COL23A1

protein-coding

collagen type XXIII alpha 1 chain, the group of Collagens

Gene summary

COL23A1 is a member of the transmembrane collagens, a subfamily of the nonfibrillar collagens that contain a single pass hydrophobic transmembrane domain (Banyard et al., 2003 [PubMed 12644459]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_173465.4

Inheritance

—

ClinVar variants

U:112B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr5:178,237,476-178,590,393

External References & Databases

Ensembl (ENSG00000050767)

Transcript & Mutation Effects

hg38 • Region Span ~352.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to COL23A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 94

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173465.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	3 clinvar		4
missense			98 clinvar			98
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			12 clinvar			12
Total	0	0	112	3	0	115

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173465.4	RefSeq	NP_775736.2	29	MANE Select
ENST00000390654.8	Ensembl	ENSP00000375069.3	29	MANE Select
ENST00000407622.3	Ensembl	ENSP00000385092.3	25	Standard
ENST00000646779.1	Ensembl	ENSP00000496734.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Collagen chain trimerization
Collagen biosynthesis and modifying enzymes
Integrin cell surface interactions
Collagen degradation
Collagen formation

Biological Process

angiogenesis
endothelial cell morphogenesis
extracellular matrix organization

Molecular Function

extracellular matrix structural constituent
protein binding

Cellular Component

collagen trimer
extracellular space
endoplasmic reticulum lumen
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000390654
Coding exons: 28
Length: 352938
Individuals with no LoFs: 124704
Homozygous LoFs: 0
Heterozygous LoFs: 97
Defined: 124801
p: 0.000389

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.696	254	287	0.884	0.0000173	3264
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00052	0.00045	rare
Latino/Admixed American	0.00064	0.00064	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00056	0.00056	rare
Finnish	0.00019	0.00019	rare
European (Non-Finnish)	0.00036	0.00036	rare
South Asian	0.00033	0.00033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0814

Intolerance Scores

LoFtool: 0.271
RVIS EVS: 0.76
RVIS percentile EVS: 86.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.812

Gene Damage Prediction

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