RXFP3

relaxin family peptide receptor 3, the group of Relaxin family peptide receptors

Basic information

Region (hg38): 5:33936386-33938918

Previous symbols: [ "RLN3R1" ]

Links

ENSG00000182631 ∙ NCBI:51289 ∙ OMIM:609445 ∙ HGNC:24883 ∙ Uniprot:Q9NSD7 ∙ 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 RXFP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RXFP3 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	1

Variants in RXFP3

This is a list of pathogenic ClinVar variants found in the RXFP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-33936798-A-C		not specified	Uncertain significance (May 25, 2022)
5-33936835-T-C		not specified	Uncertain significance (Jan 03, 2024)
5-33937017-G-A		not specified	Uncertain significance (Jan 19, 2024)
5-33937041-C-G		not specified	Uncertain significance (Aug 10, 2023)
5-33937054-T-C		not specified	Uncertain significance (Jul 06, 2021)
5-33937066-T-G		not specified	Uncertain significance (Feb 02, 2022)
5-33937086-T-C		not specified	Uncertain significance (Aug 30, 2022)
5-33937089-A-G		not specified	Uncertain significance (Sep 22, 2022)
5-33937110-C-T			Benign (Jun 14, 2018)
5-33937146-C-A		not specified	Uncertain significance (Jul 25, 2023)
5-33937167-G-T		not specified	Uncertain significance (Aug 17, 2022)
5-33937300-C-A		not specified	Uncertain significance (Aug 14, 2023)
5-33937357-T-C		not specified	Uncertain significance (Apr 03, 2023)
5-33937408-C-G		not specified	Uncertain significance (Dec 07, 2021)
5-33937576-C-T		not specified	Uncertain significance (Jan 29, 2024)
5-33937590-A-G		not specified	Uncertain significance (May 23, 2023)
5-33937628-C-G		not specified	Uncertain significance (Dec 03, 2021)
5-33937636-C-G		not specified	Uncertain significance (May 04, 2022)
5-33937687-C-T		not specified	Uncertain significance (Jun 29, 2023)
5-33937735-T-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
5-33937766-C-A		not specified	Uncertain significance (May 27, 2022)
5-33937773-C-G		not specified	Uncertain significance (Apr 18, 2024)
5-33937798-A-G		not specified	Uncertain significance (Feb 23, 2023)
5-33937885-G-A		not specified	Uncertain significance (Nov 13, 2023)
5-33937929-C-G		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RXFP3	protein_coding	protein_coding	ENST00000330120	1	2533

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.60e-13	0.00393	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.473	290	314	0.925	0.0000211	2986
Missense in Polyphen		54	61.512	0.87787		684
Synonymous	-0.506	165	157	1.05	0.0000122	1022
Loss of Function	-1.17	17	12.5	1.36	5.94e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for RNL3/relaxin-3. Binding of the ligand inhibit cAMP accumulation. {ECO:0000269|PubMed:14522968}.
• Pathway: Relaxin signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);GPCRs, Other;Signaling by GPCR;Signal Transduction;Relaxin receptors;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.743
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.0533
• hipred: N
• hipred_score: 0.486
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.235

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rxfp3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;positive regulation of cytokinesis
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;galanin receptor activity;G protein-coupled peptide receptor activity