TACR1

tachykinin receptor 1, the group of Tachykinin receptors

Basic information

Region (hg38): 2:75046462-75199520

Previous symbols: [ "TAC1R" ]

Links

ENSG00000115353 ∙ NCBI:6869 ∙ OMIM:162323 ∙ HGNC:11526 ∙ Uniprot:P25103 ∙ 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 TACR1 gene.

• Inborn genetic diseases (14 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TACR1 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in TACR1

This is a list of pathogenic ClinVar variants found in the TACR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-75049522-C-T		TACR1-related disorder	Benign (Jun 18, 2019)
2-75049551-G-T		not specified	Uncertain significance (Jul 25, 2023)
2-75049596-G-T		not specified	Uncertain significance (Sep 29, 2023)
2-75049599-G-A		not specified	Uncertain significance (Jan 23, 2023)
2-75049607-T-G		not specified	Uncertain significance (Aug 08, 2023)
2-75049637-C-T		not specified	Uncertain significance (Jun 02, 2023)
2-75049678-G-C		not specified	Uncertain significance (Jan 29, 2024)
2-75049723-C-A		not specified	Uncertain significance (Aug 30, 2022)
2-75051412-G-A		TACR1-related disorder	Likely benign (Apr 08, 2019)
2-75053621-A-G		not specified	Uncertain significance (Jul 15, 2021)
2-75053637-G-A		not specified	Uncertain significance (Apr 25, 2023)
2-75053736-C-G		not specified	Uncertain significance (Jan 03, 2024)
2-75120577-T-C		not specified	Uncertain significance (Dec 14, 2022)
2-75120594-C-T			Likely benign (Jul 06, 2018)
2-75120595-G-A		not specified	Uncertain significance (Jun 02, 2023)
2-75120618-G-C		not specified	Uncertain significance (Sep 27, 2021)
2-75120646-G-C		not specified	Uncertain significance (Dec 28, 2022)
2-75120707-T-G		not specified	Uncertain significance (Sep 27, 2022)
2-75198631-G-C		not specified	Uncertain significance (Aug 10, 2021)
2-75198817-T-C		not specified	Uncertain significance (Jul 25, 2023)
2-75198867-T-C		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TACR1	protein_coding	protein_coding	ENST00000305249	5	153237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000384	0.961	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.569	217	242	0.897	0.0000140	2678
Missense in Polyphen		68	89.936	0.7561		1035
Synonymous	0.107	99	100	0.986	0.00000648	820
Loss of Function	1.84	8	15.9	0.503	7.81e-7	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000326	0.000326
South Asian	0.000196	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This is a receptor for the tachykinin neuropeptide substance P. It is probably associated with G proteins that activate a phosphatidylinositol-calcium second messenger system. The rank order of affinity of this receptor to tachykinins is: substance P > substance K > neuromedin-K.
• Pathway: Calcium signaling pathway - Homo sapiens (human);Measles - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Peptide GPCRs;Spinal Cord Injury;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Signaling by GPCR;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Tachykinin receptors bind tachykinins;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.219

Intolerance Scores

• loftool: 0.834
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.33

Haploinsufficiency Scores

• pHI: 0.196
• hipred: N
• hipred_score: 0.490
• ghis: 0.637

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.610

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tacr1
• Phenotype: homeostasis/metabolism phenotype; 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); 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); immune system phenotype; skeleton phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: inflammatory response;G protein-coupled receptor signaling pathway;phospholipase C-activating G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;tachykinin receptor signaling pathway;detection of abiotic stimulus;response to pain;regulation of uterine smooth muscle contraction;positive regulation of flagellated sperm motility
• Cellular component: plasma membrane;integral component of plasma membrane;sperm flagellum;sperm head;sperm midpiece
• Molecular function: tachykinin receptor activity;protein binding;substance P receptor activity