COL13A1

collagen type XIII alpha 1 chain, the group of Collagens

Basic information

Region (hg38): 10:69801880-69964275

Links

ENSG00000197467 ∙ NCBI:1305 ∙ OMIM:120350 ∙ HGNC:2190 ∙ Uniprot:Q5TAT6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital myasthenic syndrome 19 (Strong), mode of inheritance: AR
• congenital myasthenic syndrome 19 (Strong), mode of inheritance: AR
• congenital myasthenic syndrome 19 (Strong), mode of inheritance: AR
• postsynaptic congenital myasthenic syndrome (Supportive), mode of inheritance: AR
• presynaptic congenital myasthenic syndrome (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myasthenic syndrome, congenital, 19	AR	Musculoskeletal	Individuals are affected by muscular weakness, including affecting the respiratory system, and medical management (with 3,4-diaminopyridine and salbutamol) has been reported as beneficial	Craniofacial; Musculoskeletal; Neurologic	26626625

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COL13A1 gene.

• not provided (8 variants)
• Congenital myasthenic syndrome 19 (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL13A1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	93	6	102
missense	1		161	3	5	170
nonsense	3	2	1			6
start loss						0
frameshift	5	2	1			8
inframe indel			2			2
splice donor/acceptor (+/-2bp)		14	2			16
splice region			26	43	11	80
non coding	1	1	12	149	93	256
Total	10	19	182	245	104

Highest pathogenic variant AF is 0.0000131

Variants in COL13A1

This is a list of pathogenic ClinVar variants found in the COL13A1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-69802014-G-A			Benign (May 10, 2021)
10-69802338-C-T			Benign (May 11, 2021)
10-69802429-A-G		COL13A1-related disorder	Likely benign (Oct 11, 2023)
10-69802430-G-A			Uncertain significance (May 31, 2021)
10-69802435-G-A			Likely benign (Oct 16, 2023)
10-69802436-C-T			Uncertain significance (Aug 27, 2021)
10-69802447-A-G			Likely benign (Dec 01, 2023)
10-69802448-G-A		Inborn genetic diseases	Uncertain significance (Apr 23, 2024)
10-69802450-G-A			Likely benign (Aug 18, 2023)
10-69802452-C-T			Uncertain significance (Mar 23, 2021)
10-69802458-C-G			Uncertain significance (Feb 21, 2022)
10-69802473-CTGGGGAGT-C			Pathogenic (Nov 10, 2021)
10-69802475-GG-AA			Uncertain significance (Oct 04, 2022)
10-69802489-G-A		COL13A1-related disorder	Likely benign (Dec 13, 2021)
10-69802489-G-T			Likely benign (Sep 07, 2022)
10-69802490-C-A		COL13A1-related disorder	Likely benign (Dec 19, 2023)
10-69802492-C-G			Likely benign (Feb 02, 2022)
10-69802497-CG-C			Pathogenic (May 23, 2023)
10-69802507-G-A			Likely benign (Jun 23, 2022)
10-69802513-G-T			Likely benign (Sep 01, 2022)
10-69802516-G-A			Likely benign (Oct 13, 2022)
10-69802525-G-T			Uncertain significance (Jul 27, 2021)
10-69802532-G-A			Uncertain significance (Mar 18, 2022)
10-69802535-C-T		Inborn genetic diseases	Uncertain significance (May 21, 2024)
10-69802536-G-C		Inborn genetic diseases	Uncertain significance (Aug 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL13A1	protein_coding	protein_coding	ENST00000398978	39	162388

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.74e-14	0.999	124458	0	218	124676	0.000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.770	364	408	0.893	0.0000226	4405
Missense in Polyphen		238	273.89	0.86895		2905
Synonymous	-1.23	168	149	1.13	0.00000851	1498
Loss of Function	3.05	31	55.6	0.558	0.00000255	684

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00517	0.00517
Ashkenazi Jewish	0.00	0.00
East Asian	0.000396	0.000389
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000234	0.000230
Middle Eastern	0.000396	0.000389
South Asian	0.000131	0.000131
Other	0.00132	0.00132

dbNSFP

Source: dbNSFP

• Function: 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 morphogenesis of lung. Binds heparin. At neuromuscular junctions, may play a role in acetylcholine receptor clustering (PubMed:26626625). {ECO:0000250|UniProtKB:Q9R1N9, ECO:0000269|PubMed:10865988, ECO:0000269|PubMed:11956183, ECO:0000269|PubMed:26626625}.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Vitamin D Receptor Pathway;Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Integrin cell surface interactions;Collagen formation;Extracellular matrix organization (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.0355
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.6

Haploinsufficiency Scores

• pHI: 0.283
• hipred: Y
• hipred_score: 0.605
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.205

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Col13a1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: morphogenesis of a branching structure;endochondral ossification;cell-matrix adhesion;cell differentiation;extracellular matrix organization;collagen catabolic process;cell-cell adhesion
• Cellular component: extracellular region;collagen type XIII trimer;extracellular space;endoplasmic reticulum lumen;plasma membrane;cell-cell junction;extracellular matrix;postsynaptic membrane;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent;protein binding;heparin binding;extracellular matrix structural constituent conferring tensile strength