GPR153

protein-coding

G protein-coupled receptor 153, the group of G protein-coupled receptors, Class A orphans

Gene summary

This gene encodes an integral membrane protein that belongs to the Class A rhodopsin superfamily of G protein coupled receptors. The encoded protein is expressed primarily in the central nervous system. A knockdown of the orthologous gene in rat is associated with a significant reduction in food intake and impaired decision making ability. Mutations in this gene are associated with schizophrenia, autism, and other neuropsychiatric disorders. The expression of this gene is activated by the glioma-associated oncogene homolog 1 transcription factor which, in turn, is activated by sonic hedgehog in normal and tumorigenic cells. [provided by RefSeq, Feb 2017]

MANE transcript

NM_207370.4

Inheritance

—

ClinVar variants

P:1U:132B:13

Top phenotype

Childhood-onset schizophrenia

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr1:6,247,353-6,261,098

External References & Databases

Ensembl (ENSG00000158292)

Transcript & Mutation Effects

hg38 • Region Span ~13.7 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 GPR153 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 133

not providedTotal: 5

Childhood-onset schizophreniaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207370.4. 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			2 clinvar	3 clinvar	1 clinvar	6
missense		1 clinvar	128 clinvar	7 clinvar	2 clinvar	138
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	132	10	3	146

Highest pathogenic variant AF is 0.000008675704

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207370.4	RefSeq	NP_997253.2	5	MANE Select
ENST00000377893.3	Ensembl	ENSP00000367125.2	5	MANE Select
ENST00000937749.1	Ensembl	ENSP00000607808.1	5	Standard
ENST00000937749.2	Ensembl	ENSP00000607808.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glucocorticoid Receptor Pathway
Nuclear Receptors Meta-Pathway

Biological Process

G protein-coupled receptor signaling pathway

Molecular Function

G protein-coupled receptor activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377893
Coding exons: 5
Length: 13630
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125735
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.669	240	271	0.886	0.0000184	3799
Missense (PolyPhen)		126	151.06	0.83413		1751
Synonymous	0.133	121	123	0.985	0.00000864	1394
Loss of Function	0.761	11	14.1	0.781	6.04e-7	184

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00025	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00027	rare
Finnish	0.000050	0.000046	rare
European (Non-Finnish)	0.00010	0.000097	rare
South Asian	0.000035	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Orphan receptor.;

Recessive Scores

pRec: 0.113

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.355

Gene Damage Prediction

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