NTSR1

neurotensin receptor 1, the group of Neurotensin receptors

Basic information

Region (hg38): 20:62708836-62762771

Links

ENSG00000101188 ∙ NCBI:4923 ∙ OMIM:162651 ∙ HGNC:8039 ∙ Uniprot:P30989 ∙ 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 NTSR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTSR1 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				4	3	7
missense			23		6	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	23	4	9

Variants in NTSR1

This is a list of pathogenic ClinVar variants found in the NTSR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-62709232-G-A		not specified	Uncertain significance (Sep 17, 2021)
20-62709239-C-G		not specified	Uncertain significance (Jul 19, 2023)
20-62709272-C-T		not specified	Uncertain significance (May 09, 2023)
20-62709287-A-G		not specified	Uncertain significance (Sep 22, 2023)
20-62709323-C-T		not specified	Uncertain significance (May 13, 2024)
20-62709324-G-A			Benign (Jun 11, 2018)
20-62709342-C-T			Benign (Apr 26, 2018)
20-62709368-T-C		not specified	Uncertain significance (Oct 05, 2022)
20-62709380-C-T			Benign (Apr 07, 2018)
20-62709422-C-T			Benign (Mar 29, 2018)
20-62709446-G-A		not specified	Uncertain significance (Mar 23, 2022)
20-62709502-A-G		not specified	Uncertain significance (Mar 21, 2023)
20-62709539-C-T		not specified	Uncertain significance (Dec 19, 2022)
20-62709549-C-T			Likely benign (Jul 02, 2018)
20-62709563-C-T		not specified	Uncertain significance (Jun 22, 2024)
20-62709671-C-T		not specified	Uncertain significance (Jun 06, 2023)
20-62709758-G-T		not specified	Uncertain significance (Dec 01, 2022)
20-62709851-A-G		not specified	Uncertain significance (Jan 26, 2022)
20-62709908-A-C		not specified	Uncertain significance (Aug 02, 2021)
20-62709910-G-A		not specified	Uncertain significance (Sep 29, 2023)
20-62754748-G-A		not specified	Uncertain significance (Aug 13, 2021)
20-62754795-A-C			Benign (Jun 10, 2018)
20-62754814-G-A		not specified	Uncertain significance (Aug 12, 2021)
20-62754852-G-T		not specified	Uncertain significance (Sep 22, 2023)
20-62754865-C-T		not specified	Uncertain significance (Jun 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTSR1	protein_coding	protein_coding	ENST00000370501	4	53935

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.93e-8	0.251	125667	0	81	125748	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.416	310	290	1.07	0.0000197	2668
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000552	0.000540
Ashkenazi Jewish	0.00201	0.00199
East Asian	0.000224	0.000217
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000306	0.000299
Middle Eastern	0.000224	0.000217
South Asian	0.0000981	0.0000980
Other	0.000495	0.000489

dbNSFP

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}.
• Pathway: Calcium signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);GPCRs, Other;Peptide GPCRs;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.311

Intolerance Scores

• loftool: 0.887
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.7

Haploinsufficiency Scores

• pHI: 0.177
• hipred: N
• hipred_score: 0.239
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.927

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ntsr1
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region 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); digestive/alimentary phenotype; normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: temperature homeostasis;negative regulation of systemic arterial blood pressure;regulation of membrane depolarization;G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;chemical synaptic transmission;learning;adult locomotory behavior;positive regulation of glutamate secretion;positive regulation of gamma-aminobutyric acid secretion;response to lipid;positive regulation of apoptotic process;negative regulation of apoptotic process;regulation of respiratory gaseous exchange;detection of temperature stimulus involved in sensory perception of pain;negative regulation of release of sequestered calcium ion into cytosol;positive regulation of release of sequestered calcium ion into cytosol;regulation of sensory perception of pain;positive regulation of inositol phosphate biosynthetic process;D-aspartate import across plasma membrane;inositol phosphate catabolic process;positive regulation of arachidonic acid secretion;positive regulation of inhibitory postsynaptic potential;L-glutamate import across plasma membrane;regulation of action potential;positive regulation of cation channel activity
• Cellular component: mitochondrion;endoplasmic reticulum;Golgi apparatus;plasma membrane;integral component of plasma membrane;cytoplasmic side of plasma membrane;cell surface;symmetric synapse;terminal bouton;dendritic spine;dendritic shaft;perikaryon;membrane raft
• Molecular function: G protein-coupled receptor activity;protein binding;G protein-coupled neurotensin receptor activity;identical protein binding;protein homodimerization activity;protein heterodimerization activity;protein N-terminus binding