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 ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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	1
missense			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	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)
2-223597553-T-C		not specified	Uncertain significance (Jan 09, 2024)
2-223597613-T-A		not specified	Uncertain significance (Feb 11, 2022)
2-223597644-T-C		not specified	Uncertain significance (Nov 21, 2023)
2-223597659-G-T		not specified	Uncertain significance (Jun 13, 2024)
2-223597769-C-A		not specified	Uncertain significance (Oct 26, 2021)
2-223597788-C-T		not specified	Uncertain significance (Sep 20, 2023)
2-223597813-T-A		not specified	Uncertain significance (Nov 10, 2022)
2-223597892-G-A		not specified	Uncertain significance (Aug 17, 2021)
2-223597952-C-T		not specified	Likely benign (Apr 20, 2024)
2-223598001-G-T		not specified	Uncertain significance (Mar 21, 2023)
2-223598034-T-C		not specified	Uncertain significance (Jul 12, 2022)
2-223598063-T-C		not specified	Uncertain significance (Jul 12, 2023)
2-223598104-G-C		not specified	Uncertain significance (Jan 31, 2024)
2-223598136-G-A		not specified	Uncertain significance (Jan 29, 2024)
2-223598171-G-A		not specified	Uncertain significance (Oct 25, 2022)
2-223598185-A-C		not specified	Uncertain significance (Dec 28, 2023)
2-223598229-T-C		not specified	Uncertain significance (Nov 28, 2023)
2-223598305-T-G		not specified	Uncertain significance (May 23, 2024)
2-223598336-C-G		not specified	Uncertain significance (Jul 26, 2021)
2-223598349-C-A		not specified	Uncertain significance (Feb 12, 2024)
2-223598351-A-T		not specified	Uncertain significance (Aug 04, 2023)
2-223598473-C-A		not specified	Uncertain significance (Jun 27, 2022)
2-223598492-T-C		not specified	Uncertain significance (Apr 28, 2023)
2-223598577-C-T		not specified	Uncertain significance (Dec 20, 2021)

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