RALGAPB

Ral GTPase activating protein non-catalytic subunit beta, the group of Armadillo like helical domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 20:38472816-38578859

Previous symbols: [ "KIAA1219" ]

Links

ENSG00000170471 ∙ NCBI:57148 ∙ OMIM:618833 ∙ HGNC:29221 ∙ Uniprot:Q86X10 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RALGAPB gene.

• Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RALGAPB 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					6	6
missense		1	51	3	5	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region						0
non coding				1	1	2
Total	1	1	51	4	12

Variants in RALGAPB

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

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

Position	Type	Phenotype	Significance	ClinVar
20-38488469-C-G		not specified	Uncertain significance (May 10, 2023)
20-38488541-G-A		not specified	Uncertain significance (Nov 10, 2024)
20-38492942-A-T		not specified	Uncertain significance (Dec 07, 2024)
20-38492994-A-G		RALGAPB-related disorder	Uncertain significance (Jan 25, 2024)
20-38493003-T-C		not specified	Uncertain significance (Aug 14, 2024)
20-38497420-C-T		Marfanoid habitus and intellectual disability	Uncertain significance (-)
20-38497421-G-A		not specified	Uncertain significance (Jul 19, 2024)
20-38497442-G-A		not specified	Uncertain significance (Feb 28, 2024)
20-38497507-A-G		not specified	Uncertain significance (Jul 26, 2022)
20-38497511-T-C		not specified	Uncertain significance (Sep 27, 2024)
20-38499437-T-C		RALGAPB-related disorder	Benign (Feb 18, 2020)
20-38499474-A-G		not specified	Uncertain significance (Jul 02, 2024)
20-38499516-C-G		not specified	Uncertain significance (Aug 04, 2021)
20-38499519-G-A		not specified	Uncertain significance (Aug 10, 2024)
20-38499621-C-G		not specified	Uncertain significance (Feb 28, 2024)
20-38509084-C-T		not specified	Uncertain significance (Nov 09, 2021)
20-38509147-C-G		RALGAPB-related disorder	Uncertain significance (Jul 26, 2023)
20-38509162-A-C		RALGAPB-related disorder	Benign (Nov 21, 2019)
20-38509201-A-G		not specified	Uncertain significance (Oct 06, 2023)
20-38517547-G-A		not specified	Uncertain significance (Jul 14, 2021)
20-38517596-C-A		not specified	Uncertain significance (Apr 09, 2024)
20-38517605-G-A		not specified	Uncertain significance (Mar 17, 2023)
20-38517634-G-A		not specified	Uncertain significance (Dec 13, 2023)
20-38517796-C-T		not specified	Uncertain significance (Dec 20, 2023)
20-38517841-T-C		High myopia • not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RALGAPB	protein_coding	protein_coding	ENST00000262879	29	106046

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.76e-10	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.18	561	816	0.687	0.0000428	9807
Missense in Polyphen		193	337.38	0.57205		4025
Synonymous	-0.312	292	285	1.02	0.0000145	2923
Loss of Function	7.58	3	72.8	0.0412	0.00000374	891

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000141	0.000139
European (Non-Finnish)	0.00000883	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-catalytic subunit of the heterodimeric RalGAP1 and RalGAP2 complexes which act as GTPase activators 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: 0.106

Intolerance Scores

• loftool: 0.00193
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.32

Haploinsufficiency Scores

• pHI: 0.644
• hipred: Y
• hipred_score: 0.768
• ghis: 0.661

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ralgapb
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of small GTPase mediated signal transduction;activation of GTPase activity
• Molecular function: GTPase activator activity;protein heterodimerization activity