COL24A1

protein-coding

collagen type XXIV alpha 1 chain, the group of Collagens

Gene summary

This gene is a member of the collagen gene family and is thought to regulate type I collagen fibrillogenesis during fetal development. [provided by RefSeq, Mar 2017]

MANE transcript

NM_152890.7

Inheritance

—

ClinVar variants

U:239B:19

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr1:85,729,233-86,156,943

External References & Databases

Ensembl (ENSG00000171502)

Transcript & Mutation Effects

hg38 • Region Span ~427.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tourette syndromeNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to COL24A1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 241

not providedTotal: 7

Prostate cancerTotal: 1

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152890.7. 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	2 clinvar	1 clinvar	4
missense			232 clinvar	13 clinvar	3 clinvar	248
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	239	15	4	258

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152890.7	RefSeq	NP_690850.2	60	MANE Select
ENST00000370571.7	Ensembl	ENSP00000359603.2	60	MANE Select
NM_001349955.1	RefSeq	NP_001336884.1	46	Standard
ENST00000426639.5	Ensembl	ENSP00000409515.1	25	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Protein digestion and absorption - Homo sapiens (human)
Collagen chain trimerization
Collagen biosynthesis and modifying enzymes
Collagen formation
Extracellular matrix organization

Biological Process

extracellular matrix organization

Molecular Function

extracellular matrix structural constituent
protein binding
extracellular matrix structural constituent conferring tensile strength

Cellular Component

extracellular region
collagen trimer
extracellular space
endoplasmic reticulum lumen
extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370571
Coding exons: 60
Length: 427711
Individuals with no LoFs: 124591
Homozygous LoFs: 0
Heterozygous LoFs: 204
Defined: 124795
p: 0.000818

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.211	908	890	1.02	0.0000421	10836
Missense (PolyPhen)		332	350.21	0.948		4040
Synonymous	0.166	289	293	0.988	0.0000143	3468
Loss of Function	2.32	82	108	0.759	0.00000513	1415

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00072	0.00071	rare
Latino/Admixed American	0.0013	0.0013	notable
Ashkenazi Jewish	0.0011	0.0011	notable
East Asian	0.00034	0.00033	rare
Finnish	0.00081	0.00079	rare
European (Non-Finnish)	0.00086	0.00085	rare
South Asian	0.00047	0.00042	rare
Other	0.00099	0.00099	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May participate in regulating type I collagen fibrillogenesis at specific anatomical locations during fetal development. {ECO:0000269|PubMed:12874293}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.174
RVIS EVS: 0.8
RVIS percentile EVS: 87.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.116

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High