RALGPS2

Ral GEF with PH domain and SH3 binding motif 2, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 1:178725164-178921842

Links

ENSG00000116191 ∙ NCBI:55103 ∙ OMIM:617819 ∙ HGNC:30279 ∙ Uniprot:Q86X27 ∙ 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 RALGPS2 gene.

• Inborn genetic diseases (42 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RALGPS2 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						0
missense			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			19		1	20
Total	0	0	42	0	1

Variants in RALGPS2

This is a list of pathogenic ClinVar variants found in the RALGPS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-178776799-A-T		not specified	Uncertain significance (Jan 03, 2024)
1-178776804-G-T		not specified	Uncertain significance (Aug 18, 2023)
1-178776805-C-G		not specified	Uncertain significance (Dec 22, 2023)
1-178776805-C-T		not specified	Uncertain significance (Dec 13, 2023)
1-178776811-C-T		not specified	Uncertain significance (Jun 07, 2023)
1-178784490-G-A		not specified	Uncertain significance (Jul 26, 2022)
1-178784515-A-G		not specified	Uncertain significance (Jul 11, 2023)
1-178785558-G-A		not specified	Uncertain significance (Aug 08, 2022)
1-178785606-A-T		not specified	Uncertain significance (Jun 12, 2023)
1-178811339-A-C		not specified	Uncertain significance (Mar 20, 2023)
1-178821634-T-C		not specified	Uncertain significance (Nov 17, 2022)
1-178821646-T-C		not specified	Uncertain significance (Feb 28, 2024)
1-178833443-A-G		not specified	Uncertain significance (May 05, 2023)
1-178833493-A-G		not specified	Uncertain significance (Jul 29, 2023)
1-178833494-A-G		not specified	Uncertain significance (Dec 13, 2021)
1-178833512-T-C		not specified	Uncertain significance (Jun 06, 2023)
1-178851136-A-T		not specified	Uncertain significance (Jan 07, 2022)
1-178851148-A-G		not specified	Uncertain significance (Oct 03, 2022)
1-178851179-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-178851199-A-C		not specified	Uncertain significance (Jul 19, 2022)
1-178851296-T-C		not specified	Uncertain significance (Oct 03, 2022)
1-178851311-A-G		not specified	Uncertain significance (Mar 02, 2023)
1-178852705-G-A			Benign (Feb 16, 2018)
1-178852710-G-C		not specified	Uncertain significance (Aug 29, 2022)
1-178852747-A-T		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RALGPS2	protein_coding	protein_coding	ENST00000367635	19	194939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.262	0.738	125718	0	29	125747	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	200	305	0.655	0.0000151	3826
Missense in Polyphen		26	67.196	0.38693		925
Synonymous	0.557	100	107	0.932	0.00000583	1052
Loss of Function	4.40	9	38.5	0.234	0.00000210	472

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000460	0.000460
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000942	0.0000924
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000109	0.000109
South Asian	0.0000336	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor for the small GTPase RALA. May be involved in cytoskeletal organization. May also be involved in the stimulation of transcription in a Ras-independent fashion (By similarity). {ECO:0000250}.
• Disease: DISEASE: Note=RALGPS2 is a potential candidate gene for susceptibility to Alzheimer disease linked to 1q24. {ECO:0000269|PubMed:17564960}.

Recessive Scores

• pRec: 0.0969

Intolerance Scores

• loftool: 0.511
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.142
• hipred: Y
• hipred_score: 0.639
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.662

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ralgps2
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: small GTPase mediated signal transduction;regulation of Ral protein signal transduction
• Cellular component: cytoplasm;plasma membrane
• Molecular function: guanyl-nucleotide exchange factor activity