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

187

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
COL27A1-related disorder	Pathogenic	rs140950220	RCV004754310
Familial cancer of breast	Likely pathogenic	rs760476125	RCV005931609
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 RCV001815630 RCV001823467 RCV005040430 RCV005040440 RCV003317536 RCV000132771 RCV002226938 RCV002244252 RCV002465079 RCV002472215 RCV003143598 RCV003143606 RCV004515788 RCV004526329 RCV000677092 RCV000677093 RCV000677205 RCV000995715 RCV000995716 RCV001255864 RCV001090006
Thyroid cancer, nonmedullary, 1	Pathogenic	rs1289391715	RCV005911066

Show/Hide Unknown Diseases (18)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Adrenocortical carcinoma, hereditary	Benign; Uncertain significance	rs113772516, rs140849642, rs201221528	RCV005914122 RCV005930617 RCV005926513
Cervical cancer	Benign	rs113772516, rs1687409	RCV005914123 RCV005912950
Cholangiocarcinoma	Benign	rs113772516, rs1687409	RCV005914131 RCV005912958
Clear cell carcinoma of kidney	Benign; Uncertain significance; Likely benign; Conflicting classifications of pathogenicity	rs1687409, rs183678867, rs768682666, rs149629527, rs146793976	RCV005912951 RCV005926724 RCV005932437 RCV005907445 RCV005902948
Colon adenocarcinoma	Benign; Likely benign	rs113772516, rs1687409, rs149629527	RCV005914120 RCV005912947 RCV005907443
Colorectal cancer	Benign	rs113772516	RCV005914124
Gastric cancer	Benign; Uncertain significance; Likely benign	rs113772516, rs1687409, rs183678867, rs138966191, rs149629527	RCV005914126 RCV005912953 RCV005926725 RCV005906058 RCV005907446
Hepatocellular carcinoma	Benign; Uncertain significance; Likely benign	rs1687409, rs183678867, rs149629527	RCV005912948 RCV005926723 RCV005907444
Lung cancer	Benign	rs113772516, rs1687409	RCV005914132 RCV005912959
Malignant lymphoma, large B-cell, diffuse	Benign	rs529746417, rs146977141	RCV005868559 RCV005904498
Malignant tumor of esophagus	Benign	rs113772516, rs1687409, rs529746417	RCV005914121 RCV005912949 RCV005868557
Melanoma	Benign; Uncertain significance	rs113772516, rs370903413, rs201221528	RCV005914130 RCV005930425 RCV005926514
Ovarian cancer	Benign	rs529746417	RCV005868558
Ovarian serous cystadenocarcinoma	Benign; Likely benign	rs1687409, rs149629527	RCV005912954 RCV005907447
Papillary renal cell carcinoma type 1	Uncertain significance	rs140849642	RCV005930616
Sarcoma	Benign	rs113772516, rs1687409	RCV005914125 RCV005912952
Thymoma	Benign	rs113772516, rs1687409, rs146977141	RCV005914128 RCV005912956 RCV005904499
Uterine carcinosarcoma	Benign	rs113772516, rs1687409	RCV005914127 RCV005912955

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Anophthalmos	Associate	31913554
Cartilage Diseases	Associate	35581901
Collagen Diseases	Associate	28895531
Coloboma	Associate	31913554
Colorectal Neoplasms	Associate	29547645
Eye Abnormalities	Associate	31913554
Funnel Chest	Associate	35581901
Genetic Diseases Inborn	Associate	28895531
Growth Disorders	Associate	28895531
Hearing Loss	Associate	31913554
Meier Blumberg Imahorn syndrome	Associate	31913554
Microphthalmos	Associate	31913554
Myotonia with Skeletal Abnormalities and Mental Retardation	Associate	35581901
Osteoarthritis	Associate	33055079
Osteogenesis Imperfecta	Associate	35581901
Patellofemoral Pain Syndrome	Associate	31482140
Scoliosis	Associate	35186112
Supranuclear Palsy Progressive	Associate	24986830, 31913554, 35581901
Tourette Syndrome	Associate	22889924, 26235311

COL27A1 (collagen type XXVII alpha 1 chain)