COL24A1

collagen type XXIV alpha 1 chain, the group of Collagens

Basic information

Region (hg38): 1:85729232-86156943

Links

ENSG00000171502 ∙ NCBI:255631 ∙ OMIM:610025 ∙ HGNC:20821 ∙ Uniprot:Q17RW2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COL24A1 gene.

• Inborn genetic diseases (60 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL24A1 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				1	1	2
missense			58	2	3	63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	3	4

Variants in COL24A1

This is a list of pathogenic ClinVar variants found in the COL24A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-85730563-A-T		not specified	Uncertain significance (Nov 09, 2021)
1-85730574-A-G		not specified	Uncertain significance (Nov 12, 2021)
1-85734780-A-C		not specified	Uncertain significance (Nov 14, 2023)
1-85734870-G-A		not specified	Uncertain significance (Apr 07, 2023)
1-85737410-C-G		not specified	Uncertain significance (Sep 29, 2022)
1-85737440-T-G		not specified	Uncertain significance (Aug 22, 2023)
1-85737458-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-85737460-A-G		not specified	Uncertain significance (Jul 06, 2021)
1-85744780-T-A		not specified	Uncertain significance (Jul 26, 2022)
1-85745485-C-T		not specified	Uncertain significance (Aug 08, 2022)
1-85745490-T-C		not specified	Uncertain significance (Jun 13, 2022)
1-85745506-T-C		not specified	Uncertain significance (Oct 25, 2022)
1-85761419-G-A		not specified	Uncertain significance (Mar 01, 2024)
1-85781230-G-T		not specified	Uncertain significance (Mar 29, 2022)
1-85781250-T-G		not specified	Uncertain significance (Jun 12, 2023)
1-85783525-A-G		not specified	Uncertain significance (Mar 07, 2024)
1-85784117-G-A		not specified	Uncertain significance (Jun 22, 2021)
1-85784266-C-T		not specified	Uncertain significance (Apr 26, 2023)
1-85784271-C-T			Likely benign (Sep 01, 2022)
1-85784281-T-A		not specified	Uncertain significance (Feb 06, 2024)
1-85784314-C-T		not specified	Likely benign (Apr 04, 2023)
1-85786449-C-T		not specified	Likely benign (Dec 12, 2023)
1-85816811-G-C		not specified	Uncertain significance (Jul 26, 2022)
1-85816865-T-C		not specified	Uncertain significance (Jan 23, 2024)
1-85816892-G-A		not specified	Uncertain significance (Aug 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL24A1	protein_coding	protein_coding	ENST00000370571	60	427711

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.98e-44	0.0134	124591	0	204	124795	0.000818

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.211	908	890	1.02	0.0000421	10836
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00202	0.00201
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.000344	0.000334
Finnish	0.000806	0.000789
European (Non-Finnish)	0.000865	0.000848
Middle Eastern	0.000344	0.000334
South Asian	0.000471	0.000425
Other	0.000992	0.000990

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in regulating type I collagen fibrillogenesis at specific anatomical locations during fetal development. {ECO:0000269|PubMed:12874293}.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization;ATF-2 transcription factor network (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.174
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.41

Haploinsufficiency Scores

• pHI: 0.160
• hipred: Y
• hipred_score: 0.552
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.116

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col24a1
• Phenotype: immune system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: extracellular matrix organization
• Cellular component: extracellular region;collagen trimer;extracellular space;endoplasmic reticulum lumen;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent;protein binding;extracellular matrix structural constituent conferring tensile strength