SCT

secretin, the group of Neuropeptides

Basic information

Region (hg38): 11:626308-627181

Links

ENSG00000070031 ∙ NCBI:6343 ∙ OMIM:182099 ∙ HGNC:10607 ∙ Uniprot:P09683 ∙ 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 SCT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCT 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	0

Variants in SCT

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

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

Position	Type	Phenotype	Significance	ClinVar
11-626517-C-T		not specified	Likely benign (Oct 27, 2022)
11-626520-C-T		not specified	Uncertain significance (Nov 17, 2022)
11-626736-A-C		not specified	Uncertain significance (Oct 27, 2022)
11-626788-C-T		not specified	Uncertain significance (Sep 17, 2021)
11-626931-C-T		not specified	Uncertain significance (Oct 06, 2021)
11-626933-C-T		not specified	Uncertain significance (Oct 03, 2022)
11-626938-C-T			Likely benign (Nov 13, 2017)
11-626939-C-G		not specified	Uncertain significance (Dec 28, 2023)
11-626946-G-A		not specified	Uncertain significance (May 01, 2022)
11-627131-G-A		not specified	Uncertain significance (Jun 28, 2023)
11-627134-G-A		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCT	protein_coding	protein_coding	ENST00000176195	4	713

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.44e-7	0.0343	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.203	62	57.7	1.08	0.00000323	729
Missense in Polyphen		13	5.6104	2.3171		60
Synonymous	-1.40	34	25.1	1.36	0.00000148	285
Loss of Function	-2.05	8	3.72	2.15	1.59e-7	48

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stimulates formation of NaHCO(3)-rich pancreatic juice and secretion of NaHCO(3)-rich bile and inhibits HCl production by the stomach.
• Pathway: Gastric acid production;Signaling by GPCR;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;G alpha (s) signalling events;Glucagon-type ligand receptors;Class B/2 (Secretin family receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;GPCR signaling-G alpha i;GPCR downstream signalling (Consensus)

Haploinsufficiency Scores

• pHI: 0.0740
• hipred: N
• hipred_score: 0.180
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.560

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sct
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;brain development;regulation of signaling receptor activity;pancreatic juice secretion;positive regulation of cAMP-mediated signaling;embryonic digestive tract development;positive regulation of pancreatic juice secretion;positive regulation of somatostatin secretion;negative regulation of gastrin-induced gastric acid secretion
• Cellular component: cellular_component;extracellular region;extracellular space
• Molecular function: G protein-coupled receptor binding;signaling receptor binding;hormone activity;protein N-terminus binding