NTSR1

protein-coding

neurotensin receptor 1, the group of Neurotensin receptors

Gene summary

Neurotensin receptor 1 belongs to the large superfamily of G-protein coupled receptors. NTSR1 mediates the multiple functions of neurotensin, such as hypotension, hyperglycemia, hypothermia, antinociception, and regulation of intestinal motility and secretion. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002531.3

Inheritance

—

ClinVar variants

U:78B:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr20:62,708,836-62,762,771

External References & Databases

Ensembl (ENSG00000101188)

Transcript & Mutation Effects

hg38 • Region Span ~53.9 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 NTSR1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002531.3. 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	5 clinvar	3 clinvar	9
missense			76 clinvar	2 clinvar	6 clinvar	84
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	78	7	9	94

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002531.3	RefSeq	NP_002522.2	4	MANE Select
ENST00000370501.4	Ensembl	ENSP00000359532.3	4	MANE Select
ENST00001005831.1	Ensembl	ENSP00000675648.1	4	Standard
ENST00001132939.1	Ensembl	ENSP00000809737.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Calcium signaling pathway - Homo sapiens (human)
Neuroactive ligand-receptor interaction - Homo sapiens (human)
GPCRs, Other
Peptide GPCRs
GPCRs, Class A Rhodopsin-like

Biological Process

temperature homeostasis
negative regulation of systemic arterial blood pressure
regulation of membrane depolarization
G protein-coupled receptor signaling pathway
neuropeptide signaling pathway

Molecular Function

G protein-coupled receptor activity
protein binding
G protein-coupled neurotensin receptor activity
identical protein binding
protein homodimerization activity

Cellular Component

mitochondrion
endoplasmic reticulum
Golgi apparatus
plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370501
Coding exons: 4
Length: 53935
Individuals with no LoFs: 125667
Homozygous LoFs: 0
Heterozygous LoFs: 81
Defined: 125748
p: 0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.416	310	290	1.07	0.0000197	2668
Missense (PolyPhen)		128	105.59	1.2122		1059
Synonymous	0.663	132	142	0.929	0.0000108	901
Loss of Function	0.494	13	15.1	0.863	9.24e-7	133

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00012	rare
Latino/Admixed American	0.00042	0.00040	rare
Ashkenazi Jewish	0.0020	0.0020	notable
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00031	0.00030	rare
South Asian	0.000098	0.000098	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: G-protein coupled receptor for the tridecapeptide neurotensin (NTS) (PubMed:8381365, PubMed:21725197, PubMed:23140271). Signaling is effected via G proteins that activate a phosphatidylinositol-calcium second messenger system. Signaling leads to the activation of downstream MAP kinases and protects cells against apoptosis (PubMed:21725197). {ECO:0000269|PubMed:21725197, ECO:0000269|PubMed:23140271, ECO:0000269|PubMed:8381365}.;

Recessive Scores

pRec: 0.311

Intolerance Scores

LoFtool: 0.887
RVIS EVS: 0.67
RVIS percentile EVS: 84.7

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.927

Gene Damage Prediction

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