RCN3 reticulocalbin 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RCN3provided by HGNC
Official Full Name: reticulocalbin 3provided by HGNC
Primary source: HGNC:HGNC:21145
See related: Ensembl:ENSG00000142552 MIM:619032; AllianceGenome:HGNC:21145
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: RLP49
Summary: Enables calcium ion binding activity. Involved in several processes, including collagen biosynthetic process; positive regulation of peptidase activity; and regulation of protein kinase B signaling. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in fat (RPKM 12.8), placenta (RPKM 11.9) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.33

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (49528003..49543633)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (52527996..52543626)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (50031260..50046890)

Chromosome 19 - NC_000019.10 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?

An Expanded Genome-Wide Association Study of Fructosamine Levels Identifies RCN3 as a Replicating Locus and Implicates FCGRT as the Effector Transcript.
Title: An Expanded Genome-Wide Association Study of Fructosamine Levels Identifies RCN3 as a Replicating Locus and Implicates FCGRT as the Effector Transcript.
Rcn3 Suppression Was Responsible for Partial Relief of Emphysema as Shown by Specific Type II Alveolar Epithelial Cell Rcn3 CKO Mouse Model.
Title: Rcn3 Suppression Was Responsible for Partial Relief of Emphysema as Shown by Specific Type II Alveolar Epithelial Cell Rcn3 CKO Mouse Model.
Study identified reticulocalbin-3 (RCN-3) as a common molecule down-regulated by aldosterone (Aldo), galectin-3 and cardiotrophin-1 - key factors in the cardiac remodeling induced by Aldo associated with cardiac hypertrophy and fibrosis. Moreover, RCN-3 emerges as a new potential negative regulator of collagen production.
Title: Differential Proteomics Identifies Reticulocalbin-3 as a Novel Negative Mediator of Collagen Production in Human Cardiac Fibroblasts.
genome-wide association study in US: Data suggest, among white subjects, an SNP in RCN3 (rs34459162) and a missense mutation in GCKR (rs1260236) are associated with serum levels of glycated albumin; among black subjects, an intergenic SNP in PRKCA (rs2438321) is associated with fructosamine levels and intronic variant in PRKCA (rs59443763) is associated with glycated albumin levels. (GCKR = glucokinase regulatory protein)
Title: Genome-Wide Association Study of Serum Fructosamine and Glycated Albumin in Adults Without Diagnosed Diabetes: Results From the Atherosclerosis Risk in Communities Study.
RCN3 expression in systemic sclerosis was not statistically significantly different to healthy controls.
Title: Circulating Reticulocalbin 1 and Reticulocalbin 3 in Systemic Sclerosis Patients: Results of a Case Control Study.
Autoactivation & secretion of rat PACE4 was increased upon co-expression with recombinant human RCN-3. Selective and transient association of RCN-3 with the precursor of PACE4 plays an important role in the biosynthesis of PACE4.
Title: A proteomic approach reveals transient association of reticulocalbin-3, a novel member of the CREC family, with the precursor of subtilisin-like proprotein convertase, PACE4.

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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
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of hematological and biochemical traits in a Japanese population. 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

SHGC-12954 (e-PCR)
- UniSTS:20850

RH78760 (e-PCR)
- UniSTS:68782

STS-W95460 (e-PCR)
- UniSTS:49854

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in ERAD pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in collagen biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lung epithelium development	ISS Inferred from Sequence or Structural Similarity more info
involved_in phospholipid homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of peptidase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in surfactant homeostasis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum lumen	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: reticulocalbin-3

Names: EF-hand calcium-binding protein RLP49; reticulocabin; reticulocalbin 3, EF-hand calcium binding domain

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.

mRNA and Protein(s)

NM_020650.3 → NP_065701.2 reticulocalbin-3 precursor

See identical proteins and their annotated locations for NP_065701.2

Status: VALIDATED

Source sequence(s)

AY195859

Consensus CDS

CCDS12771.1

UniProtKB/Swiss-Prot

Q96D15, Q9HBZ8

Related

ENSP00000270645.2, ENST00000270645.8

Conserved Domains (1) summary

cd16230
Location:44 → 311

EFh_CREC_RCN3; EF-hand, calcium binding motif, found in reticulocalbin-3 (RCN-3)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

49528003..49543633

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047439116.1 → XP_047295072.1 reticulocalbin-3 isoform X1
XM_047439118.1 → XP_047295074.1 reticulocalbin-3 isoform X2

UniProtKB/Swiss-Prot

Q96D15, Q9HBZ8
XM_047439115.1 → XP_047295071.1 reticulocalbin-3 isoform X1
XM_047439117.1 → XP_047295073.1 reticulocalbin-3 isoform X2

UniProtKB/Swiss-Prot

Q96D15, Q9HBZ8
XM_024451620.2 → XP_024307388.1 reticulocalbin-3 isoform X1

Conserved Domains (1) summary

cd16230
Location:44 → 348

EFh_CREC_RCN3; EF-hand, calcium binding motif, found in reticulocalbin-3 (RCN-3)