SCG5

secretogranin V, the group of Granins

Basic information

Region (hg38): 15:32641676-32697098

Previous symbols: [ "SGNE1" ]

Links

ENSG00000166922 ∙ NCBI:6447 ∙ OMIM:173120 ∙ HGNC:10816 ∙ Uniprot:P05408 ∙ 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 SCG5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCG5 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				5		5
missense			2			2
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				9	16	25
Total	0	0	3	14	16

Variants in SCG5

This is a list of pathogenic ClinVar variants found in the SCG5 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-32641718-C-G			Likely benign (Jun 15, 2019)
15-32641718-C-T			Likely benign (Aug 19, 2019)
15-32641754-A-T			Benign (Jul 14, 2018)
15-32641892-G-A			Benign (Jul 06, 2018)
15-32643526-T-C			Benign (Jul 20, 2018)
15-32643603-G-A		not specified	Uncertain significance (Dec 07, 2021)
15-32643664-A-G			Likely benign (Sep 01, 2023)
15-32643947-T-C			Benign (Jul 14, 2018)
15-32643993-A-G			Likely benign (Jun 22, 2019)
15-32679557-G-A			Benign (Jul 06, 2018)
15-32679727-G-T			Likely benign (Apr 01, 2020)
15-32679733-C-T			Benign (Jul 06, 2018)
15-32679762-G-A			Likely benign (Oct 28, 2020)
15-32679821-C-T			Likely benign (Apr 01, 2023)
15-32680053-G-A			Benign (Jul 06, 2018)
15-32684591-T-C			Likely benign (May 01, 2022)
15-32684639-G-A			Likely benign (Sep 24, 2020)
15-32684662-G-T		not specified	Uncertain significance (Jan 24, 2023)
15-32684900-A-G			Benign (Jul 06, 2018)
15-32691524-G-A			Likely benign (Jul 15, 2018)
15-32691727-C-T			Likely benign (Jun 01, 2023)
15-32691752-C-T		Hereditary mixed polyposis syndrome	Uncertain significance (Aug 01, 2023)
15-32691771-G-A			Likely benign (Jul 01, 2024)
15-32691995-A-G			Benign (Jul 06, 2018)
15-32692014-C-T			Likely benign (Jul 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCG5	protein_coding	protein_coding	ENST00000300175	5	55423

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000629	0.731	124599	0	40	124639	0.000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.613	97	116	0.839	0.00000590	1385
Missense in Polyphen		35	52.2	0.6705		627
Synonymous	-0.471	45	41.2	1.09	0.00000194	413
Loss of Function	1.02	8	11.8	0.678	7.44e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000347	0.000346
Ashkenazi Jewish	0.000795	0.000795
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000159
Middle Eastern	0.000111	0.000111
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a molecular chaperone for PCSK2/PC2, preventing its premature activation in the regulated secretory pathway. Binds to inactive PCSK2 in the endoplasmic reticulum and facilitates its transport from there to later compartments of the secretory pathway where it is proteolytically matured and activated. Also required for cleavage of PCSK2 but does not appear to be involved in its folding. Plays a role in regulating pituitary hormone secretion. The C-terminal peptide inhibits PCSK2 in vitro. {ECO:0000269|PubMed:7913882}.

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.488
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.0827
• hipred: N
• hipred_score: 0.350
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.603

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scg5
• Phenotype: respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: scg5
• Affected structure: ventricular system
• Phenotype tag: abnormal
• Phenotype quality: hydrocephalic

Gene ontology

• Biological process: intracellular protein transport;neuropeptide signaling pathway;peptide hormone processing;negative regulation of catalytic activity;regulation of hormone secretion
• Cellular component: extracellular region;secretory granule
• Molecular function: enzyme inhibitor activity;protein binding;GTP binding;unfolded protein binding