RTP1

receptor transporter protein 1, the group of Receptor transporter proteins|Zinc fingers 3CxxC-type

Basic information

Region (hg38): 3:187197486-187201462

Links

ENSG00000175077 ∙ NCBI:132112 ∙ OMIM:609137 ∙ HGNC:28580 ∙ Uniprot:P59025 ∙ 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 RTP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTP1 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			20	3		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	3	0

Variants in RTP1

This is a list of pathogenic ClinVar variants found in the RTP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-187197532-C-T		not specified	Uncertain significance (Dec 22, 2023)
3-187197544-G-T		not specified	Uncertain significance (Aug 08, 2022)
3-187197618-G-A		not specified	Likely benign (Dec 13, 2022)
3-187197621-A-T		not specified	Uncertain significance (Nov 13, 2023)
3-187197670-A-T		not specified	Uncertain significance (Feb 26, 2024)
3-187197766-T-C		not specified	Uncertain significance (May 13, 2024)
3-187199594-G-C		not specified	Likely benign (Dec 06, 2021)
3-187199594-G-T		not specified	Likely benign (Jul 06, 2021)
3-187199631-A-G		not specified	Uncertain significance (Feb 05, 2024)
3-187199645-G-A		not specified	Uncertain significance (Jun 28, 2022)
3-187199649-G-A		not specified	Uncertain significance (Aug 13, 2021)
3-187199654-C-T		not specified	Uncertain significance (Jun 16, 2023)
3-187199657-G-A		not specified	Uncertain significance (Mar 28, 2024)
3-187199700-A-G		not specified	Uncertain significance (Feb 03, 2022)
3-187199706-C-T		not specified	Uncertain significance (Dec 19, 2022)
3-187199711-A-C		not specified	Uncertain significance (Jun 18, 2021)
3-187199712-T-C		not specified	Uncertain significance (Feb 10, 2022)
3-187199727-T-A		not specified	Uncertain significance (Feb 28, 2024)
3-187199733-G-T		not specified	Uncertain significance (Jul 09, 2021)
3-187199778-G-A		not specified	Uncertain significance (Apr 19, 2023)
3-187199783-C-G		not specified	Uncertain significance (Apr 19, 2023)
3-187199784-G-A		not specified	Uncertain significance (Apr 19, 2023)
3-187199820-A-G		not specified	Uncertain significance (Feb 22, 2023)
3-187199983-C-A		not specified	Uncertain significance (Sep 26, 2023)
3-187200035-A-G		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTP1	protein_coding	protein_coding	ENST00000312295	2	3980

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000856	0.541	125485	0	263	125748	0.00105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.450	193	176	1.10	0.0000122	1710
Missense in Polyphen		46	42.145	1.0915		467
Synonymous	-0.441	85	80.0	1.06	0.00000610	509
Loss of Function	0.726	9	11.7	0.771	5.05e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000302	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000126	0.000123
Middle Eastern	0.000327	0.000326
South Asian	0.00759	0.00761
Other	0.000656	0.000652

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: 0.117

Intolerance Scores

• loftool: 0.755
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.85

Haploinsufficiency Scores

• pHI: 0.790
• hipred: N
• hipred_score: 0.234
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rtp1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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: olfactory receptor binding