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GeneBe

SCT

secretin, the group of Neuropeptides

Basic information

Region (hg38): 11:626308-627181

Links

ENSG00000070031NCBI:6343OMIM:182099HGNC:10607Uniprot:P09683AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (9 variants)
  • not provided (1 variants)

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
clinvar
1
missense
8
clinvar
1
clinvar
9
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 8 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 Inborn genetic diseases Likely benign (Oct 27, 2022)2361956
11-626520-C-T Inborn genetic diseases Uncertain significance (Nov 17, 2022)2326754
11-626736-A-C Inborn genetic diseases Uncertain significance (Oct 27, 2022)2321166
11-626788-C-T Inborn genetic diseases Uncertain significance (Sep 17, 2021)2412089
11-626931-C-T Inborn genetic diseases Uncertain significance (Oct 06, 2021)2219532
11-626933-C-T Inborn genetic diseases Uncertain significance (Oct 03, 2022)2363551
11-626938-C-T Likely benign (Nov 13, 2017)721157
11-626946-G-A Inborn genetic diseases Uncertain significance (May 01, 2022)2391399
11-627131-G-A Inborn genetic diseases Uncertain significance (Jun 28, 2023)2596698
11-627134-G-A Inborn genetic diseases Uncertain significance (Dec 28, 2022)2361274

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCTprotein_codingprotein_codingENST00000176195 4713
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.44e-70.034300000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2036257.71.080.00000323729
Missense in Polyphen135.61042.317160
Synonymous-1.403425.11.360.00000148285
Loss of Function-2.0583.722.151.59e-748

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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