SCTR

secretin receptor, the group of Glucagon receptor family

Basic information

Region (hg38): 2:119439843-119525301

Links

ENSG00000080293 ∙ NCBI:6344 ∙ OMIM:182098 ∙ HGNC:10608 ∙ Uniprot:P47872 ∙ 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 SCTR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCTR 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					3	3
missense			28	3	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	28	3	5

Variants in SCTR

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

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

Position	Type	Phenotype	Significance	ClinVar
2-119440195-G-A			Benign (Aug 11, 2017)
2-119440214-C-T		not specified	Uncertain significance (Oct 12, 2021)
2-119441584-C-T		not specified	Uncertain significance (Mar 08, 2024)
2-119446811-T-C		not specified	Uncertain significance (Feb 23, 2023)
2-119446866-G-C		not specified	Uncertain significance (Sep 06, 2022)
2-119448731-A-C		not specified	Uncertain significance (Nov 06, 2023)
2-119452035-C-T		not specified	Uncertain significance (Nov 30, 2022)
2-119452050-A-C		not specified	Uncertain significance (Oct 14, 2021)
2-119452051-T-C		not specified	Uncertain significance (Oct 10, 2023)
2-119452057-C-T			Likely benign (Jun 25, 2018)
2-119453277-G-A			Benign (Aug 15, 2017)
2-119461867-C-T		not specified	Uncertain significance (Nov 09, 2021)
2-119461901-T-C		not specified	Uncertain significance (Sep 07, 2022)
2-119461945-G-A		not specified	Uncertain significance (May 20, 2024)
2-119461945-G-C		not specified	Uncertain significance (Feb 14, 2023)
2-119461980-C-A		not specified	Uncertain significance (Jun 18, 2024)
2-119461980-C-G		not specified	Uncertain significance (Jan 23, 2024)
2-119461998-C-T			Benign (Aug 11, 2017)
2-119464128-G-A		not specified	Uncertain significance (Oct 29, 2021)
2-119464134-C-T		not specified	Uncertain significance (Jun 03, 2024)
2-119464135-G-A			Benign (Jun 25, 2018)
2-119464137-A-G		not specified	Uncertain significance (May 17, 2023)
2-119464154-G-A		not specified	Uncertain significance (May 31, 2023)
2-119464191-G-A			Benign (Jun 25, 2018)
2-119464247-T-A		not specified	Uncertain significance (May 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCTR	protein_coding	protein_coding	ENST00000019103	13	84652

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.43e-12	0.241	125613	2	133	125748	0.000537

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0243	249	248	1.00	0.0000139	2852
Missense in Polyphen		83	90.152	0.92066		1105
Synonymous	0.232	97	100	0.970	0.00000584	855
Loss of Function	0.981	21	26.4	0.794	0.00000130	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00113
Ashkenazi Jewish	0.00	0.00
East Asian	0.000752	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.000637	0.000624
Middle Eastern	0.000752	0.000707
South Asian	0.000491	0.000457
Other	0.000818	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This is a receptor for secretin. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase.
• Pathway: Bile secretion - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);GPCRs, Class B Secretin-like;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Glucagon-type ligand receptors;Class B/2 (Secretin family receptors);GPCR ligand binding;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.177

Intolerance Scores

• loftool: 0.864
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.6

Haploinsufficiency Scores

• pHI: 0.0729
• hipred: N
• hipred_score: 0.296

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.659

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sctr
• Phenotype: immune system phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); renal/urinary system phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;brain development
• Cellular component: cytoplasmic microtubule;plasma membrane;integral component of membrane
• Molecular function: G protein-coupled peptide receptor activity;secretin receptor activity;peptide hormone binding