COL20A1

collagen type XX alpha 1 chain, the group of Fibronectin type III domain containing|Collagens

Basic information

Region (hg38): 20:63293186-63334851

Links

ENSG00000101203 ∙ NCBI:57642 ∙ OMIM:619390 ∙ HGNC:14670 ∙ Uniprot:Q9P218 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary palmoplantar keratoderma (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COL20A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL20A1 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				2	2	4
missense			93	14		107
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	93	16	2

Variants in COL20A1

This is a list of pathogenic ClinVar variants found in the COL20A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63295131-C-A		not specified	Uncertain significance (Apr 18, 2023)
20-63295180-C-G		not specified	Uncertain significance (Oct 27, 2023)
20-63297930-G-C		not specified	Uncertain significance (Apr 11, 2023)
20-63305479-A-C		not specified	Uncertain significance (Jun 27, 2022)
20-63305506-A-G		not specified	Uncertain significance (Feb 03, 2022)
20-63305531-G-C		not specified	Uncertain significance (Feb 28, 2024)
20-63305552-A-C		not specified	Uncertain significance (Jan 03, 2024)
20-63305901-T-A		not specified	Uncertain significance (Apr 13, 2022)
20-63305931-G-A		not specified	Likely benign (Jan 23, 2024)
20-63305935-C-G		Palmoplantar keratoderma i, striate, focal, or diffuse	Uncertain significance (Jul 06, 2021)
20-63305956-C-G		not specified	Uncertain significance (Jan 26, 2022)
20-63305961-C-A		not specified	Uncertain significance (May 30, 2024)
20-63305966-G-A			Benign (Jul 21, 2018)
20-63307518-C-T			Likely benign (Sep 01, 2022)
20-63307997-C-G		not specified	Uncertain significance (Mar 22, 2023)
20-63308055-G-A		not specified	Likely benign (Aug 12, 2021)
20-63308064-G-A		not specified	Uncertain significance (Sep 25, 2023)
20-63308559-G-A		not specified	Uncertain significance (Jan 05, 2022)
20-63308577-C-G			Likely benign (Mar 01, 2022)
20-63308595-C-T		not specified	Uncertain significance (May 13, 2024)
20-63308611-A-G		not specified	Uncertain significance (Sep 22, 2023)
20-63308630-G-A			Benign (Jul 21, 2018)
20-63308633-C-T			Likely benign (Sep 01, 2022)
20-63308667-C-T		not specified	Uncertain significance (Aug 05, 2023)
20-63308688-G-A		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL20A1	protein_coding	protein_coding	ENST00000358894	34	41666

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.38e-40	0.00000290	124454	1	343	124798	0.00138

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.455	778	743	1.05	0.0000471	7961
Missense in Polyphen		232	235.42	0.98545		2845
Synonymous	-2.49	394	336	1.17	0.0000239	2787
Loss of Function	0.189	62	63.6	0.974	0.00000349	702

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00511	0.00494
Ashkenazi Jewish	0.00121	0.00119
East Asian	0.000519	0.000501
Finnish	0.000913	0.000882
European (Non-Finnish)	0.00131	0.00127
Middle Eastern	0.000519	0.000501
South Asian	0.00119	0.00114
Other	0.00208	0.00198

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable collagen protein.
• Pathway: Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization (Consensus)

Recessive Scores

• pRec: 0.0822

Intolerance Scores

• loftool: 0.447
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.12

Haploinsufficiency Scores

• pHI: 0.0925
• hipred: N
• hipred_score: 0.207
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.761

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col20a1
• Phenotype: normal phenotype

Gene ontology

• Biological process: complement activation, lectin pathway;growth plate cartilage chondrocyte morphogenesis
• Cellular component: extracellular region;collagen trimer;extracellular space;endoplasmic reticulum lumen;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: calcium ion binding;mannose binding