COL22A1

collagen type XXII alpha 1 chain, the group of Collagens

Basic information

Region (hg38): 8:138588234-138914041

Links

ENSG00000169436 ∙ NCBI:169044 ∙ OMIM:610026 ∙ HGNC:22989 ∙ Uniprot:Q8NFW1 ∙ 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 COL22A1 gene.

• Inborn genetic diseases (86 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL22A1 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	1	3
missense			83	6	2	91
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	83	8	3

Variants in COL22A1

This is a list of pathogenic ClinVar variants found in the COL22A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-138589275-G-A		not specified	Uncertain significance (Sep 17, 2021)
8-138589300-A-G		not specified	Uncertain significance (Jan 10, 2023)
8-138589347-G-A		not specified	Uncertain significance (Oct 13, 2023)
8-138589392-G-A		not specified	Uncertain significance (Jan 17, 2024)
8-138589432-C-T		not specified	Uncertain significance (Jun 05, 2023)
8-138594081-C-A		not specified	Uncertain significance (Sep 06, 2022)
8-138594089-C-T		not specified	Uncertain significance (Aug 15, 2023)
8-138594119-G-A		not specified	Uncertain significance (Dec 28, 2022)
8-138594122-G-A		not specified	Uncertain significance (Oct 13, 2023)
8-138594138-T-G		not specified	Uncertain significance (Sep 27, 2022)
8-138594184-A-T			Likely benign (Nov 01, 2022)
8-138596939-C-T		not specified	Uncertain significance (Jan 26, 2022)
8-138598724-G-C		not specified	Uncertain significance (May 31, 2023)
8-138598795-G-A		not specified	Uncertain significance (Apr 25, 2022)
8-138598812-G-C		not specified	Uncertain significance (Nov 17, 2023)
8-138606391-C-T			Uncertain significance (Jan 29, 2024)
8-138606392-G-A		not specified	Uncertain significance (Sep 13, 2023)
8-138606428-T-G		not specified	Uncertain significance (Mar 01, 2024)
8-138607956-G-T		not specified	Uncertain significance (Dec 22, 2023)
8-138607985-T-C		not specified	Uncertain significance (Dec 16, 2023)
8-138613869-G-T		not specified	Uncertain significance (Mar 01, 2023)
8-138616915-C-T		not specified	Uncertain significance (Mar 17, 2023)
8-138616933-G-C		not specified	Uncertain significance (Dec 27, 2023)
8-138619487-G-C		not specified	Uncertain significance (Feb 28, 2024)
8-138623752-G-A		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL22A1	protein_coding	protein_coding	ENST00000303045	64	325772

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.49e-45	0.00627	125511	1	236	125748	0.000943

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.367	996	964	1.03	0.0000593	10061
Missense in Polyphen		63	59.301	1.0624		616
Synonymous	-1.08	389	363	1.07	0.0000232	3492
Loss of Function	2.23	83	108	0.768	0.00000586	1245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00267	0.00264
Ashkenazi Jewish	0.000804	0.000794
East Asian	0.00145	0.00141
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000714	0.000695
Middle Eastern	0.00145	0.00141
South Asian	0.00181	0.00177
Other	0.000655	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a cell adhesion ligand for skin epithelial cells and fibroblasts.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization (Consensus)

Intolerance Scores

• loftool: 0.0681
• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.93

Haploinsufficiency Scores

• pHI: 0.0831
• hipred: Y
• hipred_score: 0.539
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0576

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col22a1

Gene ontology

• Biological process: extracellular matrix organization
• Cellular component: extracellular region;collagen trimer;extracellular space;endoplasmic reticulum lumen;extracellular matrix
• Molecular function: extracellular matrix structural constituent