NTSR2

neurotensin receptor 2, the group of Neurotensin receptors

Basic information

Region (hg38): 2:11658178-11670195

Links

ENSG00000169006 ∙ NCBI:23620 ∙ OMIM:605538 ∙ HGNC:8040 ∙ Uniprot:O95665 ∙ 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 NTSR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTSR2 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			20	3	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	6	1

Variants in NTSR2

This is a list of pathogenic ClinVar variants found in the NTSR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-11658496-G-T		not specified	Uncertain significance (May 21, 2024)
2-11658548-C-T			Likely benign (Jul 01, 2022)
2-11658558-C-T		not specified	Uncertain significance (Dec 14, 2021)
2-11658559-G-A		not specified	Uncertain significance (Feb 23, 2023)
2-11658595-C-T		not specified	Uncertain significance (Jun 04, 2024)
2-11658596-G-A		not specified	Likely benign (Sep 19, 2023)
2-11658640-A-G		not specified	Uncertain significance (Sep 25, 2023)
2-11660052-G-A		not specified	Uncertain significance (Dec 02, 2022)
2-11660056-C-T		not specified	Uncertain significance (Mar 29, 2022)
2-11660119-T-C		not specified	Likely benign (Jun 10, 2022)
2-11660125-C-T		not specified	Uncertain significance (Jun 27, 2023)
2-11661984-C-T		not specified	Likely benign (Sep 14, 2022)
2-11662005-C-T		not specified	Uncertain significance (Jan 08, 2024)
2-11662020-C-T			Benign (Apr 04, 2018)
2-11662108-G-T			Likely benign (Apr 04, 2018)
2-11662128-G-A		not specified	Likely benign (Apr 22, 2024)
2-11662213-G-A		not specified	Uncertain significance (Mar 11, 2024)
2-11669541-G-C		not specified	Uncertain significance (Jan 24, 2023)
2-11669609-A-G		not specified	Uncertain significance (Jul 20, 2021)
2-11669673-G-A		not specified	Uncertain significance (Sep 22, 2023)
2-11669690-A-G		not specified	Uncertain significance (Jun 26, 2023)
2-11669815-G-C		not specified	Uncertain significance (Mar 02, 2023)
2-11669837-T-C		not specified	Uncertain significance (May 24, 2023)
2-11669842-C-A		not specified	Uncertain significance (Jun 13, 2022)
2-11669938-G-T			Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTSR2	protein_coding	protein_coding	ENST00000306928	4	11987

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00487	0.892	125692	1	44	125737	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.635	203	230	0.882	0.0000144	2550
Missense in Polyphen		47	63.07	0.74521		813
Synonymous	0.616	103	111	0.926	0.00000751	916
Loss of Function	1.39	5	9.66	0.517	4.87e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00116	0.00116
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000594	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000594	0.0000544
South Asian	0.000229	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for the tridecapeptide neurotensin. It is associated with G proteins that activate a phosphatidylinositol- calcium second messenger system.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);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: 0.111

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.324
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.287

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ntsr2
• 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); 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)

Gene ontology

• Biological process: cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;phospholipase C-activating G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;sensory perception;regulation of membrane potential
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;G protein-coupled neurotensin receptor activity