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

Gene ID: 84570, updated on 5-Mar-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
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Genomic context

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Location:
4q25
Exon count:
49
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (108808725..109302658, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (112110611..112604870, complement)
105.20220307 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
  • 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. 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
  2. Recessive COL25A1 mutations cause isolated congenital ptosis or exotropic Duane syndrome with synergistic divergence. Khan AO, et al. J AAPOS, 2015 Oct. PMID 26486031
  3. Recessive mutations in COL25A1 are a cause of congenital cranial dysinnervation disorder. Shinwari JM, et al. Am J Hum Genet, 2015 Jan 8. PMID 25500261, Free PMC Article
  4. Association of COL25A1 with comorbid antisocial personality disorder and substance dependence. Li D, et al. Biol Psychiatry, 2012 Apr 15. PMID 22297151, Free PMC Article
  5. Genetic association to the amyloid plaque associated protein gene COL25A1 in Alzheimer's disease. Forsell C, et al. Neurobiol Aging, 2010 Mar. PMID 18501477

See all (28) 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
Compare labs

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)

Genotypes

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 
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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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_2023_10

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

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