RTP2

receptor transporter protein 2, the group of Receptor transporter proteins|Zinc fingers 3CxxC-type

Basic information

Region (hg38): 3:187698259-187702557

Links

ENSG00000198471 ∙ NCBI:344892 ∙ OMIM:609138 ∙ HGNC:32486 ∙ Uniprot:Q5QGT7 ∙ 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 RTP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTP2 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			12	3		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	4	0

Variants in RTP2

This is a list of pathogenic ClinVar variants found in the RTP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-187698572-A-G		not specified	Uncertain significance (Sep 04, 2024)
3-187698585-C-A		not specified	Likely benign (Mar 02, 2023)
3-187698598-C-T		not specified	Uncertain significance (Jul 14, 2024)
3-187698649-A-C		not specified	Uncertain significance (Feb 23, 2023)
3-187698672-G-T		not specified	Uncertain significance (Sep 26, 2023)
3-187698689-C-T		not specified	Uncertain significance (May 23, 2023)
3-187698690-G-C		not specified	Uncertain significance (Aug 22, 2022)
3-187698706-G-A		not specified	Uncertain significance (Jun 28, 2023)
3-187698776-C-T		not specified	Uncertain significance (Dec 06, 2024)
3-187698779-C-G		not specified	Uncertain significance (Aug 11, 2024)
3-187698783-C-G		not specified	Likely benign (Jan 10, 2022)
3-187698784-T-C		not specified	Likely benign (Jan 10, 2022)
3-187698907-C-T		not specified	Uncertain significance (Aug 12, 2021)
3-187698914-G-A		not specified	Uncertain significance (Nov 13, 2024)
3-187698925-G-T		not specified	Uncertain significance (Jun 02, 2023)
3-187698938-G-T		not specified	Uncertain significance (May 22, 2023)
3-187698975-A-C			Likely benign (Dec 01, 2022)
3-187701975-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-187702058-G-A		not specified	Uncertain significance (Sep 16, 2021)
3-187702080-T-C		not specified	Uncertain significance (Jun 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTP2	protein_coding	protein_coding	ENST00000358241	2	4299

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000671	0.291	124892	13	842	125747	0.00341

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.968	182	149	1.22	0.00000988	1478
Missense in Polyphen		49	44.445	1.1025		465
Synonymous	-1.43	78	63.5	1.23	0.00000457	419
Loss of Function	0.0896	8	8.28	0.966	3.54e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0791	0.0434
Ashkenazi Jewish	0.00631	0.00308
East Asian	0.000163	0.000109
Finnish	0.000467	0.000231
European (Non-Finnish)	0.00137	0.000703
Middle Eastern	0.000163	0.000109
South Asian	0.000543	0.000327
Other	0.00649	0.00359

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically promotes functional cell surface expression of olfactory receptors, but not of other GPCRs. {ECO:0000250}.
• Pathway: Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.538
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.170

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	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rtp2
• Phenotype: reproductive system phenotype

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: plasma membrane;cell surface;integral component of membrane
• Molecular function: protein binding;olfactory receptor binding