C2CD4A C2 calcium dependent domain containing 4A [Homo sapiens (human)] - Gene

Summary

Official Symbol: C2CD4Aprovided by HGNC
Official Full Name: C2 calcium dependent domain containing 4Aprovided by HGNC
Primary source: HGNC:HGNC:33627
See related: Ensembl:ENSG00000198535 MIM:610343; AllianceGenome:HGNC:33627
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NLF1; FAM148A
Summary: Involved in positive regulation of acute inflammatory response; regulation of cell adhesion; and regulation of vascular permeability involved in acute inflammatory response. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in endometrium (RPKM 1.1), colon (RPKM 0.5) and 14 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q22.2

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (62066977..62070917)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (59870950..59874893)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (62359176..62363116)

Chromosome 15 - NC_000015.10 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
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?

C2CD4A/B variants in the predisposition of lung cancer in the Chinese Han population.
Title: C2CD4A/B variants in the predisposition of lung cancer in the Chinese Han population.
C2CD4A is a transcriptional coregulator of the glycolytic pathway whose dysfunction accounts for the diabetes susceptibility associated with the chromosome 15 GWAS locus.
Title: Identification of C2CD4A as a human diabetes susceptibility gene with a role in β cell insulin secretion.
rs7163757 contributes to genetic risk of islet dysfunction and type 2 diabetes by increasing NFAT-mediated islet enhancer activity and modulating C2CD4B, and possibly C2CD4A, expression in (patho)physiologic states.
Title: A Common Type 2 Diabetes Risk Variant Potentiates Activity of an Evolutionarily Conserved Islet Stretch Enhancer and Increases C2CD4A and C2CD4B Expression.
The present data thus provide evidence for a limited role for changes in VPS13C expression in conferring altered type 2 diabetes risk at this locus, particularly in females, and suggest that C2CD4A, but not C2CD4B, may also be involved.
Title: Changes in the expression of the type 2 diabetes-associated gene VPS13C in the β-cell are associated with glucose intolerance in humans and mice.
C2CD4A expression is significantly upregulated in human masticatory mucosa during wound healing
Title: Human gingiva transcriptome during wound healing.
An endoplasmic reticulum protein, NLF-1, delivers a sodium leak channel critical for rhythmic locomotion.
Title: NLF-1 delivers a sodium leak channel to regulate neuronal excitability and modulate rhythmic locomotion.
Single nucleotide polymorphism in C2CD4A is associated with type 2 diabetes.
Title: A genome-wide association study in the Japanese population identifies susceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: A genome-wide association study in the Japanese population identifies susceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B.
NLF1 may play a role in regulating genes which control cellular architecture.
Title: A novel gene family induced by acute inflammation in endothelial cells.

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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
A genome-wide association study confirms previously reported loci for type 2 diabetes in Han Chinese. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study in the Japanese population identifies susceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies three novel loci for type 2 diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. EBI GWAS Catalog EBI GWAS CatalogPubMed
Hundreds of variants clustered in genomic loci and biological pathways affect human height. 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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Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in positive regulation of acute inflammatory response	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of cell adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of vascular permeability involved in acute inflammatory response	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: C2 calcium-dependent domain-containing protein 4A

Names: family with sequence similarity 148, member A; nuclear localized factor 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.