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GeneBe

SCG2

secretogranin II, the group of Granins

Basic information

Region (hg38): 2:223596939-223602361

Links

ENSG00000171951NCBI:7857OMIM:118930HGNC:10575Uniprot:P13521AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCG2 gene.

  • Inborn genetic diseases (20 variants)
  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCG2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
1
clinvar
1
missense
20
clinvar
20
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 20 0 1

Variants in SCG2

This is a list of pathogenic ClinVar variants found in the SCG2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
2-223597489-G-A Benign (Apr 10, 2018)783210
2-223597553-T-C not specified Uncertain significance (Jan 09, 2024)3158393
2-223597613-T-A not specified Uncertain significance (Feb 11, 2022)2366049
2-223597644-T-C not specified Uncertain significance (Nov 21, 2023)3158392
2-223597769-C-A not specified Uncertain significance (Oct 26, 2021)2257219
2-223597788-C-T not specified Uncertain significance (Sep 20, 2023)3158391
2-223597813-T-A not specified Uncertain significance (Nov 10, 2022)2384241
2-223597892-G-A not specified Uncertain significance (Aug 17, 2021)2375435
2-223598001-G-T not specified Uncertain significance (Mar 21, 2023)2527598
2-223598034-T-C not specified Uncertain significance (Jul 12, 2022)2300717
2-223598063-T-C not specified Uncertain significance (Jul 12, 2023)2610941
2-223598104-G-C not specified Uncertain significance (Jan 31, 2024)3158390
2-223598136-G-A not specified Uncertain significance (Jan 29, 2024)3158389
2-223598171-G-A not specified Uncertain significance (Oct 25, 2022)2223160
2-223598185-A-C not specified Uncertain significance (Dec 28, 2023)3158388
2-223598229-T-C not specified Uncertain significance (Nov 28, 2023)3158387
2-223598336-C-G not specified Uncertain significance (Jul 26, 2021)2355659
2-223598349-C-A not specified Uncertain significance (Feb 12, 2024)3158395
2-223598351-A-T not specified Uncertain significance (Aug 04, 2023)2596822
2-223598473-C-A not specified Uncertain significance (Jun 27, 2022)2367153
2-223598492-T-C not specified Uncertain significance (Apr 28, 2023)2524340
2-223598577-C-T not specified Uncertain significance (Dec 20, 2021)2268264
2-223598626-C-A not specified Uncertain significance (Jun 22, 2021)2384133
2-223598816-C-A not specified Uncertain significance (Nov 21, 2023)3158394
2-223598876-G-A not specified Uncertain significance (Jul 14, 2023)2611775

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCG2protein_codingprotein_codingENST00000305409 15564
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00002120.9781257230241257470.0000954
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.07513203161.010.00001624123
Missense in Polyphen8798.8810.879851370
Synonymous-0.5291261191.060.000006361112
Loss of Function2.071121.30.5160.00000110279

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004760.000475
Ashkenazi Jewish0.0001980.000198
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00005290.0000527
Middle Eastern0.00005440.0000544
South Asian0.00003270.0000327
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Secretogranin-2 is a neuroendocrine secretory granule protein, which is the precursor for biologically active peptides.;
Pathway
Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

pRec
0.423

Intolerance Scores

loftool
0.349
rvis_EVS
-0.67
rvis_percentile_EVS
15.76

Haploinsufficiency Scores

pHI
0.839
hipred
Y
hipred_score
0.553
ghis
0.549

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.449

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Scg2
Phenotype
cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);

Gene ontology

Biological process
MAPK cascade;angiogenesis;negative regulation of endothelial cell proliferation;positive regulation of endothelial cell proliferation;inflammatory response;protein secretion;regulation of signaling receptor activity;intracellular signal transduction;endothelial cell migration;post-translational protein modification;cellular protein metabolic process;eosinophil chemotaxis;positive chemotaxis;induction of positive chemotaxis;negative regulation of endothelial cell apoptotic process;negative regulation of extrinsic apoptotic signaling pathway
Cellular component
extracellular space;endoplasmic reticulum lumen;secretory granule;neuronal dense core vesicle
Molecular function
cytokine activity;protein binding;chemoattractant activity