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Aliases for COL25A1 Gene

Aliases for COL25A1 Gene

  • Collagen Type XXV Alpha 1 Chain 2 3 5
  • Alzheimer Disease Amyloid-Associated Protein 3 4
  • CLAC-P 3 4
  • AMY 3 4
  • Collagen-Like Alzheimer Amyloid Plaque Component 3
  • Collagenous Alzheimer Amyloid Plaque Component 3
  • Collagen Alpha-1(XXV) Chain 3
  • Collagen, Type XXV, Alpha 1 2
  • CFEOM5 3
  • CLACP 3
  • CLAC 3

External Ids for COL25A1 Gene

Previous GeneCards Identifiers for COL25A1 Gene

  • GC04M110125
  • GC04M110203
  • GC04M110193
  • GC04M110092
  • GC04M109954
  • GC04M109731
  • GC04M105467

Summaries for COL25A1 Gene

Entrez Gene Summary for COL25A1 Gene

  • 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]

GeneCards Summary for COL25A1 Gene

COL25A1 (Collagen Type XXV Alpha 1 Chain) is a Protein Coding gene. Diseases associated with COL25A1 include Fibrosis Of Extraocular Muscles, Congenital, 5 and Congenital Ptosis. Among its related pathways are ERK Signaling and Collagen chain trimerization. Gene Ontology (GO) annotations related to this gene include heparin binding and amyloid-beta binding. An important paralog of this gene is COL23A1.

UniProtKB/Swiss-Prot for COL25A1 Gene

  • Inhibits fibrillization of amyloid-beta peptide during the elongation phase. Has also been shown to assemble amyloid fibrils into protease-resistant aggregates. Binds heparin.

Gene Wiki entry for COL25A1 Gene

Additional gene information for COL25A1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL25A1 Gene

Genomics for COL25A1 Gene

GeneHancer (GH) Regulatory Elements for COL25A1 Gene

Promoters and enhancers for COL25A1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J109302 Promoter/Enhancer 1.3 Ensembl ENCODE 650.7 -0.2 -245 1.2 KLF17 ZNF2 ZNF335 GLIS2 ZNF366 SCRT2 SP3 ZBTB11 ZNF398 REST COL25A1 ZCCHC23 RBMXP4
GH04J108830 Enhancer 0.7 ENCODE 11.6 +472.0 471972 0.2 ZSCAN26 ZBTB6 INSM2 MZF1 FEZF1 ZNF335 ZSCAN5C ZNF600 GFI1B ZNF501 CYP2U1 ZCCHC23 COL25A1 ETNPPL SEC24B-AS1 GC04M108805 GC04M108908
GH04J108880 Enhancer 0.7 Ensembl ENCODE 5 +421.3 421308 1.9 JUN CREB1 FOS NFE2 ATF2 COL25A1 GC04M108908 GC04M108805
GH04J109365 Enhancer 0.3 ENCODE 10.9 -63.4 -63369 0.8 JUN GC04P109364 ZCCHC23 COL25A1 SEC24B-AS1 PIR37678
GH04J108884 Enhancer 0.5 FANTOM5 ENCODE 5.3 +417.8 417811 1.6 COL25A1 GC04M108908 GC04M108805
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COL25A1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the COL25A1 gene promoter:
  • FOXF2
  • MIF-1
  • E2F-1
  • E2F
  • MyoD
  • NF-1
  • NF-1/L
  • C/EBPbeta
  • HFH-1
  • POU2F1

Genomic Locations for COL25A1 Gene

Genomic Locations for COL25A1 Gene
494,028 bases
Minus strand
491,937 bases
Minus strand

Genomic View for COL25A1 Gene

Genes around COL25A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL25A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL25A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL25A1 Gene

Proteins for COL25A1 Gene

  • Protein details for COL25A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Collagen alpha-1(XXV) chain
    Protein Accession:
    Secondary Accessions:
    • A8MPZ6
    • Q9BXR9

    Protein attributes for COL25A1 Gene

    654 amino acids
    Molecular mass:
    64771 Da
    Quaternary structure:
    • Forms homodimers and homotrimers. Binds to the fibrillized forms of amyloid-beta protein 40 (beta-APP40) and amyloid-beta protein 42 (beta-APP42). Found associated with beta-APP42 more frequently than with beta-APP40.

    Alternative splice isoforms for COL25A1 Gene


neXtProt entry for COL25A1 Gene

Post-translational modifications for COL25A1 Gene

  • Undergoes proteolytic cleavage by furin protease to yield the soluble collagen-like Alzheimer amyloid plaque component.
  • Glycosylated.
  • Hydroxylated on 11% of proline residues and 49% of lysine residues.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for COL25A1 Gene

Domains & Families for COL25A1 Gene

Gene Families for COL25A1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for COL25A1 Gene

Suggested Antigen Peptide Sequences for COL25A1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with COL25A1: view

No data available for UniProtKB/Swiss-Prot for COL25A1 Gene

Function for COL25A1 Gene

Molecular function for COL25A1 Gene

UniProtKB/Swiss-Prot Function:
Inhibits fibrillization of amyloid-beta peptide during the elongation phase. Has also been shown to assemble amyloid fibrils into protease-resistant aggregates. Binds heparin.

Phenotypes From GWAS Catalog for COL25A1 Gene

Gene Ontology (GO) - Molecular Function for COL25A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001540 amyloid-beta binding IDA 11927537
GO:0008201 heparin binding IDA,IEA 15522881
genes like me logo Genes that share ontologies with COL25A1: view
genes like me logo Genes that share phenotypes with COL25A1: view

Human Phenotype Ontology for COL25A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for COL25A1 Gene

MGI Knock Outs for COL25A1:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for COL25A1 Gene

Localization for COL25A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL25A1 Gene

Membrane; Single-pass type II membrane protein. Note=After proteolytic cleavage, CLAC is secreted.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COL25A1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 5
cytosol 3
mitochondrion 2
peroxisome 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Endoplasmic reticulum (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for COL25A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS,IDA --
GO:0005581 collagen trimer IEA --
GO:0005615 extracellular space IDA 11927537
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with COL25A1: view

Pathways & Interactions for COL25A1 Gene

genes like me logo Genes that share pathways with COL25A1: view

Gene Ontology (GO) - Biological Process for COL25A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030574 collagen catabolic process TAS --
GO:0060385 axonogenesis involved in innervation IEA --
genes like me logo Genes that share ontologies with COL25A1: view

No data available for SIGNOR curated interactions for COL25A1 Gene

Drugs & Compounds for COL25A1 Gene

No Compound Related Data Available

Transcripts for COL25A1 Gene

Unigene Clusters for COL25A1 Gene

Collagen, type XXV, alpha 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL25A1 Gene

No ASD Table

Relevant External Links for COL25A1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for COL25A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COL25A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL25A1 Gene

This gene is overexpressed in Testis (x11.2), Adipose - Subcutaneous (x4.5), and Adipose - Visceral (Omentum) (x4.4).

Protein differential expression in normal tissues from HIPED for COL25A1 Gene

This gene is overexpressed in Plasma (45.9) and Platelet (23.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for COL25A1 Gene

Protein tissue co-expression partners for COL25A1 Gene

NURSA nuclear receptor signaling pathways regulating expression of COL25A1 Gene:


SOURCE GeneReport for Unigene cluster for COL25A1 Gene:


mRNA Expression by UniProt/SwissProt for COL25A1 Gene:

Tissue specificity: Expressed predominantly in brain. Deposited preferentially in primitive or neuritic amyloid plaques which are typical of Alzheimer disease.

Phenotype-based relationships between genes and organs from Gene ORGANizer for COL25A1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cranial nerve
  • eye
  • eyelid
  • face
  • forehead
  • head
  • lip
  • skull
  • chest wall
  • rib
  • rib cage
  • sternum
  • pelvis
  • rectum
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with COL25A1: view

No data available for Evidence on tissue expression from TISSUES for COL25A1 Gene

Orthologs for COL25A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL25A1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia COL25A1 34 33
  • 99.39 (n)
(Canis familiaris)
Mammalia COL25A1 34 33
  • 92.66 (n)
(Bos Taurus)
Mammalia COL25A1 34 33
  • 92.2 (n)
(Ornithorhynchus anatinus)
Mammalia COL25A1 34
  • 92 (a)
(Mus musculus)
Mammalia Col25a1 16 34 33
  • 89.19 (n)
(Monodelphis domestica)
Mammalia COL25A1 34
  • 89 (a)
(Gallus gallus)
Aves COL25A1 34 33
  • 79.61 (n)
(Anolis carolinensis)
Reptilia COL25A1 34
  • 86 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia col25a1.2 33
  • 75.75 (n)
(Danio rerio)
Actinopterygii COL25A1 34
  • 75 (a)
LOC101882764 33
  • 68.37 (n)
(Caenorhabditis elegans)
Secernentea col-135 34
  • 33 (a)
Species where no ortholog for COL25A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for COL25A1 Gene

Gene Tree for COL25A1 (if available)
Gene Tree for COL25A1 (if available)
Evolutionary constrained regions (ECRs) for COL25A1: view image

Paralogs for COL25A1 Gene

Paralogs for COL25A1 Gene

(4) SIMAP similar genes for COL25A1 Gene using alignment to 7 proteins:

  • D6R8Y2_HUMAN
  • Q4W5I4_HUMAN
  • Q8NE08_HUMAN
genes like me logo Genes that share paralogs with COL25A1: view

Variants for COL25A1 Gene

Sequence variations from dbSNP and Humsavar for COL25A1 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs780209390 pathogenic, Fibrosis of extraocular muscles, congenital, 5, Fibrosis of extraocular muscles, congenital, 5 (CFEOM5) [MIM:616219] 108,863,327(-) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs886037741 pathogenic, Fibrosis of extraocular muscles, congenital, 5 108,846,165(-) C/A coding_sequence_variant, intron_variant, stop_gained
rs766049644 uncertain-significance, not specified 108,824,222(-) G/A/C coding_sequence_variant, missense_variant, non_coding_transcript_variant, synonymous_variant
rs1000000688 -- 108,888,767(-) T/C intron_variant
rs1000010569 -- 108,977,599(-) T/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for COL25A1 Gene

Variant ID Type Subtype PubMed ID
dgv113e19 CNV gain 19470904
dgv2875n106 CNV deletion 24896259
esv2436931 CNV insertion 19546169
esv26012 CNV loss 19812545
esv2657117 CNV deletion 23128226
esv2664386 CNV deletion 23128226
esv2728123 CNV deletion 23290073
esv2728124 CNV deletion 23290073
esv2728125 CNV deletion 23290073
esv275332 CNV loss 21479260
esv3302701 CNV tandem duplication 20981092
esv3304254 CNV mobile element insertion 20981092
esv3305609 CNV mobile element insertion 20981092
esv3309451 CNV mobile element insertion 20981092
esv3329381 CNV insertion 20981092
esv3365857 CNV insertion 20981092
esv3380051 CNV insertion 20981092
esv3564424 CNV deletion 23714750
esv3569650 CNV loss 25503493
esv3569651 CNV loss 25503493
esv3601731 CNV loss 21293372
esv3601732 CNV loss 21293372
esv3601734 OTHER inversion 21293372
esv7089 CNV gain 19470904
esv8308 CNV gain 19470904
nsv1073790 CNV deletion 25765185
nsv1128086 CNV deletion 24896259
nsv1136899 CNV deletion 24896259
nsv1143102 CNV tandem duplication 24896259
nsv1153416 CNV insertion 26484159
nsv293715 CNV insertion 16902084
nsv4459 CNV insertion 18451855
nsv461613 CNV gain 19166990
nsv461614 CNV loss 19166990
nsv476458 CNV novel sequence insertion 20440878
nsv515893 CNV loss 19592680
nsv519227 CNV loss 19592680
nsv595128 CNV loss 21841781
nsv595129 CNV gain 21841781
nsv595130 CNV loss 21841781
nsv595131 CNV loss 21841781
nsv830034 CNV loss 17160897
nsv830035 CNV gain 17160897

Variation tolerance for COL25A1 Gene

Residual Variation Intolerance Score: 11.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.60; 45.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COL25A1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL25A1 Gene

Disorders for COL25A1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for COL25A1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards


  • Fibrosis of extraocular muscles, congenital, 5 (CFEOM5) [MIM:616219]: An ocular motility disorder characterized by congenital dysinnervation of various cranial nerves to ocular muscles. Clinical features are ophthalmoplegia, anchoring of the eyes in downward gaze, ptosis, and backward tilt of the head. {ECO:0000269 PubMed:25500261}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for COL25A1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with COL25A1: view

No data available for Genatlas for COL25A1 Gene

Publications for COL25A1 Gene

  1. CLAC: a novel Alzheimer amyloid plaque component derived from a transmembrane precursor, CLAC-P/collagen type XXV. (PMID: 11927537) Hashimoto T … Iwatsubo T (The EMBO journal 2002) 2 3 4 22 58
  2. Genetic association to the amyloid plaque associated protein gene COL25A1 in Alzheimer's disease. (PMID: 18501477) Forsell C … Graff C (Neurobiology of aging 2010) 3 22 44 58
  3. Molecular identification of AMY, an Alzheimer disease amyloid-associated protein. (PMID: 14656069) Söderberg L … Näslund J (Journal of neuropathology and experimental neurology 2003) 3 4 22 58
  4. Recessive mutations in COL25A1 are a cause of congenital cranial dysinnervation disorder. (PMID: 25500261) Shinwari JM … Al Tassan N (American journal of human genetics 2015) 3 4 58
  5. A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts. (PMID: 20332099) Kalsi G … Riley BP (Human molecular genetics 2010) 3 44 58

Products for COL25A1 Gene

Sources for COL25A1 Gene

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