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Aliases for SCG2 Gene

Aliases for SCG2 Gene

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

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 Intracranial Primitive Neuroectodermal Tumor and Lymph Node Cancer. Gene Ontology (GO) annotations related to this gene include cytokine activity and chemoattractant activity.

UniProtKB/Swiss-Prot for SCG2 Gene

  • Secretogranin-2 is a neuroendocrine secretory granule protein, which is the precursor for biologically active peptides.

Gene Wiki entry for SCG2 Gene

Additional gene information for SCG2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCG2 Gene

Genomics for SCG2 Gene

GeneHancer (GH) Regulatory Elements for SCG2 Gene

Promoters and enhancers for SCG2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J223602 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 650.7 +0.0 11 0.6 ELF3 ATF1 SIN3A RAD21 ZNF48 ZSCAN9 RARA SLC30A9 ZNF335 ZNF766 SCG2 ENSG00000235610
GH02J223603 Enhancer 0.2 FANTOM5 668.1 -0.7 -662 0.2 SCG2 GC02P223632
GH02J223956 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 9.7 -354.9 -354942 2.7 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 MRPL44 WDFY1 KCNE4 SCG2 LOC100419814 PIR34481
GH02J223587 Enhancer 0.5 FANTOM5 4.8 +14.5 14538 0.4 ATF7 ATF2 SCG2 ENSG00000235610
GH02J223203 Enhancer 0.2 ENCODE 5 +398.1 398128 1.1 SCG2 LOC105373906 GC02P223185 GC02M223063 GC02P223043
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for SCG2 Gene

Genomic Locations for SCG2 Gene
5,564 bases
Minus strand
5,564 bases
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 StructureGene Density

RefSeq DNA sequence for SCG2 Gene

Proteins for SCG2 Gene

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

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2R662
    • Q53T11
    • Q8TBH3

    Protein attributes for SCG2 Gene

    617 amino acids
    Molecular mass:
    70941 Da
    Quaternary structure:
    No Data Available
    • Binds calcium with a low-affinity.

neXtProt entry for SCG2 Gene

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

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

Protein Domains for SCG2 Gene

Suggested Antigen Peptide Sequences for SCG2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



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

Function for SCG2 Gene

Molecular function for SCG2 Gene

UniProtKB/Swiss-Prot Function:
Secretogranin-2 is a neuroendocrine secretory granule protein, which is the precursor for biologically active peptides.
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 Model Products

CRISPR Products

miRNA for SCG2 Gene

miRTarBase miRNAs that target SCG2

Inhibitory RNA Products

  • 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

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
golgi apparatus 2
cytoskeleton 1

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 --
GO:0031045 dense core granule IEA --
genes like me logo Genes that share ontologies with SCG2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SCG2 Gene

Pathways & Interactions 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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0

(12) 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

mRNA/cDNA for SCG2 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(188) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SCG2 Gene

Secretogranin II:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • 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: - -

Relevant External Links for SCG2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SCG2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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

NURSA nuclear receptor signaling pathways regulating expression of SCG2 Gene:


SOURCE GeneReport for Unigene cluster for SCG2 Gene:


Evidence on tissue expression from TISSUES for SCG2 Gene

  • Nervous system(5)
  • Adrenal gland(3.6)
  • Pancreas(3.4)
  • Kidney(2.2)
  • Intestine(2)
genes like me logo Genes that share expression patterns with SCG2: view

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
(Pan troglodytes)
Mammalia SCG2 34 33
  • 99.35 (n)
(Canis familiaris)
Mammalia SCG2 34 33
  • 89.99 (n)
(Bos Taurus)
Mammalia SCG2 34 33
  • 89.69 (n)
(Mus musculus)
Mammalia Scg2 16 34 33
  • 83.2 (n)
(Rattus norvegicus)
Mammalia Scg2 33
  • 82.01 (n)
(Monodelphis domestica)
Mammalia SCG2 34
  • 71 (a)
(Ornithorhynchus anatinus)
Mammalia SCG2 34
  • 66 (a)
(Gallus gallus)
Aves SCG2 34 33
  • 67.1 (n)
(Anolis carolinensis)
Reptilia SCG2 34
  • 59 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia scg2 33
  • 59.52 (n)
African clawed frog
(Xenopus laevis)
Amphibia LOC397939 33
(Danio rerio)
Actinopterygii scg2b 34 33
  • 46.75 (n)
scg2a 34
  • 24 (a)
Species where no ortholog for SCG2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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

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

Paralogs for SCG2 Gene

No data available for Paralogs for SCG2 Gene

Variants for SCG2 Gene

Sequence variations from dbSNP and Humsavar for SCG2 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000064865 -- 223,603,204(-) A/T upstream_transcript_variant
rs1000188768 -- 223,600,246(-) G/T intron_variant
rs1000998095 -- 223,601,899(-) A/G intron_variant
rs1001743708 -- 223,599,891(-) C/G intron_variant
rs1002207653 -- 223,597,802(-) T/C coding_sequence_variant, missense_variant

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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for SCG2 Gene

MalaCards: The human disease database

(6) MalaCards diseases for SCG2 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
intracranial primitive neuroectodermal tumor
  • intracranial pnet
lymph node cancer
  • lymph node neoplasm
collagenous colitis
  • microscopic colitis, collagenous type
neuroendocrine tumor
  • neuroendocrine neoplasm
  • pheochromocytoma, susceptibility to
- 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

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. 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 44 58
  2. Chromogranin peptides in amyotrophic lateral sclerosis. (PMID: 18721831) Schrott-Fischer A … Marksteiner J (Regulatory peptides 2009) 3 22 58
  3. Secretogranin II: a key AP-1-regulated protein that mediates neuronal differentiation and protection from nitric oxide-induced apoptosis of neuroblastoma cells. (PMID: 18239671) Li L … Porter AG (Cell death and differentiation 2008) 3 22 58
  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 22 58
  5. An ancestral variant of Secretogranin II confers regulation by PHOX2 transcription factors and association with hypertension. (PMID: 17584765) Wen G … Hamilton BA (Human molecular genetics 2007) 3 22 58

Products for SCG2 Gene

Sources for SCG2 Gene

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