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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	1305
Gene name Gene Name - the full gene name approved by the HGNC.	Collagen type XIII alpha 1 chain
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	COL13A1
Synonyms (NCBI Gene) Gene synonyms aliases	CMS19, COLXIIIA1
Disease Acronyms (UniProt) Disease acronyms from UniProt database	CMS19
Chromosome Chromosome number	10
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	10q22.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes the alpha chain of one of the nonfibrillar collagens. The function of this gene product is not known, however, it has been detected at low levels in all connective tissue-producing cells so it may serve a general function in connective t

Show/Hide all(7)

SNP ID	Visualize variation	Clinical significance	Consequence
rs375471249	T>C	Likely-pathogenic	Splice donor variant, intron variant
rs763281993	A>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs769426298	C>G,T	Pathogenic	Stop gained, 5 prime UTR variant, coding sequence variant, missense variant, non coding transcript variant
rs864309662	G>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs864309663	G>-	Pathogenic	Non coding transcript variant, coding sequence variant, 5 prime UTR variant, splice acceptor variant
rs1554943789	T>C	Likely-pathogenic	Intron variant, splice donor variant
rs1554967575	->A	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant

Show/Hide all(64)

miRTarBase ID	miRNA	Experiments	Reference
MIRT706674	hsa-miR-124-3p	HITS-CLIP	21572407
MIRT706695	hsa-miR-3714	HITS-CLIP	21572407
MIRT706696	hsa-miR-3910	HITS-CLIP	21572407
MIRT706694	hsa-miR-3664-5p	HITS-CLIP	21572407
MIRT706693	hsa-miR-6808-5p	HITS-CLIP	21572407
MIRT706692	hsa-miR-6893-5p	HITS-CLIP	21572407
MIRT706691	hsa-miR-940	HITS-CLIP	21572407
MIRT706690	hsa-miR-1182	HITS-CLIP	21572407
MIRT706689	hsa-miR-4639-3p	HITS-CLIP	21572407
MIRT706688	hsa-miR-1304-3p	HITS-CLIP	21572407
MIRT706687	hsa-miR-1267	HITS-CLIP	21572407
MIRT706686	hsa-miR-367-5p	HITS-CLIP	21572407
MIRT706685	hsa-miR-4746-3p	HITS-CLIP	21572407
MIRT706684	hsa-miR-3135b	HITS-CLIP	21572407
MIRT706683	hsa-miR-504-3p	HITS-CLIP	21572407
MIRT706682	hsa-miR-122-5p	HITS-CLIP	21572407
MIRT706681	hsa-miR-1207-5p	HITS-CLIP	21572407
MIRT706680	hsa-miR-4763-3p	HITS-CLIP	21572407
MIRT706679	hsa-miR-3652	HITS-CLIP	21572407
MIRT706678	hsa-miR-4430	HITS-CLIP	21572407
MIRT706677	hsa-miR-3944-5p	HITS-CLIP	21572407
MIRT706676	hsa-miR-6501-5p	HITS-CLIP	21572407
MIRT706675	hsa-miR-4423-5p	HITS-CLIP	21572407
MIRT706674	hsa-miR-124-3p	HITS-CLIP	21572407
MIRT706673	hsa-miR-506-3p	HITS-CLIP	21572407
MIRT706672	hsa-miR-6794-3p	HITS-CLIP	21572407
MIRT706671	hsa-miR-744-3p	HITS-CLIP	21572407
MIRT706670	hsa-miR-4477b	HITS-CLIP	21572407
MIRT706669	hsa-miR-7856-5p	HITS-CLIP	21572407
MIRT706674	hsa-miR-124-3p	HITS-CLIP	21572407
MIRT706695	hsa-miR-3714	HITS-CLIP	21572407
MIRT706696	hsa-miR-3910	HITS-CLIP	21572407
MIRT706694	hsa-miR-3664-5p	HITS-CLIP	21572407
MIRT706693	hsa-miR-6808-5p	HITS-CLIP	21572407
MIRT706692	hsa-miR-6893-5p	HITS-CLIP	21572407
MIRT706691	hsa-miR-940	HITS-CLIP	21572407
MIRT706690	hsa-miR-1182	HITS-CLIP	21572407
MIRT706689	hsa-miR-4639-3p	HITS-CLIP	21572407
MIRT706688	hsa-miR-1304-3p	HITS-CLIP	21572407
MIRT706687	hsa-miR-1267	HITS-CLIP	21572407
MIRT706686	hsa-miR-367-5p	HITS-CLIP	21572407
MIRT706685	hsa-miR-4746-3p	HITS-CLIP	21572407
MIRT706684	hsa-miR-3135b	HITS-CLIP	21572407
MIRT706683	hsa-miR-504-3p	HITS-CLIP	21572407
MIRT706682	hsa-miR-122-5p	HITS-CLIP	21572407
MIRT706681	hsa-miR-1207-5p	HITS-CLIP	21572407
MIRT706680	hsa-miR-4763-3p	HITS-CLIP	21572407
MIRT706679	hsa-miR-3652	HITS-CLIP	21572407
MIRT706678	hsa-miR-4430	HITS-CLIP	21572407
MIRT706677	hsa-miR-3944-5p	HITS-CLIP	21572407
MIRT706676	hsa-miR-6501-5p	HITS-CLIP	21572407
MIRT706675	hsa-miR-4423-5p	HITS-CLIP	21572407
MIRT706674	hsa-miR-124-3p	HITS-CLIP	21572407
MIRT706673	hsa-miR-506-3p	HITS-CLIP	21572407
MIRT706672	hsa-miR-6794-3p	HITS-CLIP	21572407
MIRT706671	hsa-miR-744-3p	HITS-CLIP	21572407
MIRT706670	hsa-miR-4477b	HITS-CLIP	21572407
MIRT706669	hsa-miR-7856-5p	HITS-CLIP	21572407
MIRT902467	hsa-miR-3665	CLIP-seq
MIRT902468	hsa-miR-657	CLIP-seq
MIRT1967698	hsa-miR-1303	CLIP-seq
MIRT1967699	hsa-miR-4716-5p	CLIP-seq
MIRT1967700	hsa-miR-579	CLIP-seq
MIRT2203514	hsa-miR-1972	CLIP-seq

Show/Hide all(29)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001501	Process	Skeletal system development	IBA	21873635
GO:0001763	Process	Morphogenesis of a branching structure	IBA	21873635
GO:0001763	Process	Morphogenesis of a branching structure	ISS
GO:0001958	Process	Endochondral ossification	ISS
GO:0005201	Function	Extracellular matrix structural constituent	IBA	21873635
GO:0005515	Function	Protein binding	IPI	11956183
GO:0005576	Component	Extracellular region	TAS
GO:0005581	Component	Collagen trimer	IBA	21873635
GO:0005600	Component	Collagen type XIII trimer	TAS	2459707
GO:0005615	Component	Extracellular space	IBA	21873635
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0005886	Component	Plasma membrane	TAS
GO:0005911	Component	Cell-cell junction	IBA	21873635
GO:0007160	Process	Cell-matrix adhesion	IBA	21873635
GO:0007160	Process	Cell-matrix adhesion	IPI	11956183
GO:0008201	Function	Heparin binding	IBA	21873635
GO:0008201	Function	Heparin binding	IDA	11956183
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	RCA	25037231, 28675934
GO:0030154	Process	Cell differentiation	IEA
GO:0030198	Process	Extracellular matrix organization	IBA	21873635
GO:0030198	Process	Extracellular matrix organization	TAS
GO:0030199	Process	Collagen fibril organization	IBA	21873635
GO:0030574	Process	Collagen catabolic process	TAS
GO:0030903	Process	Notochord development	IBA	21873635
GO:0031012	Component	Extracellular matrix	IBA	21873635
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0062023	Component	Collagen-containing extracellular matrix	HDA	25037231, 28675934
GO:0098609	Process	Cell-cell adhesion	IBA	21873635
GO:0098609	Process	Cell-cell adhesion	IEP	10865988

MIM	HGNC	e!Ensembl
120350	2190	ENSG00000197467

Protein

UniProt ID

Q5TAT6

Protein name

Collagen alpha-1(XIII) chain (COLXIIIA1)

Protein function

Involved in cell-matrix and cell-cell adhesion interactions that are required for normal development. May participate in the linkage between muscle fiber and basement membrane. May play a role in endochondral ossification of bone and branching m

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01391	Collagen	156 → 216	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	257 → 322	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	285 → 340	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	318 → 383	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	382 → 441	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	463 → 522	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	506 → 567	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	566 → 625	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	643 → 712	Collagen triple helix repeat (20 copies)	Repeat

Tissue specificity

TISSUE SPECIFICITY: Widely expressed in both fetal and adult ocular tissues (at protein level). In the eye, expression is accentuated in the ciliary muscle, optic nerve and the neural retina. In early placenta, localized to fibroblastoid stromal cells of

Sequence

MVAERTHKAAATGARGPGELGAPGTVALVAARAERGARLPSPGSCGLLTLALCSLALSLL
AHFRTAELQARVLRLEAERGEQQMETAILGRVNQLLDEKWKLHSRRRREAPKTSPGCNCP
PGPPGPTGRPGLPGDKGAIGMPGRVGSPGDAGLSIIGPRGPPGQPGTRGFPGFPGPIGLD
GKPGHPGPKGDMGLTGPPGQPGPQGQKGEKGQCGEYPHRECLSSMPAALRSSQIIALKLL
PLLNSVRLAPPPVIKRRTFQGEQSQASIQGPPGPPGPPGPSGPLGHPGLPGPMGPPGLPG
PPGPKGDPGIQGYHGRKGERGMPGMPGKHGAKGAPGIAVAGMKGEPGIPGTKGEKGAEGS
PGLPGLLGQKGEKGDAGNSIGGGRGEPGPPGLPGPPGPKGEAGVDGQVGPPGQPGDKGER
GAAGEQGPDGPKGSKGEPGKGEMVDYNGNINEALQEIRTLALMGPPGLPGQIGPPGAPGI
PGQKGEIGLPGPPGHDGEKGPRGKPGDMGPPGPQGPPGKDGPPGVKGENGHPGSPGEKGE
KGETGQAGSPGEKGEAGEKGNPGAEVPGLPGPEGPPGPPGLQGVPGPKGEAGLDGAKGEK
GFQGEKGDRGPLGLPGASGLDGRPGPPGTPGPIGVPGPAGPKGERGSKGDPGMTGPTGAA
GLPGLHGPPGDKGNRGERGKKGSRGPKGDKGDQGAPGLDAPCPLGEDGLPVQGCWNK

Sequence length

717

Interactions

View interactions

	KEGG		Reactome
	Protein digestion and absorption		Collagen degradation Collagen biosynthesis and modifying enzymes Integrin cell surface interactions Collagen chain trimerization

Show/Hide Causal Diseases (9)

Disease term	Disease name	dbSNP ID	References
Causal
Arthrogryposis multiplex congenita	Arthrogryposis	rs1586285494, rs80358233, rs137853305, rs1559154278, rs398124167, rs398124172, rs587780399, rs786204576, rs786204430, rs769345284, rs749355583, rs793888524, rs793888525, rs878854368, rs555445835 View all (138 more)
Myasthenic syndrome	Congenital Myasthenic Syndromes, Postsynaptic, Congenital Myasthenic Syndromes, Presynaptic, Presynaptic congenital myasthenic syndromes, Postsynaptic congenital myasthenic syndromes, Myasthenic Syndromes, Congenital, Myasthenic Syndromes, Congenital, Slow Channel, MYASTHENIC SYNDROME, CONGENITAL, 19	rs606231128, rs606231129, rs606231130, rs606231131, rs606231132, rs118203994, rs118203995, rs863223277, rs606231133, rs121908547, rs121908553, rs121908557, rs104893733, rs104893734, rs121908922 View all (237 more)	26626625
Developmental delay	Gross motor development delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291 View all (32 more)
Hearing loss	Sensorineural Hearing Loss (disorder)	rs267607135, rs267606855, rs779841884, rs267606854, rs28942097, rs121908073, rs121908076, rs74315289, rs121908144, rs111033313, rs74315437, rs121908348, rs121908349, rs121908350, rs397515359 View all (184 more)
Mental retardation	Intellectual Disability	rs5742905, rs267607136, rs267607137, rs2131714307, rs267607038, rs267607042, rs80338685, rs137853127, rs80338815, rs28940893, rs387906309, rs121908096, rs121908099, rs587784365, rs121918315 View all (1024 more)
Myasthenia gravis	Myasthenias	rs5030818, rs121912815, rs121912817, rs121912818, rs121912821, rs75466054, rs121912822, rs121912823, rs794727516, rs764497513, rs376808313, rs1279554995, rs1554802792, rs369251527, rs372760913 View all (8 more)
Nystagmus	Nystagmus	rs137852207, rs137852208, rs1928435502, rs137852209, rs137852210, rs1929191668, rs137852211, rs137852212, rs2124209414, rs387906720, rs387906721, rs1602791884, rs786205896
Parkinson disease	Parkinson Disease	rs33939927, rs35801418, rs34805604, rs35870237, rs34995376, rs74315355, rs28940284, rs74315356, rs74315357, rs28940285, rs730880302, rs750664040, rs74315359, rs74315360, rs45539432 View all (84 more)	23793441
Polyneuropathy	Polyneuropathy, Motor	rs1597597437

Show/Hide Unknown Diseases (5)

Disease term	Disease name	References	Source
Unknown
Distal amyotrophy	Distal amyotrophy		ClinVar
Myocardial infarction	Myocardial Infarction	21211798	ClinVar
Ptosis	Blepharoptosis, Ptosis		ClinVar
Myasthenic Syndrome	congenital myasthenic syndrome 19, postsynaptic congenital myasthenic syndrome, presynaptic congenital myasthenic syndrome		GenCC
Ulcerative colitis	Ulcerative colitis		GWAS

Show/Hide Text Mining Associations (16)

Disease Name	Relationship Type	References
Associations from Text Mining
Dyspnea	Associate	31081514
Fatty Liver Alcoholic	Associate	26845607
Inflammation	Associate	20708005
Muscle Weakness	Associate	31081514
Myasthenic Syndromes Congenital	Associate	31081514, 35337379, 36308527
Neoplasms	Associate	28837258
Neuromuscular Junction Diseases	Associate	31081514, 35337379
Non alcoholic Fatty Liver Disease	Associate	29307798
Non Muscle Invasive Bladder Neoplasms	Associate	28837258
Osteoarthritis	Associate	20060954
Osteosarcoma	Associate	33926256
Scleroderma Diffuse	Associate	27111861
Squamous Cell Carcinoma of Head and Neck	Associate	34999279
Thyroid Cancer Papillary	Associate	27779685
Urethral Neoplasms	Associate	28837258
Urinary Bladder Neoplasms	Stimulate	28837258

COL13A1 (collagen type XIII alpha 1 chain)