GeneBe

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
  • congenital myasthenic syndrome 19 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Myasthenic syndrome, congenital, 19ARMusculoskeletalIndividuals are affected by muscular weakness, including affecting the respiratory system, and medical management (with 3,4-diaminopyridine and salbutamol) has been reported as beneficialCraniofacial; Musculoskeletal; Neurologic26626625

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. These statistics are base on transcript: . Only rare variants are included in the table.

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
1
clinvar
97
clinvar
9
clinvar
 107
missense
1
clinvar
181
clinvar
3
clinvar
5
clinvar
 190
nonsense
3
clinvar
2
clinvar
1
clinvar
 6
start loss
0
frameshift
5
clinvar
2
clinvar
1
clinvar
 8
splice donor/acceptor (+/-2bp)
16
clinvar
3
clinvar
 19
Total 9 20 187 100 14

Highest pathogenic variant AF is 0.0000131491

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
COL13A1protein_codingprotein_codingENST00000398978 39162388
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
3.74e-140.99912445802181246760.000875
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7703644080.8930.00002264405
Missense in Polyphen238273.890.868952905
Synonymous-1.231681491.130.000008511498
Loss of Function3.053155.60.5580.00000255684

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.005170.00517
Ashkenazi Jewish0.000.00
East Asian0.0003960.000389
Finnish0.00004650.0000464
European (Non-Finnish)0.0002340.000230
Middle Eastern0.0003960.000389
South Asian0.0001310.000131
Other0.001320.00132

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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