PAQR3

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

Basic information

Region (hg38): 4:78887126-78939438

Links

ENSG00000163291 ∙ NCBI:152559 ∙ OMIM:614577 ∙ HGNC:30130 ∙ Uniprot:Q6TCH7 ∙ 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 PAQR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAQR3 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	2		6
Total	0	0	12	4	0

Variants in PAQR3

This is a list of pathogenic ClinVar variants found in the PAQR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-78887246-A-G		not specified	Uncertain significance (Oct 22, 2021)
4-78910693-C-T		not specified	Uncertain significance (Aug 17, 2021)
4-78910864-A-G		not specified	Uncertain significance (Sep 17, 2021)
4-78911338-G-A		not specified	Likely benign (Jul 13, 2021)
4-78911632-T-A		not specified	Uncertain significance (Jul 13, 2021)
4-78912028-C-T		not specified	Benign/Likely benign (Dec 31, 2019)
4-78923917-T-C		not specified	Likely benign (Jan 05, 2022)
4-78923932-C-A		not specified	Uncertain significance (Dec 08, 2023)
4-78926529-T-C		not specified	Uncertain significance (Apr 01, 2024)
4-78926532-G-A		not specified	Uncertain significance (Dec 03, 2021)
4-78926549-T-C		not specified	Uncertain significance (Dec 07, 2021)
4-78926571-T-C		not specified	Uncertain significance (Jun 11, 2021)
4-78926573-G-C			Uncertain significance (-)
4-78926610-T-C		not specified	Uncertain significance (Mar 20, 2024)
4-78926660-G-A		not specified	Uncertain significance (Sep 22, 2022)
4-78926685-C-T		not specified	Uncertain significance (Jun 11, 2021)
4-78930187-C-A		not specified	Uncertain significance (Apr 23, 2024)
4-78930261-C-T		not specified	Uncertain significance (Oct 16, 2023)
4-78935171-C-T		not specified	Uncertain significance (Mar 30, 2024)
4-78939135-C-T			Likely benign (Sep 01, 2022)
4-78939143-T-C		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAQR3	protein_coding	protein_coding	ENST00000512733	6	52312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000374	0.955	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.597	153	175	0.873	0.00000891	2013
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000110	0.000109
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.000110	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a spatial regulator of RAF1 kinase by sequestrating it to the Golgi. {ECO:0000269|PubMed:18547165}.
• Pathway: Signal Transduction;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.732
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.481
• hipred: N
• hipred_score: 0.394
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.183

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Paqr3
• Phenotype: cellular 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); neoplasm

Gene ontology

• 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;negative regulation of MAP kinase activity
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: protein binding;signaling receptor activity