COL24A1 collagen type XXIV alpha 1 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL24A1provided by HGNC
Official Full Name: collagen type XXIV alpha 1 chainprovided by HGNC
Primary source: HGNC:HGNC:20821
See related: Ensembl:ENSG00000171502 MIM:610025; AllianceGenome:HGNC:20821
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
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]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 1p22.3

Exon count:: 66

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (85729233..86156984, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (85570083..85997700, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (86194916..86622667, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The authors show that maternal COL24A1 variants have a significant genome-wide interaction with maternal pre-pregnancy overweight/obesity on Preterm birth risk, with rs11161721 (PG x E=1.8 x 10(-8); empirical PG x E=1.2 x 10(-8)) as the top hit.
Title: Genome-wide approach identifies a novel gene-maternal pre-pregnancy BMI interaction on preterm birth.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
collagen XXIV is an ancient molecule that may contribute to the regulation of type I collagen fibrillogenesis at specific anatomical locations during fetal development
Title: Collagen XXIV, a vertebrate fibrillar collagen with structural features of invertebrate collagens: selective expression in developing cornea and bone.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D14S120 (e-PCR)
- UniSTS:15876

G63181 (e-PCR)
- UniSTS:140298

COL24A1_2246 (e-PCR)
- UniSTS:280617

SHGC-75097 (e-PCR)
- UniSTS:65879

SHGC-156139 (e-PCR)
- UniSTS:182120

AL010103 (e-PCR)
- UniSTS:34932

AL009471 (e-PCR)
- UniSTS:60287

G62518 (e-PCR)
- UniSTS:139648

SHGC-148676 (e-PCR)
- UniSTS:176542

AL009422 (e-PCR)
- UniSTS:8626

RH92641 (e-PCR)
- UniSTS:90358

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: collagen alpha-1(XXIV) chain

Names: collagen, type XXIV, alpha 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_053093.1 RefSeqGene

Range

5265..432804

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001349955.1 → NP_001336884.1 collagen alpha-1(XXIV) chain isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) encodes isoform 2.

Source sequence(s)

AC099561, AC104455, AL356059, AL359971, AL445427

Conserved Domains (3) summary

pfam01391
Location:603 → 662

Collagen; Collagen triple helix repeat (20 copies)

pfam03157
Location:208 → 711

Glutenin_hmw; High molecular weight glutenin subunit

cl02436
Location:816 → 1013

COLFI; Fibrillar collagen C-terminal domain
NM_152890.7 → NP_690850.2 collagen alpha-1(XXIV) chain isoform 1 precursor

See identical proteins and their annotated locations for NP_690850.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AC099561, AC104455, AL356059, AL359971, AL445427

Consensus CDS

CCDS41353.1

UniProtKB/Swiss-Prot

C9J1X6, Q14BD7, Q17RW2, Q59EX5, Q5VY50, Q7Z5L5

Related

ENSP00000359603.2, ENST00000370571.7

Conserved Domains (3) summary

pfam01391
Location:1303 → 1362

Collagen; Collagen triple helix repeat (20 copies)

cl02436
Location:1516 → 1713

COLFI; Fibrillar collagen C-terminal domain

cl22861
Location:41 → 227

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...