RALGDS

ral guanine nucleotide dissociation stimulator

Basic information

Region (hg38): 9:133097720-133149334

Links

ENSG00000160271 ∙ NCBI:5900 ∙ OMIM:601619 ∙ HGNC:9842 ∙ Uniprot:Q12967 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RALGDS 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			1	12	12	25
missense			50	7	1	58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1		1
Total	0	0	51	20	13

Variants in RALGDS

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

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

Position	Type	Phenotype	Significance	ClinVar
9-133098600-T-C		not specified	Uncertain significance (Apr 18, 2023)
9-133098609-T-C		not specified	Uncertain significance (Dec 07, 2023)
9-133098621-T-C		not specified	Uncertain significance (Jun 11, 2021)
9-133098651-C-G		not specified	Uncertain significance (Mar 29, 2022)
9-133098652-C-T		not specified	Uncertain significance (Mar 23, 2022)
9-133098653-G-A			Likely benign (Jun 20, 2018)
9-133098737-G-A			Likely benign (Dec 26, 2018)
9-133098745-T-C		not specified	Uncertain significance (Aug 04, 2023)
9-133100311-C-T			Benign (Dec 31, 2019)
9-133100327-T-C		not specified	Uncertain significance (Oct 20, 2023)
9-133100365-C-T			Uncertain significance (Oct 01, 2016)
9-133101552-C-G		not specified	Uncertain significance (Dec 28, 2023)
9-133101589-C-T			Benign (Dec 31, 2019)
9-133101634-T-C			Likely benign (Feb 01, 2023)
9-133101663-C-T		not specified	Likely benign (Dec 13, 2023)
9-133101729-T-A		not specified	Uncertain significance (Mar 07, 2024)
9-133101736-G-A			Likely benign (Feb 12, 2018)
9-133101966-G-A		not specified	Uncertain significance (Jun 18, 2024)
9-133101970-C-T		not specified	Uncertain significance (Dec 21, 2022)
9-133101994-C-T		not specified	Uncertain significance (Sep 27, 2021)
9-133101995-G-A			Benign (May 20, 2018)
9-133102013-G-A			Benign (Dec 31, 2019)
9-133102017-G-A		not specified	Uncertain significance (Apr 05, 2023)
9-133102039-C-T		not specified	Uncertain significance (Jan 25, 2023)
9-133102048-C-T		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RALGDS	protein_coding	protein_coding	ENST00000372050	18	66195

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.888	0.112	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	424	518	0.819	0.0000339	5846
Missense in Polyphen		68	86.103	0.78975		981
Synonymous	-1.23	247	224	1.10	0.0000162	1869
Loss of Function	4.89	8	42.4	0.189	0.00000200	511

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000437	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000711	0.0000703
Middle Eastern	0.000437	0.000435
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stimulates the dissociation of GDP from the Ras-related RalA and RalB GTPases which allows GTP binding and activation of the GTPases. Interacts and acts as an effector molecule for R-Ras, H-Ras, K-Ras, and Rap.
• Pathway: Choline metabolism in cancer - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Pancreatic cancer - Homo sapiens (human);Colorectal cancer - Homo sapiens (human);Human Thyroid Stimulating Hormone (TSH) signaling pathway;Chromosomal and microsatellite instability in colorectal cancer;Ras Signaling;EGF-EGFR Signaling Pathway;Signal Transduction;ras signaling pathway;p38MAPK events;Signalling to RAS;Signalling to ERKs;Signaling by NTRK1 (TRKA);Signaling by NTRKs;EGFR1;ErbB1 downstream signaling;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.515
• rvis_EVS: -1.34
• rvis_percentile_EVS: 4.64

Haploinsufficiency Scores

• pHI: 0.482
• hipred: Y
• hipred_score: 0.695
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.758

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: Ras protein signal transduction;regulation of catalytic activity
• Cellular component: nucleus;cytosol;brush border
• Molecular function: guanyl-nucleotide exchange factor activity;protein binding;GTPase regulator activity