COL25A1 (collagen type XXV alpha 1 chain)

Gene

• Entrez ID: 84570
• Gene name: Collagen type XXV alpha 1 chain
• Gene symbol: COL25A1
• Synonyms (NCBI Gene): AMY, CFEOM5, CLAC, CLAC-P, CLACP
• Chromosome: 4
• Chromosome location: 4q25
• 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs780209390	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs886037741	C>A	Pathogenic	Coding sequence variant, intron variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2447434	hsa-miR-4694-3p	CLIP-seq
MIRT2447435	hsa-miR-548c-3p	CLIP-seq
MIRT2447436	hsa-miR-711	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001540	Function	Amyloid-beta binding	IBA
GO:0001540	Function	Amyloid-beta binding	IDA	11927537, 15215182, 15522881, 15615705
GO:0005576	Component	Extracellular region	IDA	11927537
GO:0005576	Component	Extracellular region	TAS
GO:0005581	Component	Collagen trimer	IEA
GO:0005615	Component	Extracellular space	IDA	11927537
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0005886	Component	Plasma membrane	IDA	11927537
GO:0005886	Component	Plasma membrane	TAS
GO:0008201	Function	Heparin binding	IDA	15522881
GO:0008201	Function	Heparin binding	IEA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	NAS	11927537
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	RCA	25037231
GO:0031012	Component	Extracellular matrix	HDA	25037231
GO:0042802	Function	Identical protein binding	IPI	15522881
GO:0060385	Process	Axonogenesis involved in innervation	IEA

Other IDs

• MIM: 610004
• HGNC: 18603
• e!Ensembl: ENSG00000188517

Protein

• UniProt ID: Q9BXS0
• Protein name: Collagen alpha-1(XXV) chain (Alzheimer disease amyloid-associated protein) (AMY) (CLAC-P) [Cleaved into: Collagen-like Alzheimer amyloid plaque component (CLAC)]
• Protein 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. {ECO:0000269|PubMed:15522881, ECO:0000269|PubMed:15615705, ECO:000026
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01391	Collagen	118 → 165	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	310 → 372	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	371 → 427	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	447 → 505	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	574 → 647	Collagen triple helix repeat (20 copies)	Repeat

• Tissue specificity: TISSUE SPECIFICITY: Expressed predominantly in brain. Deposited preferentially in primitive or neuritic amyloid plaques which are typical of Alzheimer disease. {ECO:0000269|PubMed:11927537}.
• Sequence:

  MLLKKHAGKGGGREPRSEDPTPAEQHCARTMPPCAVLAALLSVVAVVSCLYLGVKTNDLQ
  ARIAALESAKGAPSIHLLPDTLDHLKTMVQEKVERLLAQKSYEHMAKIRIAREAPSECNC
  PAGPPGKRGKRGRRGESGPPGQPGPQGPPGPKGDKGEQGDQGPRMVFPKINHGFLSADQQ
  LIKRRLIKGDQGQAGPPGPPGPPGPRGPPGDTGKDGPRGMPGVPGEPGKPGEQGLMGPLG
  PPGQKGSIGAPGIPGMNGQKGEPGLPGAVGQNGIPGPKGEPGEQGEKGDAGENGPKGDTG
  EKGDPGSSAAGIKGEPGESGRPGQKGEPGLPGLPGLPGIKGEPGFIGPQGEPGLPGLPGT
  KGERGEAGPPGRGERGEPGAPGPKGKQGESGTRGPKGSKGDRGEKGDSGAQGPRGPPGQK
  GDQGATEIIDYNGNLHEALQRITTLTVTGPPGPPGPQGLQGPKGEQGSPGIPGMDGEQGL
  KGSKGDMGDPGMTGEKGGIGLPGLPGANGMKGEKGDSGMPGPQGPSIIGPPGPPGPHGPP
  GPMGPHGLPGPKGTDGPMGPHGPAGPKGERGEKGAMGEPGPRGPYGLPGKDGEPGLDGFP
  GPRGEKGDLGEKGEKGFRGVKGEKGEPGQPGLDGLDAPCQLGPDGLPMPGCWQK

• Sequence length: 654

Pathways

KEGG:

Protein digestion and absorption

Reactome:

Collagen degradation
Collagen biosynthesis and modifying enzymes
Collagen chain trimerization

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Arthrogryposis	Likely pathogenic	rs1274380766	RCV004764971
Fibrosis of extraocular muscles, congenital, 5	Likely pathogenic; Pathogenic	rs1274380766, rs759316372, rs2125927453, rs780209390, rs886037741, rs2476579225	RCV001780813 RCV002272850 RCV002272920 RCV000157645 RCV000157646 RCV003228197

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
COL25A1-related disorder	Likely benign; Benign	rs2476723415, rs202176344, rs749261897, rs754236027, rs17531474, rs760493024, rs577543045, rs375017466, rs756928692, rs183625583, rs140998459, rs773786786, rs202121124	RCV003909279 RCV003924101 RCV003974290 RCV003977102 RCV003977405 RCV003909611 RCV003961841 RCV003963878 RCV003969600 RCV003953348 RCV003918452 RCV003975709 RCV003970529
Uterine corpus endometrial carcinoma	Benign	rs114761964	RCV005903339

Associations from Text Mining
Disease Name	Relationship Type	References
Alzheimer Disease	Associate	15522881, 15615705, 22297151
Antisocial Personality Disorder	Associate	22297151
Arthrogryposis	Associate	35077597
Carcinogenesis	Associate	23018867
Congenital Cranial Dysinnervation Disorders	Associate	25500261, 35077597
Mouth Diseases	Associate	23018867
Plaque Amyloid	Associate	15522881, 15615705
Substance Related Disorders	Associate	22297151