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	1308
Gene name	Collagen type XVII alpha 1 chain
Gene symbol	COL17A1
Synonyms (NCBI Gene)	BA16H23.2BP180BPA-2BPAG2EREDJEB4LAD-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

Show/Hide all (32)

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

Show/Hide all (11)

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

Show/Hide all (22)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	12482924, 32296183
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005581	Component	Collagen trimer	IEA
GO:0005604	Component	Basement membrane	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0005886	Component	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:0016020	Component	Membrane	IEA
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	HDA	28344315
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	IBA
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	RCA	25037231
GO:0030056	Component	Hemidesmosome	IBA
GO:0030056	Component	Hemidesmosome	IDA	12482924
GO:0030056	Component	Hemidesmosome	IEA
GO:0031012	Component	Extracellular matrix	HDA	25037231, 28344315
GO:0031012	Component	Extracellular matrix	IBA
GO:0031581	Process	Hemidesmosome assembly	IDA	12482924
GO:0070161	Component	Anchoring junction	IEA

MIM	HGNC	e!Ensembl
113811	2194	ENSG00000065618

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

Tissue specificity

TISSUE SPECIFICITY: Detected in skin (PubMed:8618013). In the cornea, it is detected in the epithelial basement membrane, the epithelial cells, and at a lower level in stromal cells (at protein level) (PubMed:25676728). Stratified squamous epithelia. Foun

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

Interactions

View interactions

	KEGG		Reactome
	Protein digestion and absorption		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

435

Show/Hide Causal Diseases (11)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the skin	Likely pathogenic; Pathogenic	rs1237394833	RCV001814335
Amelogenesis imperfecta	Pathogenic	rs1295957061, rs2086265807, rs2493339279	RCV003482917 RCV003883505 RCV003883506
Amelogenesis imperfecta - hypoplastic autosomal dominant - local	Likely pathogenic	rs531930614	RCV004527426
Amelogenesis imperfecta type 1A	Likely pathogenic; Pathogenic	rs766864711, rs1224647778, rs771188543, rs2493278474, rs2134567157, rs765243124, rs2493375263, rs2493333188, rs751749614, rs2493307366, rs2493294655, rs2086331407, rs199527325, rs1564685400	RCV003314753 RCV003314764 RCV003314766 RCV003314767 RCV003314768 RCV003314770 RCV003314771 RCV003314772 RCV003314773 RCV003314774 RCV003314775 RCV003314776 RCV003314641 RCV003314672
COL17A1-related disorder	Likely pathogenic; Pathogenic	rs2086256572, rs766864711, rs2493327107, rs2493277518, rs147734242, rs121912771, rs765243124, rs775244527	RCV003399147 RCV004744636 RCV003399540 RCV003392893 RCV004742374 RCV004742230 RCV003396313 RCV004742630
Corneal dystrophy	Pathogenic	rs760714959	RCV003447515
Epidermolysis bullosa, junctional 4, intermediate	Likely pathogenic; Pathogenic	rs760697124, rs2086256572, rs773423028, rs754247557, rs766864711, rs1195164931, rs886041555, rs1380132254, rs2493277518, rs1295957061, rs373469159, rs2493312925, rs1215427707, rs369035370, rs112151584 View all (26 more)	RCV003446917 RCV002291305 RCV002279944 RCV002285206 RCV005028339 RCV003142433 RCV003992256 RCV003323273 RCV005055218 RCV003444430 RCV005030115 RCV005030184 RCV005030211 RCV005030217 RCV005036998 RCV002279955 RCV005392710 RCV005025448 RCV003990326 RCV002279920 RCV002279921 RCV002279922 RCV002279923 RCV002279924 RCV002279925 RCV002279926 RCV002279927 RCV002279928 RCV002279929 RCV002279930 RCV002279931 RCV004547225 RCV003989535 RCV005208138 RCV005027698 RCV005027728 RCV003444654 RCV003333755 RCV005029404 RCV003989120 RCV002279941
Epithelial recurrent erosion dystrophy	Likely pathogenic; Pathogenic	rs760697124, rs1274167395, rs797045142, rs760714959, rs766864711, rs2493294749, rs373469159, rs2493312925, rs1215427707, rs369035370, rs112151584, rs113218289, rs147734242, rs121912771, rs1554848576 View all (6 more)	RCV005023253 RCV002249371 RCV000190896 RCV000190897 RCV005028339 RCV003333855 RCV005030115 RCV005030184 RCV005030211 RCV005030217 RCV005036998 RCV005392710 RCV005025448 RCV002247369 RCV005027698 RCV005027728 RCV005392335 RCV004596333 RCV005036089 RCV001197378 RCV001197379
Junctional epidermolysis bullosa	Pathogenic; Likely pathogenic	rs373469159, rs2086249404, rs751058779, rs2086256572, rs768705886, rs2086359795, rs2086520075, rs121912769, rs754289857, rs775196743, rs1554848576, rs1210666598, rs775244527, rs2086266709	RCV001352791 RCV001352790 RCV001352742 RCV001352740 RCV001352739 RCV001352738 RCV001352736 RCV001352741 RCV001824762 RCV005239089 RCV001352737 RCV000604168 RCV003235384 RCV001250156
Junctional epidermolysis bullosa, non-Herlitz type	Pathogenic; Likely pathogenic	rs1564684815, rs945600680, rs2134567157, rs763578030, rs2134611028, rs797045084, rs2493375635, rs752317971, rs1064793760, rs775196743, rs760094345, rs775244527, rs1478395810, rs1589572214	RCV001331280 RCV001528110 RCV001823566 RCV001823665 RCV002238740 RCV000190573 RCV003388764 RCV000376543 RCV000625554 RCV000991294 RCV000710066 RCV000761266 RCV000778270 RCV000991295
See cases	Likely pathogenic	rs2134590604	RCV002252486

Show/Hide Unknown Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Colon adenocarcinoma	Likely benign	rs143263539	RCV005931389
Familial cancer of breast	Benign	rs139524792	RCV005907755
Gastric cancer	Benign; Likely benign	rs199679027, rs777978017	RCV005929804 RCV005936597
High myopia	Uncertain significance	rs201280800	RCV000785670
Late-onset junctional epidermolysis bullosa	Uncertain significance	rs144220426	RCV003331044
Malignant tumor of esophagus	Likely benign	rs759919625	RCV005934950
Thymoma	Benign	rs805715	RCV005921885
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	rs138824013	RCV005893883

Show/Hide Text Mining Associations (61)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma	Associate	28751461
Adenocarcinoma of Lung	Associate	27891193
Allergic Fungal Sinusitis	Associate	24167818
Amelogenesis Imperfecta	Associate	26502894
Anodontia	Associate	28813618
Anophthalmia with pulmonary hypoplasia	Associate	39376555
Autoimmune Diseases	Associate	20471095
Barrett Esophagus	Associate	28751461
Blister	Associate	11406649, 11710917, 21685452, 22318390, 32235430, 33805154
Breast Neoplasms	Associate	27891193, 32964046, 34293053, 37178414
Carcinoma Basal Cell	Associate	9424087
Carcinoma Non Small Cell Lung	Associate	31449902
Carcinoma Pancreatic Ductal	Associate	40379788
Carcinoma Squamous Cell	Associate	27891193
Cardiovascular Diseases	Stimulate	31449902
Chromosome Disorders	Associate	38459694
Colorectal Neoplasms	Associate	37803411
Corneal Dystrophies Hereditary	Associate	27309958
Dermatitis Atopic	Associate	37540585
Diabetes Mellitus Type 2	Associate	35958564
Disease	Associate	7790367
Dystonic Disorders	Associate	16252234, 9038345
Ectodermal Dysplasia Skin Fragility Syndrome	Associate	8669466, 9457914
Epidermolysis Bullosa	Associate	16252234, 17476356, 20574443, 21685452, 36578049, 39636096
Epidermolysis Bullosa Dystrophica	Stimulate	24007552
Epidermolysis Bullosa Junctional	Associate	10330419, 10577906, 10636730, 10951237, 11851893, 15008985, 16354180, 21357940, 23958762, 33764477, 33805154, 35490295, 38157931, 38522573, 39636096 View all (12 more)
Epidermolysis Bullosa Junctional	Inhibit	7883981
Epidermolysis Bullosa Junctional Non Herlitz Type	Associate	11168815, 11406649, 16252234, 22318390, 33805154, 35717189, 38522573, 39636096
Epidermolysis Bullosa Pruriginosa	Associate	36578049
Epidermolysis Bullosa Simplex	Associate	11851893
Epithelial Recurrent Erosion Dystrophy	Associate	27309958, 29708937, 37289141
Genetic Diseases Inborn	Associate	35717189
Laryngo onycho cutaneous syndrome	Associate	38157931
Leukocyte adhesion deficiency type 1	Associate	9284104
Linear IgA Bullous Dermatosis	Associate	9077469
Lymphatic Metastasis	Associate	31713298
Mixed Connective Tissue Disease	Associate	22053914
Muscular Dystrophy Duchenne	Associate	33764477
Nasal Polyps	Associate	24167818
Neoplasm Metastasis	Associate	35054979
Neoplasms	Associate	27891193, 34293053, 40379788
Neoplasms	Stimulate	37803411
Neoplasms	Inhibit	39354571
Opitz Kaveggia syndrome	Associate	7790367
Ossification of Posterior Longitudinal Ligament	Associate	24668667
Pain	Associate	39636096
Pancreatic Neoplasms	Associate	28611293, 35722628, 36275722, 40486509
Pemphigoid Benign Mucous Membrane	Associate	22053914, 8592065
Pemphigoid Bullous	Associate	11710917, 12445194, 1324962, 14962097, 15008985, 16424234, 1846881, 20471095, 21488867, 23337823, 24167818, 25255430, 28273946, 28351660, 30484821 View all (16 more)
Pemphigoid Gestationis	Associate	20471095, 22535610, 8592065
Pemphigus	Associate	22053914
Retinal Dystrophies	Associate	27309958
Skin Diseases	Associate	14962097, 30837635, 31449902, 33805154
Skin Diseases Vesiculobullous	Associate	8592065
Squamous Cell Carcinoma of Head and Neck	Associate	27891193
Stomach Neoplasms	Associate	39354571
Tooth Abnormalities	Associate	8669466
Tooth Erosion	Associate	33805154
Triple Negative Breast Neoplasms	Associate	31713298
Uniparental Disomy	Associate	35717189
Uterine Cervical Neoplasms	Associate	27891193

COL17A1 (collagen type XVII alpha 1 chain)