RTP3

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

Basic information

Region (hg38): 3:46494610-46500950

Previous symbols: [ "TMEM7" ]

Links

ENSG00000163825 ∙ NCBI:83597 ∙ OMIM:607181 ∙ HGNC:15572 ∙ Uniprot:Q9BQQ7 ∙ 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 RTP3 gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTP3 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in RTP3

This is a list of pathogenic ClinVar variants found in the RTP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-46498213-G-A		not specified	Uncertain significance (Feb 02, 2022)
3-46500361-A-C		not specified	Uncertain significance (Apr 12, 2022)
3-46500386-G-C		not specified	Uncertain significance (Aug 12, 2022)
3-46500417-A-G		not specified	Uncertain significance (Jan 07, 2022)
3-46500429-G-A		not specified	Likely benign (Jun 09, 2022)
3-46500445-G-T		not specified	Uncertain significance (Jul 21, 2021)
3-46500456-A-G		not specified	Uncertain significance (Mar 22, 2023)
3-46500465-T-C		not specified	Uncertain significance (Feb 06, 2024)
3-46500498-C-G		not specified	Uncertain significance (Jul 08, 2021)
3-46500502-T-C		not specified	Uncertain significance (Feb 13, 2024)
3-46500519-A-G		not specified	Uncertain significance (Nov 03, 2022)
3-46500566-T-G		not specified	Uncertain significance (Oct 12, 2021)
3-46500667-C-T		not specified	Uncertain significance (Jan 19, 2024)
3-46500718-C-G		not specified	Uncertain significance (May 04, 2023)
3-46500732-A-G		not specified	Uncertain significance (Dec 21, 2022)
3-46500844-G-C		not specified	Uncertain significance (Sep 06, 2022)
3-46500894-A-G		not specified	Uncertain significance (Aug 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTP3	protein_coding	protein_coding	ENST00000296142	2	3459

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.201	0.659	125700	0	14	125714	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.343	116	127	0.914	0.00000612	1540
Missense in Polyphen		39	31.653	1.2321		423
Synonymous	0.867	38	45.4	0.836	0.00000227	425
Loss of Function	0.990	1	2.78	0.359	1.19e-7	29

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)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.000392	0.000392
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes functional cell surface expression of the bitter taste receptors TAS2R16 and TAS2R43. {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: 0.0712

Intolerance Scores

• loftool: 0.550
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.0423
• hipred: N
• hipred_score: 0.173
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0986

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rtp3

Gene ontology

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