TPRA1

transmembrane protein adipocyte associated 1, the group of 7TM uncharacterized proteins|MicroRNA protein coding host genes

Basic information

Region (hg38): 3:127571232-127598267

Previous symbols: [ "GPR175" ]

Links

ENSG00000163870 ∙ NCBI:131601 ∙ OMIM:608336 ∙ HGNC:30413 ∙ Uniprot:Q86W33 ∙ 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 TPRA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPRA1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	0	0	2

Variants in TPRA1

This is a list of pathogenic ClinVar variants found in the TPRA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-127575176-C-T			Benign (Nov 15, 2018)
3-127577014-C-G			Benign (Feb 20, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPRA1	protein_coding	protein_coding	ENST00000355552	10	25183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0147	0.980	125706	0	29	125735	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.518	201	223	0.902	0.0000131	2369
Missense in Polyphen		86	95.252	0.90287		1085
Synonymous	-0.833	109	98.5	1.11	0.00000586	798
Loss of Function	2.44	6	16.8	0.358	7.14e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000471	0.000337
Ashkenazi Jewish	0.00	0.00
East Asian	0.000329	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000106
Middle Eastern	0.000329	0.000326
South Asian	0.0000980	0.0000980
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.0820
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.85

Haploinsufficiency Scores

• pHI: 0.262
• hipred: N
• hipred_score: 0.324
• ghis: 0.554

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: Tpra1

Gene ontology

• Biological process: lipid metabolic process;G protein-coupled receptor signaling pathway;aging
• Cellular component: integral component of membrane
• Molecular function: G protein-coupled receptor activity;protein binding