RALGAPA2

protein-coding

Ral GTPase activating protein catalytic subunit alpha 2, the group of Armadillo like helical domain containing

Gene summary

Predicted to enable GTPase activator activity and protein heterodimerization activity. Predicted to be involved in activation of GTPase activity. Predicted to act upstream of or within Ral protein signal transduction; regulation of exocyst localization; and regulation of protein localization. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C20orf74

MANE transcript

NM_020343.4

Inheritance

—

ClinVar variants

U:311B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr20:20,389,530-20,712,644

External References & Databases

Ensembl (ENSG00000188559)

Transcript & Mutation Effects

hg38 • Region Span ~323.1 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 RALGAPA2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 294

not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020343.4. 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			7 clinvar	4 clinvar	1 clinvar	12
missense			292 clinvar	9 clinvar	1 clinvar	302
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	311	13	2	326

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020343.4	RefSeq	NP_065076.2	39	MANE Select
ENST00000202677.12	Ensembl	ENSP00000202677.6	39	MANE Select
ENST00000427175.2	Ensembl	ENSP00000388695.1	6	Standard
ENST00000430436.5	Ensembl	ENSP00000400085.1	33	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Translocation of GLUT4 to the plasma membrane

Biological Process

regulation of small GTPase mediated signal transduction
activation of GTPase activity

Molecular Function

GTPase activator activity
protein heterodimerization activity

Cellular Component

extracellular space
nucleus
cytoplasm
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000202677
Coding exons: 39
Length: 322936
Individuals with no LoFs: 124537
Homozygous LoFs: 0
Heterozygous LoFs: 154
Defined: 124691
p: 0.000618

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.888	877	954	0.919	0.0000507	12173
Missense (PolyPhen)		169	220.44	0.76664		2878
Synonymous	-0.679	388	371	1.04	0.0000212	3588
Loss of Function	4.98	45	98.3	0.458	0.00000554	1192

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00053	0.00052	rare
Latino/Admixed American	0.00061	0.00058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00074	0.00072	rare
Finnish	0.0014	0.0014	notable
European (Non-Finnish)	0.00064	0.00062	rare
South Asian	0.00040	0.00039	rare
Other	0.00018	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalytic subunit of the heterodimeric RalGAP2 complex which acts as a GTPase activator for the Ras-like small GTPases RALA and RALB. {ECO:0000250}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.446
RVIS EVS: -2.31
RVIS percentile EVS: 1.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.283

Gene Damage Prediction

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