NTS

neurotensin, the group of Neuropeptides

Basic information

Region (hg38): 12:85874295-85882992

Links

ENSG00000133636 ∙ NCBI:4922 ∙ OMIM:162650 ∙ HGNC:8038 ∙ Uniprot:P30990 ∙ 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 NTS gene.

Variants pathogenicity by type

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

Variants in NTS

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

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

Position	Type	Phenotype	Significance	ClinVar
12-85874436-C-G		not specified	Uncertain significance (Jan 21, 2025)
12-85874437-A-C		not specified	Uncertain significance (Aug 02, 2023)
12-85874446-C-G		not specified	Uncertain significance (Sep 25, 2023)
12-85878394-G-A		Breast ductal adenocarcinoma	Uncertain significance (Jul 20, 2015)
12-85878508-C-T		not specified	Uncertain significance (May 26, 2022)
12-85878555-T-C		not specified	Uncertain significance (Aug 02, 2024)
12-85882274-G-C		not specified	Uncertain significance (May 18, 2023)
12-85882290-A-C		not specified	Uncertain significance (Jul 02, 2024)
12-85882331-C-T		not specified	Uncertain significance (Aug 13, 2021)
12-85882366-C-T			Benign (Jun 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTS	protein_coding	protein_coding	ENST00000256010	4	8698

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000385	0.396	125690	0	46	125736	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.234	91	84.9	1.07	0.00000377	1131
Missense in Polyphen		31	29.772	1.0412		407
Synonymous	0.173	27	28.2	0.959	0.00000121	294
Loss of Function	0.239	7	7.72	0.907	3.23e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.0000560	0.0000544
Finnish	0.000233	0.000231
European (Non-Finnish)	0.000260	0.000255
Middle Eastern	0.0000560	0.0000544
South Asian	0.000239	0.000229
Other	0.000501	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Neurotensin may play an endocrine or paracrine role in the regulation of fat metabolism. It causes contraction of smooth muscle.
• Pathway: 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;AP-1 transcription factor network (Consensus)

Recessive Scores

• pRec: 0.361

Intolerance Scores

• loftool: 0.534
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.690
• hipred: N
• hipred_score: 0.187
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nts
• 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); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: signal transduction;G protein-coupled receptor signaling pathway;regulation of signaling receptor activity;regulation of blood vessel size
• Cellular component: extracellular region;transport vesicle;axon terminus
• Molecular function: neuropeptide hormone activity;protein binding