RTP4

receptor transporter protein 4, the group of Zinc fingers 3CxxC-type|Receptor transporter proteins

Basic information

Region (hg38): 3:187368385-187372076

Links

ENSG00000136514 ∙ NCBI:64108 ∙ OMIM:609350 ∙ HGNC:23992 ∙ Uniprot:Q96DX8 ∙ 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 RTP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTP4 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						0
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in RTP4

This is a list of pathogenic ClinVar variants found in the RTP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-187368488-T-A		not specified	Uncertain significance (Jun 02, 2024)
3-187368491-A-G		not specified	Uncertain significance (May 05, 2023)
3-187368505-C-T		not specified	Likely benign (Jun 10, 2022)
3-187368506-G-T		not specified	Uncertain significance (Dec 14, 2023)
3-187370802-C-G		not specified	Uncertain significance (Apr 12, 2022)
3-187370811-G-A		not specified	Uncertain significance (May 07, 2024)
3-187370836-G-C		not specified	Uncertain significance (Jun 17, 2024)
3-187370898-T-G		not specified	Uncertain significance (Dec 15, 2023)
3-187370905-A-C		not specified	Uncertain significance (Feb 28, 2024)
3-187370919-G-A		not specified	Uncertain significance (Aug 13, 2021)
3-187370924-T-A		not specified	Uncertain significance (Jun 17, 2024)
3-187370936-G-A		not specified	Uncertain significance (Sep 21, 2023)
3-187370939-A-G		not specified	Uncertain significance (Feb 07, 2023)
3-187370993-C-G		not specified	Uncertain significance (Dec 28, 2024)
3-187371032-T-C		not specified	Uncertain significance (Dec 02, 2024)
3-187371072-G-T		not specified	Uncertain significance (Dec 19, 2023)
3-187371123-A-G		not specified	Uncertain significance (Mar 08, 2025)
3-187371143-A-G		not specified	Uncertain significance (Apr 25, 2023)
3-187371149-C-T		not specified	Uncertain significance (Aug 02, 2024)
3-187371342-T-A		not specified	Uncertain significance (Apr 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTP4	protein_coding	protein_coding	ENST00000259030	2	3745

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.596	0.369	125641	0	2	125643	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.291	122	131	0.928	0.00000665	1600
Missense in Polyphen		40	39.417	1.0148		500
Synonymous	1.74	38	54.3	0.699	0.00000281	476
Loss of Function	1.56	0	2.84	0.00	1.22e-7	28

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable chaperone protein which facilitates trafficking and functional cell surface expression of some G-protein coupled receptors (GPCRs). Promotes functional expression of the bitter taste receptor TAS2R16 (PubMed:16720576). Also promotes functional expression of the opioid receptor heterodimer OPRD1-OPRM1 (By similarity). {ECO:0000250|UniProtKB:Q9ER80, ECO:0000269|PubMed:16720576}.
• Pathway: Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0731

Intolerance Scores

• loftool: 0.813
• rvis_EVS: 1.35
• rvis_percentile_EVS: 94.35

Haploinsufficiency Scores

• pHI: 0.0507
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.125

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rtp4

Gene ontology

• Biological process: detection of chemical stimulus involved in sensory perception of bitter taste;protein targeting to membrane;protein insertion into membrane;defense response to virus
• Cellular component: cytoplasm;cell surface;integral component of membrane
• Molecular function: protein binding;olfactory receptor binding