RABGAP1

protein-coding

RAB GTPase activating protein 1

Gene summary

Enables GTPase activator activity and small GTPase binding activity. Predicted to be involved in G protein-coupled receptor signaling pathway. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_012197.4

Inheritance

ClinVar variants

P:2U:115B:6

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.02

Max pathogenic AF

—

Genomic locus

chr9:122,940,833-123,104,866

External References & Databases

Ensembl (ENSG00000011454)

Transcript & Mutation Effects

hg38 • Region Span ~164.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: G2P

neurodevelopmental disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RABGAP1 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 146

not providedTotal: 12

RABGAP1-related conditionTotal: 1

Neurodevelopmental disorder, RABGAP1-relatedTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012197.4. 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			3 clinvar	3 clinvar		6
missense			102 clinvar	3 clinvar		105
nonsense	1 clinvar		2 clinvar			3
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)		1 clinvar	5 clinvar			6
Total	1	1	115	6	0	123

Highest pathogenic variant AF is 6.899778e-7

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 77 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012197.4	RefSeq	NP_036329.3	25	MANE Select
ENST00000373647.9	Ensembl	ENSP00000362751.4	25	MANE Select
ENST00000402311.5	Ensembl	ENSP00000384119.1	2	Standard
ENST00000426918.2	Ensembl	ENSP00000416327.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
TBC/RABGAPs
Membrane Trafficking
Rab regulation of trafficking

Biological Process

intracellular protein transport
cell cycle
regulation of GTPase activity
activation of GTPase activity
regulation of cilium assembly

Molecular Function

GTPase activator activity
protein binding
tubulin binding
Rab GTPase binding

Cellular Component

centrosome
cytosol
microtubule associated complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373647
Coding exons: 25
Length: 164034
Individuals with no LoFs: 125596
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125599
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.96	368	566	0.650	0.0000303	7063
Missense (PolyPhen)		145	289.37	0.50109		3570
Synonymous	0.408	201	208	0.964	0.0000112	1967
Loss of Function	7.12	1	61.1	0.0164	0.00000318	759

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a GTPase-activating protein of RAB6A. May play a role in microtubule nucleation by centrosome. May participate in a RAB6A-mediated pathway involved in the metaphase- anaphase transition. {ECO:0000269|PubMed:10202141, ECO:0000269|PubMed:16395330}.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.265
RVIS EVS: -1.51
RVIS percentile EVS: 3.5

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.879

Gene Damage Prediction

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