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.

not_specified (248 variants)
not_provided (7 variants)

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. These statistics are base on transcript: NM_000020343.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	1 clinvar	3
missense			240 clinvar	9 clinvar	1 clinvar	250
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	242	11	2

Loading clinvar variants...

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