COL21A1

collagen type XXI alpha 1 chain, the group of Collagens

Basic information

Region (hg38): 6:56056590-56394094

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.

• not_specified (106 variants)
• not_provided (5 variants)

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. These statistics are base on transcript: NM_000030820.4. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			103	5	1	109
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	103	6	2

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