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.

not_specified (48 variants)

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. These statistics are base on transcript: NM_000153708.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			45 clinvar	3 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	45	3	0

Loading clinvar variants...

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