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	1305
Gene name	Collagen type XIII alpha 1 chain
Gene symbol	COL13A1
Synonyms (NCBI Gene)	CMS19COLXIIIA1
Chromosome	10
Chromosome location	10q22.1
Summary	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 (24)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001503	Process	Ossification	IEA
GO:0001763	Process	Morphogenesis of a branching structure	ISS
GO:0001958	Process	Endochondral ossification	ISS
GO:0005515	Function	Protein binding	IPI	11956183
GO:0005576	Component	Extracellular region	TAS
GO:0005581	Component	Collagen trimer	IEA
GO:0005600	Component	Collagen type XIII trimer	TAS	2459707, 9624150
GO:0005604	Component	Basement membrane	IBA
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	9624150
GO:0007155	Process	Cell adhesion	IEA
GO:0007160	Process	Cell-matrix adhesion	IPI	11956183
GO:0008201	Function	Heparin binding	IDA	11956183
GO:0008201	Function	Heparin binding	IEA
GO:0016020	Component	Membrane	IEA
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	IBA
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	RCA	25037231, 28675934
GO:0030154	Process	Cell differentiation	IEA
GO:0031012	Component	Extracellular matrix	HDA	25037231, 28675934
GO:0045202	Component	Synapse	IEA
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0098609	Process	Cell-cell adhesion	IEP	10865988

MIM	HGNC	e!Ensembl
120350	2190	ENSG00000197467

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

124

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Congenital myasthenic syndrome 19	Likely pathogenic; Pathogenic	rs763197055, rs2136077497, rs2134842358, rs2135829327, rs769673346, rs1480562957, rs864309662, rs864309663, rs2544717844, rs763281993, rs1057204973, rs2545815673, rs1554943789, rs2064735979, rs1564932829, rs2065959942, rs759296053 View all (2 more)	RCV003136050 RCV001543594 RCV001543595 RCV001543596 RCV001780804 RCV002272855 RCV000203254 RCV000203249 RCV002789987 RCV003492024 RCV003447874 RCV003493228 RCV000578262 RCV001253101 RCV001254694 RCV001261648 RCV005042673
See cases	Likely pathogenic	rs1589245442	RCV002253166
Thyroid cancer, nonmedullary, 1	Likely pathogenic	rs894208635	RCV005928392

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Uncertain significance	rs373955853	RCV005923999
Cervical cancer	Benign	rs2704505, rs72805194, rs114352207	RCV005923345 RCV005922349 RCV005902719
Cholangiocarcinoma	Benign	rs56173804, rs72805194	RCV005916858 RCV005922354
COL13A1-related disorder	Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity	rs375168437, rs1487796419, rs374489567, rs768223191, rs560046143, rs147220162, rs751822343, rs373882459, rs2545255516, rs777001080, rs199809931, rs530365744, rs771278874, rs1319263892, rs1195450785 View all (21 more)	RCV003395270 RCV004756344 RCV003913630 RCV003968810 RCV003951028 RCV004756377 RCV003971320 RCV003906356 RCV003394413 RCV003948980 RCV003902290 RCV003906891 RCV003976859 RCV003971751 RCV003962072 RCV003978313 RCV003960654 RCV003905901 RCV003983310 RCV003916102 RCV003967985 RCV003910518 RCV003940402 RCV003908402 RCV004756077 RCV003968293 RCV003912992 RCV003975708 RCV004756090 RCV003950641 RCV003942842 RCV003923231 RCV003932998 RCV003933040 RCV003960441 RCV003903105
Familial cancer of breast	Benign; Uncertain significance	rs35532046, rs200322111, rs181488392	RCV005922253 RCV005923934 RCV005904721
Gastric cancer	Benign	rs35532046, rs72805194, rs35268667	RCV005922254 RCV005922351 RCV005871348
Hepatocellular carcinoma	Uncertain significance	rs756426858	RCV005928373
Lung cancer	Benign	rs7100913, rs114352207	RCV005916840 RCV005902721
Malignant tumor of esophagus	Benign	rs2704505, rs72805194, rs114352207	RCV005923344 RCV005922348 RCV005902718
Nonpapillary renal cell carcinoma	Likely benign	rs761342035	RCV005926246
Ovarian serous cystadenocarcinoma	Benign	rs80290126, rs72805194	RCV005919337 RCV005922352
Sarcoma	Benign	rs80290126, rs2704505, rs72805194	RCV005919336 RCV005923346 RCV005922350
Thymoma	Benign	rs35532046	RCV005922255
Uterine carcinosarcoma	Benign	rs80290126, rs72805194	RCV005919338 RCV005922353
Uterine corpus endometrial carcinoma	Benign	rs2704505, rs72805194, rs114352207	RCV005923347 RCV005922355 RCV005902722

Show/Hide Text Mining Associations (16)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
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)