COL17A1 (collagen type XVII alpha 1 chain)

Gene

• Entrez ID: 1308
• Gene name: Collagen type XVII alpha 1 chain
• Gene symbol: COL17A1
• Synonyms: BA16H23.2, BP180, BPA-2, BPAG2, ERED, JEB4, LAD-1
• Chromosome: 10
• Chromosome location: 10q25.1
• Summary: This gene encodes the alpha chain of type XVII collagen. Unlike most collagens, collagen XVII is a transmembrane protein. Collagen XVII is a structural component of hemidesmosomes, multiprotein complexes at the dermal-epidermal basement membrane zone that

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121912769	G>A	Pathogenic	Stop gained, coding sequence variant
rs121912770	G>A	Pathogenic	Stop gained, coding sequence variant
rs121912771	C>T	Pathogenic	Missense variant, coding sequence variant
rs121912772	A>C	Pathogenic	Stop gained, coding sequence variant
rs121912773	C>T	Pathogenic	Missense variant, coding sequence variant
rs121912774	G>A	Pathogenic	Stop gained, coding sequence variant
rs199527325	C>T	Likely-pathogenic	Splice donor variant
rs201940939	C>T	Likely-pathogenic	Intron variant
rs752317971	C>A,G	Pathogenic	Coding sequence variant, stop gained, missense variant
rs753898533	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs754289857	C>T	Pathogenic	Splice acceptor variant
rs760094345	G>A,C	Pathogenic	Missense variant, coding sequence variant, stop gained
rs760714959	G>A	Pathogenic	Coding sequence variant, synonymous variant
rs765243124	CTCT>-	Pathogenic	Coding sequence variant, frameshift variant
rs767083273	C>G,T	Pathogenic	Coding sequence variant, missense variant
rs775196743	G>A	Pathogenic	Coding sequence variant, stop gained
rs775244527	A>-	Likely-pathogenic	Splice donor variant
rs775251483	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs797045084	CCCTCTGAAAAC>-	Likely-pathogenic	Coding sequence variant, intron variant, splice acceptor variant
rs797045142	G>A	Pathogenic	Coding sequence variant, missense variant
rs886041555	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs1064793760	T>-	Pathogenic	Frameshift variant, coding sequence variant
rs1131691753	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1210666598	CAGGGGGTC>C,G	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1240465846	G>A	Pathogenic	Stop gained, coding sequence variant
rs1478395810	T>C	Likely-pathogenic	Splice acceptor variant
rs1554847822	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1554849445	C>T	Pathogenic	Stop gained, coding sequence variant
rs1554850239	C>T	Pathogenic	Stop gained, coding sequence variant
rs1589562891	C>A	Pathogenic	Splice acceptor variant
rs1589567772	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1589572214	G>-	Pathogenic	Frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT022276	hsa-miR-124-3p	Microarray	18668037
MIRT1967701	hsa-miR-3942-3p	CLIP-seq
MIRT2203520	hsa-miR-1197	CLIP-seq
MIRT2203521	hsa-miR-28-5p	CLIP-seq
MIRT2203522	hsa-miR-3139	CLIP-seq
MIRT2203523	hsa-miR-4652-3p	CLIP-seq
MIRT2203524	hsa-miR-708	CLIP-seq
MIRT2447429	hsa-miR-298	CLIP-seq
MIRT2447430	hsa-miR-4303	CLIP-seq
MIRT2447431	hsa-miR-4682	CLIP-seq
MIRT2447432	hsa-miR-4802-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005201	Function	Extracellular matrix structural constituent	IBA	21873635
GO:0005515	Function	Protein binding	IPI	12482924, 32296183
GO:0005576	Component	Extracellular region	TAS
GO:0005581	Component	Collagen trimer	IEA
GO:0005604	Component	Basement membrane	IEA
GO:0005615	Component	Extracellular space	IBA	21873635
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0005886	Component	Plasma membrane	TAS
GO:0005887	Component	Integral component of plasma membrane	TAS	9012408
GO:0005911	Component	Cell-cell junction	TAS	9012408
GO:0007160	Process	Cell-matrix adhesion	TAS	9012408
GO:0008544	Process	Epidermis development	TAS	9012408
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	HDA	28344315
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	RCA	25037231
GO:0030056	Component	Hemidesmosome	IBA	21873635
GO:0030056	Component	Hemidesmosome	IDA	12482924
GO:0030198	Process	Extracellular matrix organization	IBA	21873635
GO:0031012	Component	Extracellular matrix	IBA	21873635
GO:0031581	Process	Hemidesmosome assembly	IDA	12482924
GO:0031581	Process	Hemidesmosome assembly	TAS
GO:0050776	Process	Regulation of immune response	TAS
GO:0062023	Component	Collagen-containing extracellular matrix	HDA	25037231, 28344315

Other IDs

• MIM: 113811
• HGNC: 2194
• e!Ensembl: ENSG00000065618

Protein

• UniProt ID: Q9UMD9
• Protein name: Collagen alpha-1(XVII) chain (180 kDa bullous pemphigoid antigen 2) (Bullous pemphigoid antigen 2) [Cleaved into: 120 kDa linear IgA disease antigen (120 kDa linear IgA dermatosis antigen) (Linear IgA disease antigen 1) (LAD-1); 97 kDa linear IgA disease
• Protein function: May play a role in the integrity of hemidesmosome and the attachment of basal keratinocytes to the underlying basement membrane.; The 120 kDa linear IgA disease antigen is an anchoring filament component involved in dermal-epidermal co
• PDB: 8IZS
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01391	Collagen	561 → 624	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	749 → 809	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	1434 → 1488	Collagen triple helix repeat (20 copies)	Repeat

• Sequence:

  MDVTKKNKRDGTEVTERIVTETVTTRLTSLPPKGGTSNGYAKTASLGGGSRLEKQSLTHG
  SSGYINSTGSTRGHASTSSYRRAHSPASTLPNSPGSTFERKTHVTRHAYEGSSSGNSSPE
  YPRKEFASSSTRGRSQTRESEIRVRLQSASPSTRWTELDDVKRLLKGSRSASVSPTRNSS
  NTLPIPKKGTVETKIVTASSQSVSGTYDATILDANLPSHVWSSTLPAGSSMGTYHNNMTT
  QSSSLLNTNAYSAGSVFGVPNNMASCSPTLHPGLSTSSSVFGMQNNLAPSLTTLSHGTTT
  TSTAYGVKKNMPQSPAAVNTGVSTSAACTTSVQSDDLLHKDCKFLILEKDNTPAKKEMEL
  LIMTKDSGKVFTASPASIAATSFSEDTLKKEKQAAYNADSGLKAEANGDLKTVSTKGKTT
  TADIHSYGSSGGGGSGGGGGVGGAGGGPWGPAPAWCPCGSCCSWWKWLLGLLLTWLLLLG
  LLFGLIALAEEVRKLKARVDELERIRRSILPYGDSMDRIEKDRLQGMAPAAGADLDKIGL
  HSDSQEELWMFVRKKLMMEQENGNLRGSPGPKGDMGSPGPKGDRGFPGTPGIPGPLGHPG
  PQGPKGQKGSVGDPGMEGPMGQRGREGPMGPRGEAGPPGSGEKGERGAAGEPGPHGPPGV
  PGSVGPKGSSGSPGPQGPPGPVGLQGLRGEVGLPGVKGDKGPMGPPGPKGDQGEKGPRGL
  TGEPGMRGLPGAVGEPGAKGAMGPAGPDGHQGPRGEQGLTGMPGIRGPPGPSGDPGKPGL
  TGPQGPQGLPGTPGRPGIKGEPGAPGKIVTSEGSSMLTVPGPPGPPGAMGPPGPPGAPGP
  AGPAGLPGHQEVLNLQGPPGPPGPRGPPGPSIPGPPGPRGPPGEGLPGPPGPPGSFLSNS
  ETFLSGPPGPPGPPGPKGDQGPPGPRGHQGEQGLPGFSTSGSSSFGLNLQGPPGPPGPQG
  PKGDKGDPGVPGALGIPSGPSEGGSSSTMYVSGPPGPPGPPGPPGSISSSGQEIQQYISE
  YMQSDSIRSYLSGVQGPPGPPGPPGPVTTITGETFDYSELASHVVSYLRTSGYGVSLFSS
  SISSEDILAVLQRDDVRQYLRQYLMGPRGPPGPPGASGDGSLLSLDYAELSSRILSYMSS
  SGISIGLPGPPGPPGLPGTSYEELLSLLRGSEFRGIVGPPGPPGPPGIPGNVWSSISVED
  LSSYLHTAGLSFIPGPPGPPGPPGPRGPPGVSGALATYAAENSDSFRSELISYLTSPDVR
  SFIVGPPGPPGPQGPPGDSRLLSTDASHSRGSSSSSHSSSVRRGSSYSSSMSTGGGGAGS
  LGAGGAFGEAAGDRGPYGTDIGPGGGYGAAAEGGMYAGNGGLLGADFAGDLDYNELAVRV
  SESMQRQGLLQGMAYTVQGPPGQPGPQGPPGISKVFSAYSNVTADLMDFFQTYGAIQGPP
  GQKGEMGTPGPKGDRGPAGPPGHPGPPGPRGHKGEKGDKGDQVYAGRRRRRSIAVKP

• Sequence length: 1497

Pathways

KEGG:

Protein digestion and absorption

Reactome:

Collagen biosynthesis and modifying enzymes
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Assembly of collagen fibrils and other multimeric structures
Type I hemidesmosome assembly
Collagen chain trimerization

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Amelogenesis imperfecta	Amelogenesis Imperfecta	rs267607178, rs143816093, rs606231351, rs137854435, rs137854440, rs137854441, rs137854444, rs587776587, rs121908109, rs587776588, rs140213840, rs104894704, rs387906487, rs387906488, rs387906489, rs104894733, rs104894734, rs104894736, rs387906490, rs387906491, rs104894737, rs104894738, rs144411158, rs587776911, rs587776912, rs587776913, rs587776914, rs387907215, rs866941536, rs1560562738, rs1560562630, rs146645381, rs1560558455, rs587777515, rs587777516, rs587777530, rs139620139, rs587777531, rs587777535, rs587777536, rs587777537, rs606231462, rs1553275034, rs869320671, rs786201004, rs140015315, rs730882118, rs730880297, rs730880298, rs786204825, rs786204826, rs1555409827, rs1057517671, rs1057517672, rs556734208, rs146238585, rs202073531, rs1057519277, rs767907487, rs779823931, rs1060499539, rs1085307111, rs546603773, rs1553275070, rs1553275195, rs752102959, rs1554623490, rs1553888384, rs770804941, rs1553887511, rs557128345, rs1568724130, rs199527325, rs1603038146, rs773117913, rs1560973571, rs1560782372, rs1560980659, rs1560973467, rs772929908, rs762816338, rs1565222166, rs1595312054, rs1866200282, rs2086254952	8669466
Anemia	Anemia	rs118204044, rs118204045, rs118204046, rs121918330, rs869320719, rs869312029, rs121918332, rs869320724, rs767094129, rs786205058, rs786205059, rs137853119, rs137853120, rs137853121, rs1384933966, rs137853122, rs137853123, rs786205060, rs267607121, rs121908584, rs80338697, rs80338699, rs120074166, rs120074167, rs1050828, rs74575103, rs137852314, rs5030868, rs137852316, rs137852317, rs137852318, rs137852319, rs137852320, rs137852321, rs137852322, rs137852323, rs137852324, rs72554665, rs387906468, rs5030872, rs137852326, rs137852333, rs137852327, rs137852328, rs137852329, rs137852330, rs137852331, rs137852332, rs137852334, rs137852335, rs137852336, rs137852339, rs76645461, rs137852340, rs137852341, rs78478128, rs137852343, rs137852344, rs137852345, rs587776730, rs137852346, rs137852347, rs137852349, rs2070404412, rs2070350038, rs2070350009, rs137852303, rs137852304, rs33946267, rs34378160, rs33933298, rs11549407, rs35724775, rs34598529, rs41469945, rs267607201, rs80338694, rs80338696, rs387907018, rs398123546, rs78365220, rs587777100, rs587777101, rs483352840, rs869312752, rs765487627, rs1557229599, rs1557230040, rs1555524842, rs782090947, rs1358275550, rs1557229736, rs1557230573, rs1556323334, rs1233124208, rs1293528130, rs146864395, rs1595503440, rs1603411214, rs137852325, rs1575247302, rs1603411177, rs1336651679, rs782322505
Anonychia	ANONYCHIA	rs74315420, rs74315421, rs74315422, rs74315423, rs387907026, rs387907027, rs387907028, rs780261665, rs775644973, rs370554150
Aplasia cutis congenita	Aplasia Cutis Congenita	rs587777706
Epidermolysis bullosa	EPIDERMOLYSIS BULLOSA, JUNCTIONAL, LOCALISATA VARIANT (disorder), Localized junctional epidermolysis bullosa	rs137852757, rs80356682, rs80356680, rs786205094, rs121912482, rs786205095, rs587776813, rs121912487, rs587776814, rs1558092501, rs80356683, rs118203899, rs118203900, rs1558095794, rs118203901, rs1558088792, rs121912466, rs2147483647, rs746056280, rs121912832, rs121912833, rs121912834, rs121912836, rs121912837, rs759990189, rs121912839, rs121912844, rs121912845, rs1575495784, rs121912848, rs121912849, rs121912851, rs121912852, rs121912853, rs121912854, rs121912855, rs121912769, rs1564673127, rs121912770, rs753898533, rs121912771, rs1589562891, rs2134563935, rs2134581672, rs121912772, rs121912773, rs121912774, rs121912856, rs201551805, rs769967565, rs786204774, rs797045084, rs886039330, rs886039412, rs1553277702, rs886041187, rs368007918, rs886041186, rs766902987, rs886041555, rs752657203, rs757415879, rs886058642, rs752317971, rs201307156, rs1057517096, rs774133746, rs772421306, rs758886532, rs144023803, rs1057517723, rs760063197, rs916512411, rs772381373, rs768128088, rs374718902, rs762162799, rs1064793916, rs780623622, rs747522386, rs1064793760, rs775196743, rs1131691385, rs201940939, rs200972872, rs139318843, rs1368134215, rs1203706188, rs772038362, rs1553281335, rs1181742615, rs1553853022, rs1553612928, rs1055680335, rs1057517023, rs760094345, rs1560241522, rs199527325, rs751535193, rs767539005, rs775244527, rs769808745, rs1032335328, rs1478395810, rs777672897, rs1575466699, rs776841521, rs1589572214, rs761388039, rs769294243, rs761927109, rs754621187	24550734
Epithelial erosion dystrophy	Epithelial Recurrent Erosion Dystrophy	rs121912771, rs797045142, rs760714959, rs765243124	14562173, 25676728
Junctional epidermolysis bullosa	Junctional Epidermolysis Bullosa, Adult junctional epidermolysis bullosa (disorder), Late-onset junctional epidermolysis bullosa, Intermediate generalized junctional epidermolysis bullosa	rs80356682, rs121912482, rs786205095, rs769151482, rs118203901, rs121912467, rs121912468, rs121912769, rs80356681, rs370148688, rs770302956, rs778012079, rs201307156, rs1057516759, rs1057517096, rs1057516539, rs774133746, rs754289857, rs1064793896, rs775196743, rs747916314, rs759518184, rs1554848576, rs1210666598, rs1553266871, rs1418276828, rs1158945258, rs775244527, rs1558092158, rs1571803654, rs774734592, rs778026407	10577906, 10951237, 10652291, 12813757, 10577906, 24550734, 8669466, 9077475, 10636730, 19340010, 9199555, 21357940, 11406649, 10951237, 14614394, 16354180, 11912005, 9204958
Palmoplantar keratoderma	Keratoderma, Palmoplantar	rs59616921, rs1568039793, rs746488412, rs200564757, rs1567027297, rs781596375, rs1567027610, rs398123054, rs398123055, rs398123056, rs398123057, rs398122949, rs398122950, rs397515639, rs398122951, rs397515640, rs397515641, rs142859678, rs797044479, rs577442939, rs672601344, rs568609861, rs1057518846, rs1182196436, rs1567037561

Unknown
Disease name	Disease term	dbSNP ID	References
Corneal erosion	Corneal erosion
Dental enamel hypoplasia	Dental Enamel Hypoplasia
Excessive tearing	Excessive tearing
Hyperhidrosis palmaris et plantaris	Hyperhidrosis Palmaris Et Plantaris
Hypodontia	Hypodontia
Nail diseases	NAIL DISORDER, NONSYNDROMIC CONGENITAL, 4, NAIL DISORDER, NONSYNDROMIC CONGENITAL, 9
Nail dysplasia	Nail dysplasia
Nail dystrophy	Dystrophia unguium
Biliary cirrhosis	Primary biliary cirrhosis		23000144