Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	85301
Gene name	Collagen type XXVII alpha 1 chain
Gene symbol	COL27A1
Synonyms (NCBI Gene)	STLS
Chromosome	9
Chromosome location	9q32
Summary	This gene encodes a member of the fibrillar collagen family, and plays a role during the calcification of cartilage and the transition of cartilage to bone. The encoded protein product is a preproprotein. It includes an N-terminal signal peptide, which is

Show/Hide all (10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs5900078	C>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs140950220	G>C	Pathogenic	Non coding transcript variant, genic upstream transcript variant, 5 prime UTR variant, coding sequence variant, missense variant
rs766405509	G>C	Likely-pathogenic	Intron variant, splice donor variant, genic downstream transcript variant
rs1401322428	C>A,T	Pathogenic	Stop gained, synonymous variant, coding sequence variant, genic upstream transcript variant, non coding transcript variant, 5 prime UTR variant
rs1554787366	T>-	Pathogenic	Non coding transcript variant, upstream transcript variant, coding sequence variant, frameshift variant, genic upstream transcript variant
rs1554787559	GCGGGCAG>-	Pathogenic	Non coding transcript variant, upstream transcript variant, coding sequence variant, frameshift variant, genic upstream transcript variant
rs1554816354	G>A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1554821679	A>G	Pathogenic	Splice acceptor variant
rs1588550383	G>-	Pathogenic	Coding sequence variant, frameshift variant, genic upstream transcript variant, non coding transcript variant
rs1588816777	G>A	Likely-pathogenic	Splice acceptor variant

Show/Hide all (8)

miRTarBase ID	miRNA	Experiments	Reference
MIRT025143	hsa-miR-181a-5p	Microarray	17612493
MIRT040778	hsa-miR-18a-3p	CLASH	23622248
MIRT619565	hsa-miR-6757-5p	HITS-CLIP	23824327
MIRT619564	hsa-miR-135a-3p	HITS-CLIP	23824327
MIRT619563	hsa-miR-1290	HITS-CLIP	23824327
MIRT619565	hsa-miR-6757-5p	HITS-CLIP	23824327
MIRT619564	hsa-miR-135a-3p	HITS-CLIP	23824327
MIRT619563	hsa-miR-1290	HITS-CLIP	23824327

Show/Hide all (15)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001501	Process	Skeletal system development	IBA
GO:0003431	Process	Growth plate cartilage chondrocyte development	IEA
GO:0005201	Function	Extracellular matrix structural constituent	IEA
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005581	Component	Collagen trimer	IEA
GO:0005583	Component	Fibrillar collagen trimer	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	HDA	28344315
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	IBA
GO:0030198	Process	Extracellular matrix organization	IEA
GO:0031012	Component	Extracellular matrix	HDA	28344315
GO:0031012	Component	Extracellular matrix	IBA
GO:0046872	Function	Metal ion binding	IEA

MIM	HGNC	e!Ensembl
608461	22986	ENSG00000196739

Q8IZC6

Protein name

Collagen alpha-1(XXVII) chain

Protein function

Plays a role during the calcification of cartilage and the transition of cartilage to bone.

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01391	Collagen	624 → 685	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	681 → 746	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	823 → 898	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	873 → 938	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	892 → 954	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	922 → 1007	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1075 → 1145	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1170 → 1247	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1225 → 1289	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1279 → 1339	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1338 → 1399	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1508 → 1583	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1562 → 1623	Collagen triple helix repeat (20 copies)	Repeat
PF01410	COLFI	1658 → 1744	Fibrillar collagen C-terminal domain	Family
PF01410	COLFI	1737 → 1859	Fibrillar collagen C-terminal domain	Family

Sequence

MGAGSARGARGTAAAAAARGGGFLFSWILVSFACHLASTQGAPEDVDILQRLGLSWTKAG
SPAPPGVIPFQSGFIFTQRARLQAPTGTVIPAALGTELALVLSLCSHRVNHAFLFAVRSQ
KRKLQLGLQFLPGKTVVHLGSRRSVAFDLDMHDGRWHHLALELRGRTVTLVTACGQRRVP
VLLPFHRDPALDPGGSFLFGKMNPHAVQFEGALCQFSIYPVTQVAHNYCTHLRKQCGQAD
TYQSPLGPLFSQDSGRPFTFQSDLALLGLENLTTATPALGSLPAGRGPRGTVAPATPTKP
QRTSPTNPHQHMAVGGPAQTPLLPAKLSASNALDPMLPASVGGSTRTPRPAAAQPSQKIT
ATKIPKSLPTKPSAPSTSIVPIKSPHPTQKTAPSSFTKSALPTQKQVPPTSRPVPARVSR
PAEKPIQRNPGMPRPPPPSTRPLPPTTSSSKKPIPTLARTEAKITSHASKPASARTSTHK
PPPFTALSSSPAPTPGSTRSTRPPATMVPPTSGTSTPRTAPAVPTPGSAPTGSKKPIGSE
ASKKAGPKSSPRKPVPLRPGKAARDVPLSDLTTRPSPRQPQPSQQTTPALVLAPAQFLSS
SPRPTSSGYSIFHLAGSTPFPLLMGPPGPKGDCGLPGPPGLPGLPGIPGARGPRGPPGPY
GNPGLPGPPGAKGQKGDPGLSPGKAHDGAKGDMGLPGLSGNPGPPGRKGHKGYPGPAGHP
GEQGQPGPEGSPGAKGYPGRQGLPGPVGDPGPKGSRGYIGLPGLFGLPGSDGERGLPGVP
GKRGKMGMPGFPGVFGERGPPGLDGNPGELGLPGPPGVPGLIGDLGVLGPIGYPGPKGMK
GLMGSVGEPGLKGDKGEQGVPGVSGDPGFQGDKGSQGLPGFPGARGKPGPLGKVGDKGSI
GFPGPPGPEGFPGDIGPPGDNGPEGMKGKPGARGLPGPRGQLGPEGDEGPMGPPGAPGLE
GQPGRKGFPGRPGLDGVKGEPGDPGRPGPVGEQGFMGFIGLVGEPGIVGEKGDRGMMGPP
GVPGPKGSMGHPGMPGGMGTPGEPGPQGPPGSRGPPGMRGAKGRRGPRGPDGPAGEQGSR
GLKGPPGPQGRPGRPGQQGVAGERGHLGSRGFPGIPGPSGPPGTKGLPGEPGPQGPQGPI
GPPGEMGPKGPPGAVGEPGLPGEAGMKGDLGPLGTPGEQGLIGQRGEPGLEGDSGPMGPD
GLKGDRGDPGPDGEHGEKGQEGLMGEDGPPGPPGVTGVRGPEGKSGKQGEKGRTGAKGAK
GYQGQLGEMGVPGDPGPPGTPGPKGSRGSLGPTGAPGRMGAQGEPGLAGYDGHKGIVGPL
GPPGPKGEKGEQGEDGKAEGPPGPPGDRGPVGDRGDRGEPGDPGYPGQEGVQGLRGKPGQ
QGQPGHPGPRGWPGPKGSKGAEGPKGKQGKAGAPGRRGVQGLQGLPGPRGVVGRQGLEGI
AGPDGLPGRDGQAGQQGEQGDDGDPGPMGPAGKRGNPGVAGLPGAQGPPGFKGESGLPGQ
LGPPGKRGTEGRTGLPGNQGEPGSKGQPGDSGEMGFPGMAGLFGPKGPPGDIGFKGIQGP
RGPPGLMGKEGIVGPLGILGPSGLPGPKGDKGSRGDWGLQGPRGPPGPRGRPGPPGPPGG
PIQLQQDDLGAAFQTWMDTSGALRPESYSYPDRLVLDQGGEIFKTLHYLSNLIQSIKTPL
GTKENPARVCRDLMDCEQKMVDGTYWVDPNLGCSSDTIEVSCNFTHGGQTCLKPITASKV
EFAISRVQMNFLHLLSSEVTQHITIHCLNMTVWQEGTGQTPAKQAVRFRAWNGQIFEAGG
QFRPEVSMDGCKVQDGRWHQTLFTFRTQDPQQLPIISVDNLPPASSGKQYRLEVGPACFL

Sequence length

1860

Interactions

View interactions

	KEGG		Reactome
	Cytoskeleton in muscle cells Protein digestion and absorption		Collagen biosynthesis and modifying enzymes Assembly of collagen fibrils and other multimeric structures MET activates PTK2 signaling Collagen chain trimerization

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
COL27A1-related disorder	Pathogenic	rs140950220	RCV004754310	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Familial cancer of breast	Likely pathogenic	rs760476125	RCV005931609	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Steel syndrome	Pathogenic; Likely pathogenic	rs1289391715, rs1328051341, rs2131618521, rs1849088219, rs2135594366, rs753461513, rs1848097390, rs2135531602, rs1835450838, rs1830319943, rs140950220, rs2131616036, rs1465820080, rs2490365600, rs2490547878 View all (11 more)	RCV001644994 RCV001332720 RCV005040234 RCV002499806 RCV001780545 View all (21 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Thyroid cancer, nonmedullary, 1	Pathogenic	rs1289391715	RCV005911066	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (24)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Adrenocortical carcinoma, hereditary	Benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign; Uncertain significance; Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign; Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, HIP	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, KNEE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Papillary renal cell carcinoma type 1	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TOURETTE SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (27)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Anophthalmos	Anophthalmia	Pubtator	31913554	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cartilage Diseases	Cartilage disease	Pubtator	35581901	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Coloboma	Coloboma	Pubtator	31913554	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	29547645		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	29547645	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital dislocation of radial head	Dislocated radial head	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysmorphic features	Dysmorphic Features	CLINVAR_DG	12714037, 12766169, 15922909, 17331945, 17693149, 19204719, 19414009, 20041163, 22206015, 24986830, 28276056, 7990924, 8001137		★★★★★ ★☆☆☆☆ Found in Text Mining only
Eye Abnormalities	Eye abnormalities	Pubtator	31913554	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Gilles de la Tourette syndrome	Tourette Syndrome	GWASDB_DG	22889924		★★★★★ ★☆☆☆☆ Found in Text Mining only
Gilles de la Tourette syndrome	Tourette Syndrome	GWASCAT_DG	22889924		★★★★★ ★☆☆☆☆ Found in Text Mining only
Gilles de la Tourette syndrome	Tourette Syndrome	BEFREE	26235311		★★★★★ ★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	28895531	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	31913554	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	Pubtator	31913554	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Multiple congenital anomalies	Multiple Congenital Anomalies	CLINVAR_DG	12714037, 12766169, 15922909, 17331945, 17693149, 19204719, 19414009, 20041163, 22206015, 24986830, 28276056, 7990924, 8001137		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteoarthritis	Osteoarthritis	Pubtator	33055079	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteogenesis Imperfecta	Osteogenesis imperfecta	Pubtator	35581901	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Scoliosis	Scoliosis	Pubtator	35186112	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
STEEL SYNDROME	Steel Syndrome	BEFREE	24986830, 28276056, 28322503		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
STEEL SYNDROME	Steel Syndrome	ORPHANET_DG	24986830		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
STEEL SYNDROME	Steel Syndrome	UNIPROT_DG	24986830		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Steel syndrome	Steel Syndrome	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
STEEL SYNDROME	Steel Syndrome	CLINVAR_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Supranuclear Palsy Progressive	Progressive supranuclear palsy	Pubtator	24986830, 31913554, 35581901	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Tourette Syndrome	Tourette syndrome	Pubtator	22889924, 26235311	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

COL27A1 (collagen type XXVII alpha 1 chain)