GRTP1

growth hormone regulated TBC protein 1

Basic information

Region (hg38): 13:113324163-113364148

Links

ENSG00000139835 ∙ NCBI:79774 ∙ ∙ HGNC:20310 ∙ Uniprot:Q5TC63 ∙ 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 GRTP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRTP1 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			25	3		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				17	1	18
Total	0	0	25	20	1

Variants in GRTP1

This is a list of pathogenic ClinVar variants found in the GRTP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-113324508-G-A		not specified	Uncertain significance (Oct 04, 2022)
13-113324531-T-C		not specified	Likely benign (Aug 08, 2023)
13-113324534-G-A		not specified	Uncertain significance (Apr 26, 2023)
13-113325668-A-G		not specified	Uncertain significance (Sep 22, 2023)
13-113325671-G-A		not specified	Uncertain significance (Mar 29, 2022)
13-113325704-A-G		not specified	Uncertain significance (Jun 02, 2023)
13-113325718-A-C		not specified	Likely benign (Jul 13, 2021)
13-113325767-T-G		not specified	Uncertain significance (Jan 23, 2024)
13-113325810-C-A		not specified	Uncertain significance (Dec 09, 2023)
13-113325938-A-G		not specified	Uncertain significance (Aug 16, 2021)
13-113325959-C-T		not specified	Uncertain significance (Sep 16, 2021)
13-113325968-A-T		not specified	Uncertain significance (Mar 27, 2023)
13-113325987-C-T		not specified	Uncertain significance (Sep 22, 2021)
13-113325992-C-T		not specified	Uncertain significance (Mar 28, 2023)
13-113326014-C-G		not specified	Uncertain significance (May 15, 2023)
13-113326025-G-A		not specified	Uncertain significance (Mar 17, 2023)
13-113326028-C-T		not specified	Uncertain significance (Sep 06, 2022)
13-113326029-G-A		not specified	Uncertain significance (Apr 01, 2024)
13-113326041-C-G		not specified	Uncertain significance (Feb 17, 2022)
13-113346103-C-A			Likely benign (Jan 01, 2023)
13-113346176-G-A			Likely benign (Dec 01, 2023)
13-113346217-TGTGGCTGA-T			Likely benign (Nov 01, 2022)
13-113346241-G-C			Likely benign (Jan 01, 2023)
13-113346252-CCG-C			Likely benign (Jan 01, 2023)
13-113346301-C-T			Likely benign (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRTP1	protein_coding	protein_coding	ENST00000375431	8	39942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.04e-13	0.0130	125637	0	111	125748	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.444	230	212	1.09	0.0000136	2161
Missense in Polyphen		88	73.28	1.2009		739
Synonymous	-1.17	104	89.9	1.16	0.00000602	674
Loss of Function	-0.410	18	16.2	1.11	6.94e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000635	0.000635
Ashkenazi Jewish	0.00	0.00
East Asian	0.00104	0.00103
Finnish	0.000332	0.000277
European (Non-Finnish)	0.000365	0.000360
Middle Eastern	0.00104	0.00103
South Asian	0.000854	0.000850
Other	0.000672	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a GTPase-activating protein for Rab family protein(s).

Intolerance Scores

• loftool: 0.903
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.49

Haploinsufficiency Scores

• pHI: 0.395
• hipred: N
• hipred_score: 0.289
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grtp1
• Phenotype: endocrine/exocrine gland phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: intracellular protein transport;activation of GTPase activity
• Cellular component: cell
• Molecular function: GTPase activator activity;Rab GTPase binding