SCGN

secretagogin, EF-hand calcium binding protein, the group of EF-hand domain containing

Basic information

Region (hg38): 6:25652200-25701783

Links

ENSG00000079689 ∙ NCBI:10590 ∙ OMIM:609202 ∙ HGNC:16941 ∙ Uniprot:O76038 ∙ 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 SCGN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCGN 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	17	2	1

Variants in SCGN

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

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

Position	Type	Phenotype	Significance	ClinVar
6-25652411-G-A		not specified	Uncertain significance (Dec 26, 2023)
6-25652453-T-G		not specified	Uncertain significance (Mar 04, 2024)
6-25653380-AG-A		SCGN-related disorder	Benign (Jun 05, 2020)
6-25653388-G-A		not specified	Uncertain significance (Mar 20, 2023)
6-25653394-T-C		not specified	Uncertain significance (Dec 17, 2023)
6-25653402-A-G		not specified	Uncertain significance (Apr 25, 2022)
6-25661589-A-G		not specified	Uncertain significance (Sep 16, 2021)
6-25661630-A-T		not specified	Uncertain significance (Apr 07, 2022)
6-25665018-G-A		not specified	Uncertain significance (Oct 29, 2021)
6-25669518-G-T		not specified	Uncertain significance (Dec 09, 2023)
6-25669555-T-C			Likely benign (Jan 01, 2024)
6-25670035-G-A		not specified	Uncertain significance (Nov 18, 2022)
6-25670042-C-T		not specified	Uncertain significance (Mar 27, 2023)
6-25670054-T-A		SCGN-related disorder	Likely benign (Jul 30, 2023)
6-25681981-C-T		not specified	Uncertain significance (Jan 26, 2022)
6-25681993-A-G		not specified	Uncertain significance (Dec 20, 2023)
6-25701213-A-G		not specified	Uncertain significance (Feb 28, 2024)
6-25701262-G-A		not specified	Uncertain significance (May 03, 2023)
6-25701267-G-T		not specified	Uncertain significance (Dec 12, 2023)
6-25701327-A-G		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCGN	protein_coding	protein_coding	ENST00000377961	11	49548

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.34e-11	0.0722	125201	6	541	125748	0.00218

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.349	148	160	0.923	0.00000869	1865
Missense in Polyphen		40	47.135	0.84863		606
Synonymous	1.26	43	54.9	0.784	0.00000306	469
Loss of Function	0.237	17	18.1	0.940	9.53e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0278	0.0277
Ashkenazi Jewish	0.00149	0.00149
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000336	0.000334
Middle Eastern	0.000109	0.000109
South Asian	0.000233	0.000229
Other	0.00164	0.00163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.527
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.0671
• hipred: Y
• hipred_score: 0.544
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.758

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scgn

Zebrafish Information Network

• Gene name: scgn
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: biological_process;regulation of cytosolic calcium ion concentration;regulation of presynaptic cytosolic calcium ion concentration;regulation of long-term synaptic potentiation
• Cellular component: extracellular region;nucleus;cytoplasm;cytosol;dendrite;transport vesicle membrane;neuron projection;synapse;presynapse
• Molecular function: calcium ion binding