SCGN secretagogin, EF-hand calcium binding protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: SCGNprovided by HGNC
Official Full Name: secretagogin, EF-hand calcium binding proteinprovided by HGNC
Primary source: HGNC:HGNC:16941
See related: Ensembl:ENSG00000079689 MIM:609202; AllianceGenome:HGNC:16941
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
Also known as: SEGN; CALBL; SECRET; setagin; DJ501N12.8
Summary: The encoded protein is a secreted calcium-binding protein which is found in the cytoplasm. It is related to calbindin D-28K and calretinin. This protein is thought to be involved in KCL-stimulated calcium flux and cell proliferation. [provided by RefSeq, Jul 2008]
Expression: Biased expression in stomach (RPKM 11.2), colon (RPKM 8.7) and 8 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p22.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (25652215..25701783)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (25518025..25567550)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (25652443..25702011)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

SCGN deficiency is a risk factor for autism spectrum disorder.
Title: SCGN deficiency is a risk factor for autism spectrum disorder.
Differential expression of secretagogin immunostaining in the hippocampal formation and the entorhinal and perirhinal cortices of humans, rats, and mice.
Title: Differential expression of secretagogin immunostaining in the hippocampal formation and the entorhinal and perirhinal cortices of humans, rats, and mice.
In this study, the authors report the identification of an ultrarare missense variant (NM_006998.3:c.230G > A;p.Arg77His) in the SCGN gene causing Mendelian early-onset ulcerative colitis.
Title: SCGN deficiency results in colitis susceptibility.
the overexpression of SCGN in SW480 human colorectal cancer cells promoted cell apoptosis and inhibited cell migration and invasion.
Title: Overexpression of secretagogin promotes cell apoptosis and inhibits migration and invasion of human SW480 human colorectal cancer cells.
Glucose-dependent de-SUMOylation of tomosyn1 at K298 releases syntaxin1A and controls the amplification of exocytosis in concert with a recently-identified tomosyn1-interacting partner; the Ca(2+)-binding protein secretagogin, which dissociates from tomosyn1 in response to Ca(2+)-raising stimuli and is required for insulin granule trafficking and exocytosis downstream of Ca(2+) influx.
Title: SUMOylation and calcium control syntaxin-1A and secretagogin sequestration by tomosyn to regulate insulin exocytosis in human ß cells.
secretagogin is a potential biomarker, reflecting stress and islet cell dysfunction in T2D patients
Title: Secretagogin is increased in plasma from type 2 diabetes patients and potentially reflects stress and islet dysfunction.
Secretagogin-dependent MMP2 release from neurons regulates neuroblast migration.
Title: Secretagogin-dependent matrix metalloprotease-2 release from neurons regulates neuroblast migration.
The low SCGN plasma levels in children with ASD probably indicate that SCGN might be implicated in the pathogenesis of autism. However, these data should be treated with caution until further investigations are performed using larger sample sizes to determine whether the decrease in plasma SCGN levels is a mere consequence of autism or it plays a pathogenic role in the disease.
Title: Secretagogin (SCGN) Plasma Levels and their Association with Cognitive and Social Behavior in Children with Autism Spectrum Disorder ASD).
Therefore, and considering the desensitization of TRPV1s in diabetic pancreata, a TRPV1-to-secretagogin regulatory axis seems critical to maintain the structural integrity and signal competence of beta-cells.
Title: A TRPV1-to-secretagogin regulatory axis controls pancreatic β-cell survival by modulating protein turnover.
These results suggest SCGN is involved in the chemoresistance of small cell lung cancer under the regulation of miR-494
Title: Overexpression of secretagogin inhibits cell apoptosis and induces chemoresistance in small cell lung cancer under the regulation of miR-494.

Submit: New GeneRIF Correction See all GeneRIFs (19)

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
Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels. 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

RH99089 (e-PCR)
- UniSTS:85255

D6S1468 (e-PCR)
- UniSTS:26509

AL021842 (e-PCR)
- UniSTS:29100

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	NAS Non-traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in regulation of long-term synaptic potentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of presynaptic cytosolic calcium ion concentration	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytoplasm	NAS Non-traceable Author Statement more info	PubMed
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
is_active_in dendrite	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
is_active_in terminal bouton	IBA Inferred from Biological aspect of Ancestor more info
located_in transport vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: secretagogin

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_006998.4 → NP_008929.2 secretagogin

Status: REVIEWED

Source sequence(s)

BC000336, BM511122, BQ477463, Y16752

Consensus CDS

CCDS4561.1

UniProtKB/Swiss-Prot

A8K0B2, O76038, Q5VV44, Q96QV7, Q9UJF6

UniProtKB/TrEMBL

A0A994J4C2

Related

ENSP00000367197.2, ENST00000377961.3

Conserved Domains (1) summary

cd16178
Location:17 → 273

EFh_HEF_SCGN; EF-hand, calcium binding motif, found in secretagogin (SCGN)