SCG2 Gene (Protein Coding)

Secretogranin II

GC02M223596
GIFtS:
40
The protein encoded by this gene is a member of the chromogranin/secretogranin family of neuroendocrine secretory proteins. Studies in rodents suggest that the full-length protein, secretogranin II, is involved in the packaging or sorting of peptide hormones and neuropeptides into secretory vesicles. The full-length protein is cleaved to produce the active peptide secretoneurin... See more...

Aliases for SCG2 Gene

Aliases for SCG2 Gene

  • Secretogranin II 2 3 4 5
  • CHGC 2 3 4
  • SgII 2 3 4
  • Secretogranin-2 3 4
  • Chromogranin-C 3 4
  • Secretoneurin 2 3
  • SN 2 3
  • Chromogranin C 2
  • EM66 3
  • SCG2 5

External Ids for SCG2 Gene

Previous GeneCards Identifiers for SCG2 Gene

  • GC02M222484
  • GC02M223182
  • GC02M224425
  • GC02M224664
  • GC02M224287
  • GC02M224169
  • GC02M216313

Summaries for SCG2 Gene

Entrez Gene Summary for SCG2 Gene

  • The protein encoded by this gene is a member of the chromogranin/secretogranin family of neuroendocrine secretory proteins. Studies in rodents suggest that the full-length protein, secretogranin II, is involved in the packaging or sorting of peptide hormones and neuropeptides into secretory vesicles. The full-length protein is cleaved to produce the active peptide secretoneurin, which exerts chemotaxic effects on specific cell types, and EM66, whose function is unknown. [provided by RefSeq, Jul 2008]

GeneCards Summary for SCG2 Gene

SCG2 (Secretogranin II) is a Protein Coding gene. Diseases associated with SCG2 include Collagenous Colitis and Neuroendocrine Tumor. Gene Ontology (GO) annotations related to this gene include cytokine activity and chemoattractant activity.

UniProtKB/Swiss-Prot Summary for SCG2 Gene

  • Neuroendocrine protein of the granin family that regulates the biogenesis of secretory granules.

Gene Wiki entry for SCG2 Gene

Additional gene information for SCG2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCG2 Gene

Genomics for SCG2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SCG2 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH02J223598 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 250.7 +2.0 2024 4.2 MXD4 CTCF THAP11 REST ZNF511 SAP130 MIER3 ZSCAN9 RARA TEAD3 SCG2 piR-31292-109 KCNE4
GH02J223602 Promoter 0.9 Ensembl 250.7 -0.3 -340 0.2 MXD4 CTCF THAP11 ZNF511 SAP130 REST MIER3 ZSCAN9 TCF7L2 RAD21 SCG2 lnc-MRPL44-4 AP1S3
GH02J223603 Enhancer 0.3 FANTOM5 268 -0.8 -804 0.2 CEBPB SCG2 lnc-MRPL44-4 AP1S3
GH02J223956 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 10.2 -355.8 -355784 4.1 CHD2 TBP ZBTB10 BCL11A SP1 MXD4 FEZF1 CEBPA SIX5 NR2C1 MRPL44 lnc-WDFY1-4 piR-41482 WDFY1 ANKRD49P1 SCG2 SERPINE2
GH02J224483 Promoter/Enhancer 1.2 Ensembl ENCODE 10.5 -882.8 -882804 2.8 CEBPA FOXA1 ZNF217 ELF1 ZIC2 HOMEZ KDM6A THAP11 FOXA2 SMAD4 lnc-FAM124B-1 ANKRD49P1 SCG2 CUL3 HSALNG0022637 FAM124B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCG2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SCG2

Top Transcription factor binding sites by QIAGEN in the SCG2 gene promoter:
  • AP-1
  • Nkx2-5
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4
  • POU3F2
  • RSRFC4
  • S8

Genomic Locations for SCG2 Gene

Latest Assembly
chr2:223,596,940-223,602,361
(GRCh38/hg38)
Size:
5,422 bases
Orientation:
Minus strand

Previous Assembly
chr2:224,461,658-224,467,079
(GRCh37/hg19 by Entrez Gene)
Size:
5,422 bases
Orientation:
Minus strand

chr2:224,461,658-224,467,221
(GRCh37/hg19 by Ensembl)
Size:
5,564 bases
Orientation:
Minus strand

Genomic View for SCG2 Gene

Genes around SCG2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCG2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCG2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SCG2 Gene

Proteins for SCG2 Gene

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  • Protein details for SCG2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P13521-SCG2_HUMAN
    Recommended name:
    Secretogranin-2
    Protein Accession:
    P13521
    Secondary Accessions:
    • B2R662
    • Q53T11
    • Q8TBH3

    Protein attributes for SCG2 Gene

    Size:
    617 amino acids
    Molecular mass:
    70941 Da
    Quaternary structure:
    • Interacts with Secretogranin III/SCG3.
    Miscellaneous:
    • Binds calcium with a low-affinity.

neXtProt entry for SCG2 Gene

Protein Expression for SCG2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SCG2 Gene

Other Protein References for SCG2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SCG2 Gene

Domains & Families for SCG2 Gene

Gene Families for SCG2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted secreted proteins

Protein Domains for SCG2 Gene

InterPro:
Blocks:
  • Chromogranin/secretogranin
ProtoNet:

Suggested Antigen Peptide Sequences for SCG2 Gene

GenScript: Design optimal peptide antigens:
  • Secretogranin II (SCG2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P13521

UniProtKB/Swiss-Prot:

SCG2_HUMAN :
  • Belongs to the chromogranin/secretogranin protein family.
Family:
  • Belongs to the chromogranin/secretogranin protein family.
genes like me logo Genes that share domains with SCG2: view

Function for SCG2 Gene

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  1. Animal Models for research
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  6. Cell Lines for research

Molecular function for SCG2 Gene

UniProtKB/Swiss-Prot Function:
Neuroendocrine protein of the granin family that regulates the biogenesis of secretory granules.
GENATLAS Biochemistry:
chromogranin C

Phenotypes From GWAS Catalog for SCG2 Gene

Gene Ontology (GO) - Molecular Function for SCG2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005125 cytokine activity IDA 14970115
GO:0005515 protein binding IPI 21516116
GO:0042056 chemoattractant activity IDA 9473216
genes like me logo Genes that share ontologies with SCG2: view
genes like me logo Genes that share phenotypes with SCG2: view

Animal Models for SCG2 Gene

MGI Knock Outs for SCG2:
  • Scg2 Scg2<tm1.1(KOMP)Vlcg>

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCG2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SCG2 Gene

Localization for SCG2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCG2 Gene

Secreted. Note=Neuroendocrine and endocrine secretory granules.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCG2 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
nucleus 3
plasma membrane 2
cytoskeleton 2
golgi apparatus 2
mitochondrion 1
endosome 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCG2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IDA 9473216
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0030141 secretory granule IEA,IBA 21873635
GO:0031045 dense core granule IEA --
genes like me logo Genes that share ontologies with SCG2: view

Pathways & Interactions for SCG2 Gene

PathCards logo

SuperPathways for SCG2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCG2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000165 MAPK cascade IDA 14970115
GO:0001525 angiogenesis IEA,IDA 14970115
GO:0001937 negative regulation of endothelial cell proliferation TAS 9473216
GO:0001938 positive regulation of endothelial cell proliferation IDA 14970115
GO:0006954 inflammatory response TAS 14970115
genes like me logo Genes that share ontologies with SCG2: view

No data available for Pathways by source and SIGNOR curated interactions for SCG2 Gene

Drugs & Compounds for SCG2 Gene

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(14) Drugs for SCG2 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6876

(13) Additional Compounds for SCG2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SCG2: view

Transcripts for SCG2 Gene

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  1. CRISPR products for research
  2. miRNA products for research
  3. Inhibitory RNAs for research
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mRNA/cDNA for SCG2 Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCG2

Alternative Splicing Database (ASD) splice patterns (SP) for SCG2 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c
SP1: -
SP2: - -
SP3:

Relevant External Links for SCG2 Gene

GeneLoc Exon Structure for
SCG2

Expression for SCG2 Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCG2 Gene

mRNA expression in normal human tissues for SCG2 Gene
mRNA expression by GTEx for SCG2 GenemRNA expression by BioGPS for SCG2 Gene

mRNA differential expression in normal tissues according to GTEx for SCG2 Gene

This gene is overexpressed in Brain - Hypothalamus (x10.4), Brain - Nucleus accumbens (basal ganglia) (x7.8), Pituitary (x6.0), Brain - Caudate (basal ganglia) (x4.4), and Brain - Putamen (basal ganglia) (x4.2).

Protein differential expression in normal tissues from HIPED for SCG2 Gene

This gene is overexpressed in Islet of Langerhans (22.7), Cerebrospinal fluid (9.8), Amniocyte (7.9), and Bone marrow stromal cell (7.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SCG2 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCG2

SOURCE GeneReport for Unigene cluster for SCG2 Gene:

Hs.516726

Evidence on tissue expression from TISSUES for SCG2 Gene

  • Nervous system(5)
  • Adrenal gland(3.5)
  • Pancreas(3.5)
  • Kidney(2.8)
  • Intestine(2.2)
  • Blood(2)
genes like me logo Genes that share expression patterns with SCG2: view

Primer products for research

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCG2 Gene

Orthologs for SCG2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCG2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia SCG2 30 31
  • 99.35 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia SCG2 30 31
  • 89.99 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia SCG2 30 31
  • 89.69 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Scg2 30 17 31
  • 83.2 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Scg2 30
  • 82.01 (n)
Oppossum
(Monodelphis domestica)
 Mammalia SCG2 31
  • 71 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia SCG2 31
  • 66 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves SCG2 30 31
  • 67.1 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia SCG2 31
  • 59 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia scg2 30
  • 59.52 (n)
African clawed frog
(Xenopus laevis)
 Amphibia LOC397939 30
Zebrafish
(Danio rerio)
 Actinopterygii scg2b 30 31
  • 46.75 (n)
 OneToMany
scg2a 31
  • 24 (a)
 OneToMany
Species where no ortholog for SCG2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SCG2 Gene

ENSEMBL:
Gene Tree for SCG2 (if available)
TreeFam:
Gene Tree for SCG2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCG2: view image

Paralogs for SCG2 Gene

No data available for Paralogs for SCG2 Gene

Variants for SCG2 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCG2 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs16864974 Benign: not provided 223,597,489(-) G/A
NM_003469.5(SCG2):c.1794C>T (p.Asn598=) 		SYNONYMOUS
rs1438157 - p.Ala196Val
rs16864976 - p.Tyr61His
rs17852053 - p.Asp294Gly
rs17852054 - p.Asp535Gly

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SCG2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SCG2 Gene

Variant ID Type Subtype PubMed ID
nsv584549 CNV gain 21841781
nsv834553 CNV gain 17160897

Variation tolerance for SCG2 Gene

Residual Variation Intolerance Score: 20.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.02; 37.12% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCG2 Gene

Human Gene Mutation Database (HGMD)
SCG2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCG2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCG2 Gene

Disorders for SCG2 Gene

MalaCards: The human disease database

(11) MalaCards diseases for SCG2 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
collagenous colitis
  • microscopic colitis, collagenous type
neuroendocrine tumor
  • neuroendocrine neoplasm
intracranial primitive neuroectodermal tumor
  • intracranial pnet
pheochromocytoma
  • pheochromocytoma, susceptibility to
neuroendocrine carcinoma
  • neuroendocrine cancer
- elite association - COSMIC cancer census association via MalaCards
Search SCG2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SCG2

Genetic Association Database
(GAD)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SCG2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCG2 Gene

Publications for SCG2 Gene

  1. Dispersion of chromogranin/secretogranin secretory protein family loci in mammalian genomes. (PMID: 8617499) Mahata SK … O'Connor DT (Genomics 1996) 2 3 23
  2. Genome-wide pleiotropy of osteoporosis-related phenotypes: the Framingham Study. (PMID: 20200953) Karasik D … Demissie S (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2010) 3 41
  3. Chromogranin peptides in amyotrophic lateral sclerosis. (PMID: 18721831) Schrott-Fischer A … Marksteiner J (Regulatory peptides 2009) 3 23
  4. Measurements of secretogranins II, III, V and proconvertases 1/3 and 2 in plasma from patients with neuroendocrine tumours. (PMID: 18448176) Stridsberg M … Janson ET (Regulatory peptides 2008) 3 23
  5. Knockdown of Pdcd4 results in induction of proprotein convertase 1/3 and potent secretion of chromogranin A and secretogranin II in a neuroendocrine cell line. (PMID: 18549351) Lankat-Buttgereit B … Göke R (Biology of the cell 2008) 3 23

ExternalLinks

View latest publications for SCG2 gene in Mastermind

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