RALGPS1

Ral GEF with PH domain and SH3 binding motif 1, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 9:126914773-127223166

Links

ENSG00000136828 ∙ NCBI:9649 ∙ OMIM:614444 ∙ HGNC:16851 ∙ Uniprot:Q5JS13 ∙ 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 RALGPS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RALGPS1 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			28			28
Total	0	0	46	1	0

Variants in RALGPS1

This is a list of pathogenic ClinVar variants found in the RALGPS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-126965887-A-G		not specified	Uncertain significance (Jan 04, 2024)
9-126965910-G-A		not specified	Uncertain significance (Jul 14, 2021)
9-127034485-G-A		not specified	Uncertain significance (Sep 13, 2022)
9-127050093-A-G		not specified	Uncertain significance (Sep 26, 2022)
9-127088952-T-C		not specified	Uncertain significance (Oct 03, 2022)
9-127089043-T-C		not specified	Uncertain significance (Jun 16, 2023)
9-127089046-G-A		not specified	Uncertain significance (Feb 10, 2022)
9-127091685-G-A		not specified	Uncertain significance (May 03, 2023)
9-127091715-C-T		not specified	Uncertain significance (Jan 02, 2024)
9-127091757-G-A		not specified	Uncertain significance (Aug 13, 2021)
9-127093843-G-A		not specified	Uncertain significance (Aug 09, 2021)
9-127093857-G-A		not specified	Uncertain significance (Nov 08, 2021)
9-127107929-G-A		not specified	Uncertain significance (Apr 13, 2022)
9-127107957-G-A		not specified	Uncertain significance (Mar 17, 2023)
9-127107975-G-T		not specified	Uncertain significance (May 16, 2024)
9-127108068-G-A		not specified	Uncertain significance (Dec 08, 2023)
9-127108071-G-A		not specified	Uncertain significance (Nov 08, 2022)
9-127108154-T-A		not specified	Uncertain significance (Sep 12, 2023)
9-127108163-G-C		not specified	Uncertain significance (Oct 26, 2022)
9-127108287-G-A		not specified	Uncertain significance (May 13, 2022)
9-127108389-C-T		not specified	Uncertain significance (Oct 20, 2021)
9-127108418-G-A		not specified	Uncertain significance (Aug 21, 2023)
9-127108423-G-C		not specified	Uncertain significance (Feb 21, 2024)
9-127108476-T-C		not specified	Uncertain significance (Jun 18, 2024)
9-127108478-T-G		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RALGPS1	protein_coding	protein_coding	ENST00000259351	18	308393

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000813	125720	0	2	125722	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.09	163	318	0.512	0.0000173	3643
Missense in Polyphen		30	109.65	0.27361		1355
Synonymous	0.988	110	124	0.887	0.00000735	1074
Loss of Function	5.51	1	37.3	0.0268	0.00000217	399

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) for the small GTPase RALA. May be involved in cytoskeletal organization (By similarity). Guanine nucleotide exchange factor for. {ECO:0000250, ECO:0000269|PubMed:10747847, ECO:0000269|PubMed:10889189}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.432
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.770
• hipred: Y
• hipred_score: 0.673
• ghis: 0.643

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ralgps1

Zebrafish Information Network

• Gene name: ralgps1
• Affected structure: pronephric glomerulus
• Phenotype tag: abnormal
• Phenotype quality: permeability

Gene ontology

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