RALGAPA2

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

Basic information

Region (hg38): 20:20389530-20712644

Previous symbols: [ "C20orf74" ]

Links

ENSG00000188559 ∙ NCBI:57186 ∙ OMIM:618836 ∙ HGNC:16207 ∙ Uniprot:Q2PPJ7 ∙ 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 RALGAPA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RALGAPA2 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				2	1	3
missense			151	6	1	158
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	153	8	2

Variants in RALGAPA2

This is a list of pathogenic ClinVar variants found in the RALGAPA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-20412044-T-G		not specified	Uncertain significance (Dec 15, 2022)
20-20412101-C-T		not specified	Uncertain significance (Apr 24, 2024)
20-20412135-C-T		not specified	Uncertain significance (Dec 25, 2024)
20-20412137-C-T		not specified	Uncertain significance (Dec 10, 2024)
20-20412138-G-A			Uncertain significance (Mar 01, 2022)
20-20412147-A-G		not specified	Uncertain significance (Oct 12, 2021)
20-20472841-A-G		not specified	Uncertain significance (Aug 04, 2024)
20-20472863-C-A		not specified	Uncertain significance (Jan 31, 2025)
20-20472887-C-T		not specified	Uncertain significance (Feb 25, 2025)
20-20472898-C-T		not specified	Uncertain significance (Oct 26, 2021)
20-20472945-A-C		not specified	Uncertain significance (Aug 02, 2021)
20-20495152-G-C		not specified	Uncertain significance (Mar 01, 2024)
20-20495161-T-C		not specified	Uncertain significance (Feb 18, 2025)
20-20495165-G-A			Benign (Jul 11, 2017)
20-20495173-T-C		not specified	Uncertain significance (Jan 26, 2025)
20-20495252-C-G		not specified	Uncertain significance (Oct 04, 2024)
20-20495254-C-T		not specified	Uncertain significance (Aug 04, 2024)
20-20503383-G-A		not specified	Uncertain significance (Apr 13, 2022)
20-20503388-C-T		not specified	Uncertain significance (May 23, 2023)
20-20503409-A-G		not specified	Uncertain significance (May 10, 2023)
20-20503442-G-A		not specified	Uncertain significance (Apr 07, 2022)
20-20503455-T-C		not specified	Uncertain significance (Mar 15, 2024)
20-20503473-C-T		not specified	Uncertain significance (May 15, 2024)
20-20503497-A-G		not specified	Uncertain significance (May 23, 2023)
20-20505446-C-T		not specified	Uncertain significance (Jan 01, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RALGAPA2	protein_coding	protein_coding	ENST00000202677	39	322936

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.03e-17	1.00	124537	0	154	124691	0.000618

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.888	877	954	0.919	0.0000507	12173
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00114	0.00112
Ashkenazi Jewish	0.00	0.00
East Asian	0.000735	0.000723
Finnish	0.00140	0.00139
European (Non-Finnish)	0.000643	0.000619
Middle Eastern	0.000735	0.000723
South Asian	0.000402	0.000392
Other	0.000178	0.000165

dbNSFP

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}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Translocation of GLUT4 to the plasma membrane (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.446
• rvis_EVS: -2.31
• rvis_percentile_EVS: 1.2

Haploinsufficiency Scores

• pHI: 0.214
• hipred: Y
• hipred_score: 0.544
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ralgapa2
• Phenotype: neoplasm; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of small GTPase mediated signal transduction;activation of GTPase activity
• Cellular component: extracellular space;nucleus;cytoplasm;cytosol;plasma membrane
• Molecular function: GTPase activator activity;protein heterodimerization activity