL1A1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, zebrafish, and frog.
Orthologs from Annotation Pipeline: 242 organisms have orthologs with human gene COL1A1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	HDA more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	ISS Inferred from Sequence or Structural Similarity more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables identical protein binding	IDA Inferred from Direct Assay 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 blood vessel development	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in blood vessel development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in bone trabecula formation	IEA Inferred from Electronic Annotation more info
involved_in cartilage development involved in endochondral bone morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cellular response to amino acid stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to epidermal growth factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to fibroblast growth factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to fluoride	IEA Inferred from Electronic Annotation more info
involved_in cellular response to mechanical stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to retinoic acid	IEA Inferred from Electronic Annotation more info
involved_in cellular response to transforming growth factor beta stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to tumor necrosis factor	IEA Inferred from Electronic Annotation more info
involved_in cellular response to vitamin E	IEA Inferred from Electronic Annotation more info
involved_in collagen biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in collagen fibril organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in collagen-activated tyrosine kinase receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in embryonic skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endochondral ossification	IEA Inferred from Electronic Annotation more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in face morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in intramembranous ossification	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell-substrate adhesion	IEA Inferred from Electronic Annotation more info
involved_in ossification	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in osteoblast differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of canonical Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of epithelial to mesenchymal transition	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription, DNA-templated	IDA Inferred from Direct Assay more info	PubMed
involved_in protein localization to nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in response to cAMP	IEA Inferred from Electronic Annotation more info
involved_in response to corticosteroid	IEA Inferred from Electronic Annotation more info
involved_in response to estradiol	IEA Inferred from Electronic Annotation more info
involved_in response to hydrogen peroxide	IEA Inferred from Electronic Annotation more info
involved_in response to hyperoxia	IEA Inferred from Electronic Annotation more info
involved_in response to mechanical stimulus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in response to peptide hormone	IEA Inferred from Electronic Annotation more info
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in skin development	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in skin morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tooth eruption	IEA Inferred from Electronic Annotation more info
involved_in tooth mineralization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in visual perception	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in wound healing	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
part_of collagen type I trimer	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of collagen type I trimer	IDA Inferred from Direct Assay more info	PubMed
part_of collagen type I trimer	IMP Inferred from Mutant Phenotype more info	PubMed
colocalizes_with collagen-containing extracellular matrix	HDA more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
colocalizes_with collagen-containing extracellular matrix	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
is_active_in extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in extracellular region	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in extracellular space	IMP Inferred from Mutant Phenotype more info	PubMed
located_in secretory granule	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: collagen alpha-1(I) chain

Names: alpha-1 type I collagen; alpha1(I) procollagen; collagen alpha 1 chain type I; collagen alpha-1(I) chain preproprotein; collagen of skin, tendon and bone, alpha-1 chain; collagen, type I, alpha 1; pro-alpha-1 collagen type 1; type I proalpha 1; type I procollagen alpha 1 chain

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_007400.1 RefSeqGene

Range

5001..22544

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1

mRNA and Protein(s)

NM_000088.4 → NP_000079.2 collagen alpha-1(I) chain preproprotein

See identical proteins and their annotated locations for NP_000079.2

Status: REVIEWED

Source sequence(s)

AB209597, AC015909

Consensus CDS

CCDS11561.1

UniProtKB/Swiss-Prot

P02452

Related

ENSP00000225964.6, ENST00000225964.10

Conserved Domains (5) summary

PRK07764
Location:449 → 640

PRK07764; DNA polymerase III subunits gamma and tau; Validated

PRK12678
Location:908 → 1111

PRK12678; transcription termination factor Rho; Provisional

pfam00093
Location:40 → 95

VWC; von Willebrand factor type C domain

pfam01391
Location:239 → 295

Collagen; Collagen triple helix repeat (20 copies)

pfam01410
Location:1227 → 1463

COLFI; Fibrillar collagen C-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p13 Primary Assembly

Range

50184096..50201649 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005257058.4 → XP_005257115.2 collagen alpha-1(I) chain isoform X2

See identical proteins and their annotated locations for XP_005257115.2

Conserved Domains (3) summary

pfam01391
Location:236 → 295

Collagen; Collagen triple helix repeat (20 copies)

pfam00093
Location:40 → 95

VWC; von Willebrand factor type C domain

pfam01410
Location:1140 → 1373

COLFI; Fibrillar collagen C-terminal domain
XM_005257059.4 → XP_005257116.2 collagen alpha-1(I) chain isoform X3

Conserved Domains (3) summary

pfam01391
Location:236 → 295

Collagen; Collagen triple helix repeat (20 copies)

pfam00093
Location:40 → 95

VWC; von Willebrand factor type C domain

pfam01410
Location:924 → 1157

COLFI; Fibrillar collagen C-terminal domain
XM_011524341.1 → XP_011522643.1 collagen alpha-1(I) chain isoform X1

See identical proteins and their annotated locations for XP_011522643.1

Conserved Domains (3) summary

pfam01391
Location:236 → 295

Collagen; Collagen triple helix repeat (20 copies)

pfam00093
Location:40 → 95

VWC; von Willebrand factor type C domain

pfam01410
Location:1164 → 1397

COLFI; Fibrillar collagen C-terminal domain