GRTP1

protein-coding

growth hormone regulated TBC protein 1

Gene summary

Predicted to enable GTPase activator activity. Predicted to be active in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024719.4

Inheritance

—

ClinVar variants

U:75B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.11

Max pathogenic AF

—

Genomic locus

chr13:113,324,163-113,364,148

External References & Databases

Ensembl (ENSG00000139835)

Transcript & Mutation Effects

hg38 • Region Span ~40.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GRTP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 72

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024719.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			73 clinvar	4 clinvar		77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	75	4	0	79

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024719.4	RefSeq	NP_078995.2	8	MANE Select
ENST00000375431.9	Ensembl	ENSP00000364580.3	8	MANE Select
NM_001286732.2	RefSeq	NP_001273661.1	7	Standard
NM_001286733.1	RefSeq	NP_001273662.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intracellular protein transport
activation of GTPase activity

Molecular Function

GTPase activator activity
Rab GTPase binding

Cellular Component

cell

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375431
Coding exons: 8
Length: 39942
Individuals with no LoFs: 125637
Homozygous LoFs: 0
Heterozygous LoFs: 111
Defined: 125748
p: 0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.444	230	212	1.09	0.0000136	2161
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0010	0.0010	notable
Finnish	0.00033	0.00028	rare
European (Non-Finnish)	0.00036	0.00036	rare
South Asian	0.00085	0.00085	rare
Other	0.00067	0.00065	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.162

Gene Damage Prediction

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