RABGAP1L

protein-coding

RAB GTPase activating protein 1 like

Gene summary

Enables GTPase activator activity and small GTPase binding activity. Acts upstream of or within regulation of protein localization. Located in several cellular components, including Golgi apparatus; cilium; and early endosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001366446.1

Inheritance

—

ClinVar variants

U:106B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr1:174,159,410-174,995,308

External References & Databases

Ensembl (ENSG00000152061)

UniProt (B7ZAP0, Q5R372)

Transcript & Mutation Effects

hg38 • Region Span ~835.9 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 RABGAP1L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 134

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001366446.1. 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			2 clinvar	1 clinvar	2 clinvar	5
missense			99 clinvar		1 clinvar	100
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	106	1	3	110

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 69 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001366446.1	RefSeq	NP_001353375.1	25	MANE Select
ENST00000681986.1	Ensembl	ENSP00000507884.1	25	MANE Select
NM_001035230.3	RefSeq	NP_001030307.1	3	Standard
NM_001243763.2	RefSeq	NP_001230692.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intracellular protein transport
endocytosis
regulation of protein localization
activation of GTPase activity

Molecular Function

GTPase activator activity
Rab GTPase binding

Cellular Component

nucleus
early endosome
Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000251507
Coding exons: 20
Length: 835898
Individuals with no LoFs: 125701
Homozygous LoFs: 0
Heterozygous LoFs: 47
Defined: 125748
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.12	360	425	0.847	0.0000210	5376
Missense (PolyPhen)		102	136.98	0.74466		1721
Synonymous	0.168	151	154	0.983	0.00000801	1488
Loss of Function	4.25	16	47.7	0.335	0.00000258	576

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00039	0.00038	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00012	0.00011	rare
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.00022	0.00020	rare
South Asian	0.000099	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.376
RVIS EVS: -1.09
RVIS percentile EVS: 7.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.866

Gene Damage Prediction

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