SCG2

secretogranin II, the group of Granins

Basic information

Region (hg38): 2:223596939-223602361

Links

ENSG00000171951 ∙ NCBI:7857 ∙ OMIM:118930 ∙ HGNC:10575 ∙ Uniprot:P13521 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

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 (14 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant						0
non coding						0
Total	0	0	14	0	1

Variants in SCG2

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

Position	Type	Phenotype	Significance	ClinVar
2-223597489-G-A			Benign (Apr 10, 2018)
2-223597613-T-A		Inborn genetic diseases	Uncertain significance (Feb 11, 2022)
2-223597769-C-A		Inborn genetic diseases	Uncertain significance (Oct 26, 2021)
2-223597813-T-A		Inborn genetic diseases	Uncertain significance (Nov 10, 2022)
2-223597892-G-A		Inborn genetic diseases	Uncertain significance (Aug 17, 2021)
2-223598001-G-T		Inborn genetic diseases	Uncertain significance (Mar 21, 2023)
2-223598034-T-C		Inborn genetic diseases	Uncertain significance (Jul 12, 2022)
2-223598063-T-C		Inborn genetic diseases	Uncertain significance (Jul 12, 2023)
2-223598171-G-A		Inborn genetic diseases	Uncertain significance (Oct 25, 2022)
2-223598336-C-G		Inborn genetic diseases	Uncertain significance (Jul 26, 2021)
2-223598351-A-T		Inborn genetic diseases	Uncertain significance (Aug 04, 2023)
2-223598473-C-A		Inborn genetic diseases	Uncertain significance (Jun 27, 2022)
2-223598492-T-C		Inborn genetic diseases	Uncertain significance (Apr 28, 2023)
2-223598577-C-T		Inborn genetic diseases	Uncertain significance (Dec 20, 2021)
2-223598626-C-A		Inborn genetic diseases	Uncertain significance (Jun 22, 2021)
2-223598876-G-A		Inborn genetic diseases	Uncertain significance (Jul 14, 2023)
2-223598911-C-A		Inborn genetic diseases	Uncertain significance (Sep 06, 2022)
2-223598961-C-G		Inborn genetic diseases	Uncertain significance (Jan 26, 2023)
2-223599140-T-C		Inborn genetic diseases	Uncertain significance (Apr 08, 2022)
2-223599190-C-G		Inborn genetic diseases	Uncertain significance (Sep 27, 2022)
2-223599259-C-A		Inborn genetic diseases	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCG2	protein_coding	protein_coding	ENST00000305409	1	5564

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000212	0.978	125723	0	24	125747	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0751	320	316	1.01	0.0000162	4123
Missense in Polyphen		87	98.881	0.87985		1370
Synonymous	-0.529	126	119	1.06	0.00000636	1112
Loss of Function	2.07	11	21.3	0.516	0.00000110	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000476	0.000475
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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