COL21A1

collagen type XXI alpha 1 chain, the group of Collagens

Basic information

Region (hg38): 6:56056589-56394094

Links

ENSG00000124749 ∙ NCBI:81578 ∙ OMIM:610002 ∙ HGNC:17025 ∙ Uniprot:Q96P44 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COL21A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL21A1 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					1	1
missense			48	2	1	51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	2	2

Variants in COL21A1

This is a list of pathogenic ClinVar variants found in the COL21A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-56057695-C-A		not specified	Uncertain significance (Sep 16, 2021)
6-56057833-G-C		not specified	Uncertain significance (Aug 12, 2021)
6-56059169-G-A			Benign (Sep 17, 2017)
6-56059170-G-C		not specified	Uncertain significance (Jul 27, 2021)
6-56060054-C-T		not specified	Uncertain significance (Feb 12, 2024)
6-56060085-C-A		not specified	Uncertain significance (Aug 23, 2021)
6-56060958-G-A		not specified	Uncertain significance (Jan 30, 2024)
6-56060995-A-G		not specified	Likely benign (Jul 05, 2023)
6-56061662-C-T		not specified	Uncertain significance (Jan 23, 2024)
6-56061665-T-C		not specified	Uncertain significance (Mar 01, 2023)
6-56064598-G-T		not specified	Uncertain significance (Jun 06, 2023)
6-56069062-C-T		not specified	Uncertain significance (Aug 12, 2021)
6-56069105-C-T		not specified	Uncertain significance (Jun 11, 2024)
6-56070758-G-A		not specified	Uncertain significance (Jan 26, 2023)
6-56070770-C-A			Uncertain significance (Mar 08, 2024)
6-56075504-C-T		not specified	Uncertain significance (Jan 16, 2024)
6-56075520-G-A		not specified	Uncertain significance (Aug 17, 2021)
6-56077530-T-G		not specified	Uncertain significance (Aug 17, 2022)
6-56077539-A-G		not specified	Uncertain significance (Jan 04, 2024)
6-56077567-G-A		not specified	Uncertain significance (May 23, 2023)
6-56124072-G-C			Benign (Sep 17, 2017)
6-56124073-G-A		not specified	Uncertain significance (Jun 30, 2023)
6-56124085-A-T		not specified	Uncertain significance (Aug 10, 2021)
6-56124109-G-C		not specified	Uncertain significance (May 07, 2024)
6-56124241-C-A		not specified	Uncertain significance (May 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL21A1	protein_coding	protein_coding	ENST00000244728	29	337505

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.23e-24	0.0645	124220	0	422	124642	0.00169

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.809	421	470	0.895	0.0000234	5995
Missense in Polyphen		145	181.31	0.79973		2165
Synonymous	-1.13	182	164	1.11	0.00000859	1908
Loss of Function	1.52	43	55.1	0.780	0.00000297	742

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00793	0.00741
Ashkenazi Jewish	0.000414	0.000398
East Asian	0.0102	0.00984
Finnish	0.000615	0.000603
European (Non-Finnish)	0.000544	0.000522
Middle Eastern	0.0102	0.00984
South Asian	0.000582	0.000556
Other	0.00120	0.00116

dbNSFP

Source: dbNSFP

• Pathway: Protein digestion and absorption - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Type 2 papillary renal cell carcinoma;Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.0800
• rvis_EVS: 0.72
• rvis_percentile_EVS: 85.85

Haploinsufficiency Scores

• pHI: 0.535
• hipred: N
• hipred_score: 0.273
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.230

Gene Damage Prediction

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

Gene ontology

• Biological process: growth plate cartilage chondrocyte morphogenesis
• Cellular component: extracellular region;collagen trimer;extracellular space;endoplasmic reticulum lumen;cytosol;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent conferring tensile strength