TACR1

protein-coding

tachykinin receptor 1, the group of Tachykinin receptors

Gene summary

This gene belongs to a gene family of tachykinin receptors. These tachykinin receptors are characterized by interactions with G proteins and contain seven hydrophobic transmembrane regions. This gene encodes the receptor for the tachykinin substance P, also referred to as neurokinin 1. The encoded protein is also involved in the mediation of phosphatidylinositol metabolism of substance P. [provided by RefSeq, Sep 2008]

Previous symbols:

TAC1R

MANE transcript

NM_001058.4

Inheritance

—

ClinVar variants

U:52B:7

Top phenotype

TACR1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr2:75,046,463-75,199,520

External References & Databases

Ensembl (ENSG00000115353)

Transcript & Mutation Effects

hg38 • Region Span ~153.1 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 TACR1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 52

TACR1-related disorderTotal: 5

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001058.4. 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				3 clinvar	1 clinvar	4
missense			52 clinvar	3 clinvar		55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	6	1	59

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001058.4	RefSeq	NP_001049.1	5	MANE Select
ENST00000305249.10	Ensembl	ENSP00000303522.4	5	MANE Select
NM_015727.3	RefSeq	NP_056542.1	4	Standard
ENST00000409848.3	Ensembl	ENSP00000386448.3	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Calcium signaling pathway - Homo sapiens (human)
Measles - Homo sapiens (human)
Neuroactive ligand-receptor interaction - Homo sapiens (human)
Peptide GPCRs
Spinal Cord Injury

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

Molecular Function

tachykinin receptor activity
protein binding
substance P receptor activity

Cellular Component

plasma membrane
integral component of plasma membrane
sperm flagellum
sperm head
sperm midpiece

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000305249
Coding exons: 5
Length: 153237
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125748
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.569	217	242	0.897	0.0000140	2678
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.00020	0.00020	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.219

Intolerance Scores

LoFtool: 0.834
RVIS EVS: -0.76
RVIS percentile EVS: 13.33

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.610

Gene Damage Prediction

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