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

    Gene ID: 1287, updated on 2-Nov-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
    mouse all
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    Genomic context

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    See COL4A5 in Genome Data Viewer
    Location:
    Xq22.3
    Exon count:
    57
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (108439838..108697545)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (106877380..107135128)
    RS_2024_09 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 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. Detection of mutations in the COL4A5 gene by analyzing cDNA of skin fibroblasts. Wang F, et al. Kidney Int, 2005 Apr. PMID 15780079
    2. Aromatic interactions promote self-association of collagen triple-helical peptides to higher-order structures. Kar K, et al. Biochemistry, 2009 Aug 25. PMID 19610672, Free PMC Article
    3. Atypical Alport syndrome associated with a novel COL4A5 mutation. Höpker K, et al. Clin Nephrol, 2009 Mar. PMID 19281745
    4. [A novel COL4A5 splicing mutation causing Alport syndrome in a Chinese family]. Tang Z, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2008 Dec. PMID 19065523
    5. MLPA and cDNA analysis improves COL4A5 mutation detection in X-linked Alport syndrome. Hertz JM, et al. Clin Genet, 2008 Dec. PMID 18616531

    See all (196) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Four novel mutations identified in the COL4A3, COL4A4 and COL4A5 genes in 10 families with Alport syndrome.
      Title: Four novel mutations identified in the COL4A3, COL4A4 and COL4A5 genes in 10 families with Alport syndrome.
    2. A novel COL4A5 splicing mutation causes alport syndrome in a Chinese family.
      Title: A novel COL4A5 splicing mutation causes alport syndrome in a Chinese family.
    3. Genetic diagnosis of Alport syndrome in 16 Chinese families.
      Title: Genetic diagnosis of Alport syndrome in 16 Chinese families.
    4. 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.
    5. [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].
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (114)

    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 
    enables protein binding IPI
    Inferred from Physical Interaction
    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_2024_08

    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

    Gene LinkOut

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