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    COL25A1 collagen type XXV alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 84570, updated on 3-Nov-2024

    Summary

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    Official Symbol
    COL25A1provided by HGNC
    Official Full Name
    collagen type XXV alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:18603
    See related
    Ensembl:ENSG00000188517 MIM:610004; AllianceGenome:HGNC:18603
    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
    AMY; CLAC; CLACP; CFEOM5; CLAC-P
    Summary
    This gene encodes a brain-specific membrane associated collagen. A product of proteolytic processing of the encoded protein, CLAC (collagenous Alzheimer amyloid plaque component), binds to amyloid beta-peptides found in Alzheimer amyloid plaques but CLAC inhibits rather than facilitates amyloid fibril elongation (PMID: 16300410). A study of over-expression of this collagen in mice, however, found changes in pathology and behavior suggesting that the encoded protein may promote amyloid plaque formation (PMID: 19548013). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
    Expression
    Biased expression in testis (RPKM 1.9), fat (RPKM 1.8) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See COL25A1 in Genome Data Viewer
    Location:
    4q25
    Exon count:
    49
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (108808725..109302658, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (112110611..112604870, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (109729881..110223814, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:109708719-109709219 Neighboring gene ethanolamine-phosphate phospho-lyase Neighboring gene regulator of chromosome condensation 2 pseudogene 8 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:109852739-109853343 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71593 Neighboring gene uncharacterized LOC124900756 Neighboring gene Sharpr-MPRA regulatory region 6815 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71618 Neighboring gene Sharpr-MPRA regulatory region 12117 Neighboring gene uncharacterized LOC124900754 Neighboring gene NANOG hESC enhancer GRCh37_chr4:110107576-110108103 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71641 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71659 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71681 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15620 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:110223886-110224668 Neighboring gene COL25A1 divergent transcript Neighboring gene RBMX pseudogene 4

    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. Molecular identification of AMY, an Alzheimer disease amyloid-associated protein. Söderberg L, et al. J Neuropathol Exp Neurol, 2003 Nov. PMID 14656069
    2. Recessive variants in COL25A1 gene as novel cause of arthrogryposis multiplex congenita with ocular congenital cranial dysinnervation disorder. Natera-de Benito D, et al. Hum Mutat, 2022 Apr. PMID 35077597, Free PMC Article
    3. Collagenous Alzheimer amyloid plaque component assembles amyloid fibrils into protease resistant aggregates. Söderberg L, et al. FEBS J, 2005 May. PMID 15853808
    4. CLAC binds to aggregated Abeta and Abeta fragments, and attenuates fibril elongation. Kakuyama H, et al. Biochemistry, 2005 Nov 29. PMID 16300410
    5. Recessive COL25A1 mutations cause isolated congenital ptosis or exotropic Duane syndrome with synergistic divergence. Khan AO, et al. J AAPOS, 2015 Oct. PMID 26486031

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Recessive variants in COL25A1 gene as novel cause of arthrogryposis multiplex congenita with ocular congenital cranial dysinnervation disorder.
      Title: Recessive variants in COL25A1 gene as novel cause of arthrogryposis multiplex congenita with ocular congenital cranial dysinnervation disorder.
    2. Collagenous Alzheimer amyloid plaque component impacts on the compaction of amyloid-beta plaques.
      Title: Collagenous Alzheimer amyloid plaque component impacts on the compaction of amyloid-β plaques.
    3. We highlight phenotypes of the 4 affected children from the 2 reported families: isolated congenital ptosis (one unilateral, one bilateral) and Duane syndrome (one unilateral, one bilateral) with synergistic divergence.
      Title: Recessive COL25A1 mutations cause isolated congenital ptosis or exotropic Duane syndrome with synergistic divergence.
    4. We identified COL25A1 mutations as a cause of autosomal-recessive congenital cranial dysinnervation disorder.
      Title: Recessive mutations in COL25A1 are a cause of congenital cranial dysinnervation disorder.
    5. COL25A1 methylation correlates with severity of cervical intraepithelial neoplasia
      Title: Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia.
    6. The COL25A1 single nucleotide polymorphism rs13134663 was significantly associated with antisocial personality disorder, especially in subjects with comorbid substance dependence.
      Title: Association of COL25A1 with comorbid antisocial personality disorder and substance dependence.
    7. The next best locus for gene x gender interactions for age at onset was in COL25A1 gene at 4q25
      Title: Genome-wide association analysis of age at onset in schizophrenia in a European-American sample.
    8. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    9. provides genetic evidence of association between COL25A1 and risk for Alzheimer's disease
      Title: Genetic association to the amyloid plaque associated protein gene COL25A1 in Alzheimer's disease.
    10. COL25A1 leads to Alzheimer's disease-like pathology in vivo
      Title: COL25A1 triggers and promotes Alzheimer's disease-like pathology in vivo.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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
    Fibrosis of extraocular muscles, congenital, 5
    MedGen: C4015552 OMIM: 616219 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
    EBI GWAS Catalog
    Genome-wide association analysis of age at onset in schizophrenia in a European-American sample
    EBI GWAS Catalog
    Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables amyloid-beta binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables amyloid-beta binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    enables heparin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of collagen 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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    collagen alpha-1(XXV) chain
    Names
    alzheimer disease amyloid-associated protein
    collagen-like Alzheimer amyloid plaque component
    collagenous Alzheimer amyloid plaque component

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_047204.1 RefSeqGene

      Range
      5095..499028
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001256074.3 → NP_001243003.1  collagen alpha-1(XXV) chain isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple differences in the coding region but maintains the reading frame, and also differs in the 5' and 3' UTRs, compared to variant 1. The resulting isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC004051, AC097473, BC030649
      Consensus CDS
      CCDS58922.1
      UniProtKB/TrEMBL
      A8MWQ5
      Related
      ENSP00000382078.1, ENST00000399127.5
      Conserved Domains (1) summary
      pfam01391
      Location:547 → 606
      Collagen; Collagen triple helix repeat (20 copies)

    2. NM_032518.4 → NP_115907.2  collagen alpha-1(XXV) chain isoform 2

      See identical proteins and their annotated locations for NP_115907.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks three 3' exons but includes an alternate 3' exon, resulting in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC004051, AC097473, AF293341, BC030649
      Consensus CDS
      CCDS43259.1
      UniProtKB/Swiss-Prot
      Q9BXS0
      Related
      ENSP00000382077.1, ENST00000399126.1
      Conserved Domains (1) summary
      pfam01391
      Location:553 → 611
      Collagen; Collagen triple helix repeat (20 copies)

    3. NM_198721.4 → NP_942014.1  collagen alpha-1(XXV) chain isoform 1

      See identical proteins and their annotated locations for NP_942014.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC004051, AC097473, AF293340, AF293341, BC030649, KF457803
      Consensus CDS
      CCDS43258.1
      UniProtKB/Swiss-Prot
      A8MPZ6, Q9BXR9, Q9BXS0
      Related
      ENSP00000382083.1, ENST00000399132.6
      Conserved Domains (1) summary
      pfam01391
      Location:553 → 611
      Collagen; Collagen triple helix repeat (20 copies)

    RNA

    1. NR_045756.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate 5' exon, lacks three exons and uses an alternate splice site in the central region, and uses alternate exon structure in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC004051, AC097473, BC036669
      Related
      ENST00000494183.5

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      108808725..109302658 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011532335.3 → XP_011530637.1  collagen alpha-1(XXV) chain isoform X1

      See identical proteins and their annotated locations for XP_011530637.1

      UniProtKB/TrEMBL
      A0A2R8Y760
      Conserved Domains (1) summary
      pfam01391
      Location:592 → 646
      Collagen; Collagen triple helix repeat (20 copies)

    2. XM_011532334.3 → XP_011530636.1  collagen alpha-1(XXV) chain isoform X1

      See identical proteins and their annotated locations for XP_011530636.1

      UniProtKB/TrEMBL
      A0A2R8Y760
      Conserved Domains (1) summary
      pfam01391
      Location:592 → 646
      Collagen; Collagen triple helix repeat (20 copies)

    3. XM_011532333.3 → XP_011530635.1  collagen alpha-1(XXV) chain isoform X1

      See identical proteins and their annotated locations for XP_011530635.1

      UniProtKB/TrEMBL
      A0A2R8Y760
      Related
      ENSP00000495847.1, ENST00000642955.1
      Conserved Domains (1) summary
      pfam01391
      Location:592 → 646
      Collagen; Collagen triple helix repeat (20 copies)

    4. XM_017008737.2 → XP_016864226.1  collagen alpha-1(XXV) chain isoform X2

      Conserved Domains (1) summary
      pfam01391
      Location:479 → 533
      Collagen; Collagen triple helix repeat (20 copies)

    5. XM_011532356.3 → XP_011530658.1  collagen alpha-1(XXV) chain isoform X3

      Conserved Domains (1) summary
      pfam01391
      Location:473 → 527
      Collagen; Collagen triple helix repeat (20 copies)

    6. XM_011532355.3 → XP_011530657.1  collagen alpha-1(XXV) chain isoform X2

      Conserved Domains (1) summary
      pfam01391
      Location:479 → 533
      Collagen; Collagen triple helix repeat (20 copies)

    7. XM_011532358.2 → XP_011530660.1  collagen alpha-1(XXV) chain isoform X4

      Conserved Domains (1) summary
      pfam01391
      Location:431 → 485
      Collagen; Collagen triple helix repeat (20 copies)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      112110611..112604870 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351103.1 → XP_054207078.1  collagen alpha-1(XXV) chain isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y760

    2. XM_054351101.1 → XP_054207076.1  collagen alpha-1(XXV) chain isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y760

    3. XM_054351102.1 → XP_054207077.1  collagen alpha-1(XXV) chain isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y760

    4. XM_054351105.1 → XP_054207080.1  collagen alpha-1(XXV) chain isoform X2

    5. XM_054351106.1 → XP_054207081.1  collagen alpha-1(XXV) chain isoform X3

    6. XM_054351104.1 → XP_054207079.1  collagen alpha-1(XXV) chain isoform X2

    7. XM_054351107.1 → XP_054207082.1  collagen alpha-1(XXV) chain isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BXS0.2 GenPept UniProtKB/Swiss-Prot:Q9BXS0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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