SCTR

protein-coding

secretin receptor, the group of Glucagon receptor family

Gene summary

The protein encoded by this gene is a G protein-coupled receptor and belongs to the glucagon-VIP-secretin receptor family. It binds secretin which is the most potent regulator of pancreatic bicarbonate, electrolyte and volume secretion. Secretin and its receptor are suggested to be involved in pancreatic cancer and autism. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002980.3

Inheritance

—

ClinVar variants

U:71B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr2:119,439,843-119,525,301

External References & Databases

Ensembl (ENSG00000080293)

Transcript & Mutation Effects

hg38 • Region Span ~85.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCTR variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 72

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002980.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	4 clinvar	5
missense			70 clinvar	5 clinvar	1 clinvar	76
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	71	6	5	82

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002980.3	RefSeq	NP_002971.2	13	MANE Select
ENST00000019103.8	Ensembl	ENSP00000019103.6	13	MANE Select
ENST00000627145.1	Ensembl	ENSP00000486987.1	8	Standard
ENST00000630739.2	Ensembl	ENSP00000486930.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

cell surface receptor signaling pathway
G protein-coupled receptor signaling pathway
brain development

Molecular Function

G protein-coupled peptide receptor activity
secretin receptor activity
peptide hormone binding

Cellular Component

cytoplasmic microtubule
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000019103
Coding exons: 13
Length: 84652
Individuals with no LoFs: 125613
Homozygous LoFs: 2
Heterozygous LoFs: 133
Defined: 125748
p: 0.000537

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0243	249	248	1.00	0.0000139	2852
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00095	0.00084	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00075	0.00071	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00064	0.00062	rare
South Asian	0.00049	0.00046	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: This is a receptor for secretin. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase.;

Recessive Scores

pRec: 0.177

Intolerance Scores

LoFtool: 0.864
RVIS EVS: 0.55
RVIS percentile EVS: 81.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.659

Gene Damage Prediction

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