COL23A1

collagen type XXIII alpha 1 chain, the group of Collagens

Basic information

Region (hg38): 5:178237475-178590393

Links

ENSG00000050767 ∙ NCBI:91522 ∙ OMIM:610043 ∙ HGNC:22990 ∙ Uniprot:Q86Y22 ∙ 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 COL23A1 gene.

• Inborn genetic diseases (19 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL23A1 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
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in COL23A1

This is a list of pathogenic ClinVar variants found in the COL23A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-178242076-G-A		not specified	Uncertain significance (Jan 09, 2024)
5-178242121-C-T		not specified	Uncertain significance (Nov 17, 2023)
5-178242343-T-G		not specified	Uncertain significance (Aug 02, 2021)
5-178245960-G-A			Likely benign (Feb 01, 2023)
5-178246435-C-T		not specified	Uncertain significance (Dec 13, 2023)
5-178246446-T-C		not specified	Uncertain significance (Feb 23, 2023)
5-178247778-C-T			Likely benign (Feb 01, 2023)
5-178247820-T-C		not specified	Uncertain significance (Jan 19, 2024)
5-178249172-G-A		not specified	Uncertain significance (Nov 18, 2022)
5-178252588-C-T		not specified	Uncertain significance (Sep 14, 2021)
5-178254981-C-T		not specified	Uncertain significance (Dec 13, 2022)
5-178256354-C-T		not specified	Uncertain significance (Dec 13, 2023)
5-178256372-T-C		not specified	Uncertain significance (Sep 16, 2021)
5-178256868-T-G		not specified	Uncertain significance (Dec 04, 2023)
5-178256921-G-A		not specified	Uncertain significance (May 26, 2023)
5-178257552-G-A		not specified	Uncertain significance (Jun 07, 2023)
5-178259732-G-T		not specified	Uncertain significance (Dec 05, 2022)
5-178262227-T-C		not specified	Uncertain significance (May 09, 2022)
5-178263249-C-T		not specified	Uncertain significance (Dec 27, 2023)
5-178263257-G-C		not specified	Uncertain significance (Aug 02, 2023)
5-178288332-C-G		not specified	Uncertain significance (Dec 16, 2022)
5-178288337-C-T		not specified	Uncertain significance (Dec 20, 2023)
5-178306904-C-T		not specified	Uncertain significance (May 16, 2023)
5-178320690-T-C		Vascular endothelial growth factor (VEGF) inhibitor response	association (-)
5-178560700-C-T		not specified	Uncertain significance (Oct 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL23A1	protein_coding	protein_coding	ENST00000390654	28	352938

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.65e-13	0.953	124704	0	97	124801	0.000389

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.696	254	287	0.884	0.0000173	3264
Missense in Polyphen		108	135.71	0.79584		1290
Synonymous	-1.07	129	114	1.13	0.00000768	1174
Loss of Function	2.21	26	41.4	0.629	0.00000222	484

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00116	0.00109
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000557	0.000556
Finnish	0.000186	0.000186
European (Non-Finnish)	0.000364	0.000362
Middle Eastern	0.000557	0.000556
South Asian	0.000330	0.000327
Other	0.000170	0.000165

dbNSFP

Source: dbNSFP

• Pathway: Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Integrin cell surface interactions;Collagen degradation;Collagen formation;Extracellular matrix organization;Metabolism of RNA;mRNA Splicing - Major Pathway;Degradation of the extracellular matrix;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.0814

Intolerance Scores

• loftool: 0.271
• rvis_EVS: 0.76
• rvis_percentile_EVS: 86.82

Haploinsufficiency Scores

• pHI: 0.0726
• hipred: N
• hipred_score: 0.207
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.812

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col23a1

Gene ontology

• Biological process: angiogenesis;endothelial cell morphogenesis;extracellular matrix organization
• Cellular component: collagen trimer;extracellular space;endoplasmic reticulum lumen;plasma membrane;integral component of membrane;extracellular matrix
• Molecular function: extracellular matrix structural constituent;protein binding