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COL4A5 collagen type IV alpha 5 chain [ Homo sapiens (human) ]

Gene ID: 1287, updated on 16-Apr-2024

Summary

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Official Symbol
COL4A5provided by HGNC
Official Full Name
collagen type IV alpha 5 chainprovided by HGNC
Primary source
HGNC:HGNC:2207
See related
Ensembl:ENSG00000188153 MIM:303630; AllianceGenome:HGNC:2207
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
ATS; ASLN; ATS1; CA54
Summary
This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. Mutations in this gene are associated with X-linked Alport syndrome, also known as hereditary nephritis. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Aug 2010]
Expression
Broad expression in endometrium (RPKM 21.7), skin (RPKM 10.8) and 20 other tissues See more
Orthologs
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Genomic context

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Location:
Xq22.3
Exon count:
57
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (108439838..108697545)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (106877380..107135128)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (107683068..107940775)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29839 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:107370111-107370674 Neighboring gene proteasome 26S subunit, non-ATPase 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:107399852-107400352 Neighboring gene autophagy related 4A cysteine peptidase Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:107419738-107420424 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:107420425-107421109 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:107421110-107421795 Neighboring gene uncharacterized LOC124905205 Neighboring gene collagen type IV alpha 6 chain Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:107513459-107514658 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:107596629-107597181 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:107609798-107610337 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:107634248-107634889 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:107843610-107844540 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:107884720-107885919 Neighboring gene IRS4 antisense RNA 1 Neighboring gene insulin receptor substrate 4 Neighboring gene RNA, U6 small nuclear 309, pseudogene

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. Type IV collagen α5 chain promotes luminal breast cancer progression through c-Myc-driven glycolysis. Wu Y, et al. J Mol Cell Biol, 2023 Mar 29. PMID 36484686, Free PMC Article
  2. Aberrant splicing caused by exonic single nucleotide variants positioned 2nd or 3rd to the last nucleotide in the COL4A5 gene. Okada E, et al. Clin Exp Nephrol, 2023 Mar. PMID 36371577, Free PMC Article
  3. Pathogenicity of missense variants affecting the collagen IV α5 carboxy non-collagenous domain in X-linked Alport syndrome. Gibson JT, et al. Sci Rep, 2022 Jul 4. PMID 35789182, Free PMC Article
  4. Lifelong effect of therapy in young patients with the COL4A5 Alport missense variant p.(Gly624Asp): a prospective cohort study. Boeckhaus J, et al. Nephrol Dial Transplant, 2022 Nov 23. PMID 35022790
  5. Dissecting the genotype-phenotype correlation of COL4A5 gene mutation and its response to renin-angiotensin-aldosterone system blockers in Chinese male patients with Alport syndrome. Di H, et al. Nephrol Dial Transplant, 2022 Nov 23. PMID 35020912

See all (185) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genetic diagnosis of Alport syndrome in 16 Chinese families.
    Title: Genetic diagnosis of Alport syndrome in 16 Chinese families.
  2. Three exonic variants in the COL4A5 gene alter RNA splicing in a minigene assay.
    Title: Three exonic variants in the COL4A5 gene alter RNA splicing in a minigene assay.
  3. [Genetic testing and prenatal diagnosis for two Chinese pedigrees affected with Alport syndrome due to variants of COL4A5 gene].
    Title: [Genetic testing and prenatal diagnosis for two Chinese pedigrees affected with Alport syndrome due to variants of COL4A5 gene].
  4. Collagen Type IV Alpha 5 Chain in Bronchiolitis Obliterans Syndrome After Lung Transplant: The First Evidence.
    Title: Collagen Type IV Alpha 5 Chain in Bronchiolitis Obliterans Syndrome After Lung Transplant: The First Evidence.
  5. Genetic and molecular dynamics analysis of two variants of the COL4A5 gene causing Alport syndrome.
    Title: Genetic and molecular dynamics analysis of two variants of the COL4A5 gene causing Alport syndrome.
  6. Type IV collagen alpha5 chain promotes luminal breast cancer progression through c-Myc-driven glycolysis.
    Title: Type IV collagen α5 chain promotes luminal breast cancer progression through c-Myc-driven glycolysis.
  7. Aberrant splicing caused by exonic single nucleotide variants positioned 2nd or 3rd to the last nucleotide in the COL4A5 gene.
    Title: Aberrant splicing caused by exonic single nucleotide variants positioned 2nd or 3rd to the last nucleotide in the COL4A5 gene.
  8. Genetic Variants of the COL4A3 , COL4A4 , and COL4A5 Genes Contribute to Thinned Glomerular Basement Membrane Lesions in Sporadic IgA Nephropathy Patients.
    Title: Genetic Variants of the COL4A3 , COL4A4 , and COL4A5 Genes Contribute to Thinned Glomerular Basement Membrane Lesions in Sporadic IgA Nephropathy Patients.
  9. Lifelong effect of therapy in young patients with the COL4A5 Alport missense variant p.(Gly624Asp): a prospective cohort study.
    Title: Lifelong effect of therapy in young patients with the COL4A5 Alport missense variant p.(Gly624Asp): a prospective cohort study.
  10. Dissecting the genotype-phenotype correlation of COL4A5 gene mutation and its response to renin-angiotensin-aldosterone system blockers in Chinese male patients with Alport syndrome.
    Title: Dissecting the genotype-phenotype correlation of COL4A5 gene mutation and its response to renin-angiotensin-aldosterone system blockers in Chinese male patients with Alport syndrome.
Submit: New GeneRIF Correction See all GeneRIFs (112)

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
Alport syndrome
MedGen: C1567741 GeneReviews: Not available
Compare labs
X-linked Alport syndrome
MedGen: C4746986 OMIM: 301050 GeneReviews: Alport Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-09-08)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-09-08)

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)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 and serum-free macrophage supernatant (MSP) enhance synthesis of type IV collagen by mesangial cells; anti-TGF-beta antibodies attenuate this gp160/MSP-induced collagen synthesis PubMed
Tat tat Treatment with cannabinoids inhibits HIV-1 Tat-enhanced attachment of U937 cells to collagen IV, laminin, or ECM1 proteins, which is linked to the cannabinoid receptor type 2 and the modulation of beta1-integrin and actin distribution PubMed
tat HIV-1 Tat enhances adhesion of human U937 monocyte-like cells to proteins of the extracellular matrix, such as collagen IV, laminin, and ECM1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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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

Homology

Clone Names

  • MGC42377, MGC167109, DKFZp686G1497

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables extracellular matrix structural constituent conferring tensile strength HDA 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 
Process Evidence Code Pubs
involved_in collagen-activated tyrosine kinase receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuromuscular junction development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in basement membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of collagen type IV trimer IEA
Inferred from Electronic Annotation
more info
  
located_in collagen-containing extracellular matrix HDA PubMed 
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
  
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 neuromuscular junction IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
collagen alpha-5(IV) chain
Names
collagen IV, alpha-5 polypeptide
collagen of basement membrane, alpha-5 chain
collagen, type IV, alpha 5
dA149D17.3
dA24A23.1

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

  1. NG_011977.2 RefSeqGene

    Range
    4915..262622
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_232

mRNA and Protein(s)

  1. NM_000495.5 → NP_000486.1  collagen alpha-5(IV) chain isoform 1 precursor

    See identical proteins and their annotated locations for NP_000486.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame segment in the coding region, compared to variant 2. The resulting isoform (1) lacks two Gly-X-Y repeats, compared to isoform 2.
    Source sequence(s)
    AL034369, BC035387, BC151846, BU688037, DA461056, M31115
    Consensus CDS
    CCDS14543.1
    UniProtKB/Swiss-Prot
    P29400, Q16006, Q16126, Q6LD84, Q7Z700, Q9NUB7
    Related
    ENSP00000354505.2, ENST00000361603.7
    Conserved Domains (2) summary
    pfam01391
    Location:1285 → 1344
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:1573 → 1682
    C4; C-terminal tandem repeated domain in type 4 procollagen

  2. NM_033380.3 → NP_203699.1  collagen alpha-5(IV) chain isoform 2 precursor

    See identical proteins and their annotated locations for NP_203699.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes the longer isoform (2).
    Source sequence(s)
    AL034369, BC035387, BC151846, BU688037, DA461056, M31115
    Consensus CDS
    CCDS35366.1
    UniProtKB/Swiss-Prot
    P29400
    UniProtKB/TrEMBL
    A7MBN3, Q49AM6
    Related
    ENSP00000331902.7, ENST00000328300.11
    Conserved Domains (2) summary
    pfam01391
    Location:1291 → 1350
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:1579 → 1688
    C4; C-terminal tandem repeated domain in type 4 procollagen

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    108439838..108697545
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047441810.1 → XP_047297766.1  collagen alpha-5(IV) chain isoform X4

  2. XM_047441811.1 → XP_047297767.1  collagen alpha-5(IV) chain isoform X7

  3. XM_011530849.3 → XP_011529151.2  collagen alpha-5(IV) chain isoform X1

  4. XM_017029259.3 → XP_016884748.1  collagen alpha-5(IV) chain isoform X2

  5. XM_017029260.2 → XP_016884749.1  collagen alpha-5(IV) chain isoform X3

  6. XM_017029261.2 → XP_016884750.1  collagen alpha-5(IV) chain isoform X5

  7. XM_017029262.3 → XP_016884751.1  collagen alpha-5(IV) chain isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    106877380..107135128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326438.1 → XP_054182413.1  collagen alpha-5(IV) chain isoform X4

  2. XM_054326441.1 → XP_054182416.1  collagen alpha-5(IV) chain isoform X7

  3. XM_054326435.1 → XP_054182410.1  collagen alpha-5(IV) chain isoform X1

  4. XM_054326436.1 → XP_054182411.1  collagen alpha-5(IV) chain isoform X2

  5. XM_054326437.1 → XP_054182412.1  collagen alpha-5(IV) chain isoform X3

  6. XM_054326439.1 → XP_054182414.1  collagen alpha-5(IV) chain isoform X5

  7. XM_054326440.1 → XP_054182415.1  collagen alpha-5(IV) chain isoform X6

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_033381.1: Suppressed sequence

    Description
    NM_033381.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P29400.2 GenPept UniProtKB/Swiss-Prot:P29400

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