PAQR3

protein-coding

progestin and adipoQ receptor family member 3, the group of Progestin and adipoQ receptor family

Gene summary

This gene encodes a seven-transmembrane protein localized in the Golgi apparatus in mammalian cells. The encoded protein belongs to the progestin and adipoQ receptor (PAQR) family. This protein functions as a tumor suppressor by inhibiting the Raf/MEK/ERK signaling cascade. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2017]

MANE transcript

NM_001040202.2

Inheritance

—

ClinVar variants

U:39B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr4:78,887,127-78,939,438

External References & Databases

Ensembl (ENSG00000163291)

Transcript & Mutation Effects

hg38 • Region Span ~52.3 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 PAQR3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001040202.2. 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				1 clinvar		1
missense			39 clinvar	1 clinvar		40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	2	0	41

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001040202.2	RefSeq	NP_001035292.1	6	MANE Select
ENST00000512733.5	Ensembl	ENSP00000421981.1	6	MANE Select
NM_001350105.2	RefSeq	NP_001337034.1	4	Standard
NM_001350106.2	RefSeq	NP_001337035.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
Negative regulation of MAPK pathway
RAF/MAP kinase cascade
MAPK1/MAPK3 signaling
MAPK family signaling cascades

Biological Process

MAPK cascade
negative regulation of protein phosphorylation
negative regulation of neuron projection development
negative regulation of peptidyl-serine phosphorylation
protein localization to Golgi apparatus

Molecular Function

protein binding
signaling receptor activity

Cellular Component

Golgi membrane
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000512733
Coding exons: 6
Length: 52312
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125748
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.597	153	175	0.873	0.00000891	2013
Missense (PolyPhen)		40	46.408	0.86192		521
Synonymous	-0.189	68	66.0	1.03	0.00000342	601
Loss of Function	1.83	10	18.5	0.540	9.46e-7	198

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Functions as a spatial regulator of RAF1 kinase by sequestrating it to the Golgi. {ECO:0000269|PubMed:18547165}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.732
RVIS EVS: -0.34
RVIS percentile EVS: 30.37

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.183

Gene Damage Prediction

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