RRAGC

Ras related GTP binding C, the group of Ras related GTP binding proteins

Basic information

Region (hg38): 1:38838198-38859772

Links

ENSG00000116954 ∙ NCBI:64121 ∙ OMIM:608267 ∙ HGNC:19902 ∙ Uniprot:Q9HB90 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Long-Olsen-Distelmaier syndrome	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Cardiovascular; Neurologic; Ophthalmologic	27234373; 37057673

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RRAGC 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		1	20			21
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	1	20	0	1

Variants in RRAGC

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

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

Position	Type	Phenotype	Significance	ClinVar
1-38839558-T-C		Inborn genetic diseases	Uncertain significance (Sep 25, 2023)
1-38839580-G-T		Inborn genetic diseases	Uncertain significance (Aug 23, 2021)
1-38839633-G-C		Inborn genetic diseases	Uncertain significance (Dec 04, 2024)
1-38846038-T-C		Inborn genetic diseases	Uncertain significance (Sep 27, 2021)
1-38846087-C-T		Inborn genetic diseases	Likely benign (Dec 27, 2023)
1-38851747-A-C		Inborn genetic diseases	Uncertain significance (Jun 13, 2023)
1-38851750-C-A		Inborn genetic diseases	Uncertain significance (May 26, 2022)
1-38855750-T-A		RRAGC-related condition	Uncertain significance (Sep 21, 2024)
1-38855750-T-C		Inborn genetic diseases	Uncertain significance (Jul 16, 2024)
1-38855861-T-C		Inborn genetic diseases	Uncertain significance (May 02, 2024)
1-38855886-T-C		Inborn genetic diseases	Uncertain significance (May 01, 2023)
1-38856967-G-A		Long-Olsen-Distelmaier syndrome	Pathogenic (Mar 07, 2025)
1-38856977-A-G		See cases • Long-Olsen-Distelmaier syndrome	Likely pathogenic (Aug 15, 2022)
1-38856978-T-C		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
1-38856997-G-A		Inborn genetic diseases	Uncertain significance (Jun 13, 2022)
1-38857003-T-C		Inborn genetic diseases	Uncertain significance (Feb 07, 2025)
1-38857051-G-T		Long-Olsen-Distelmaier syndrome	Pathogenic (Mar 07, 2025)
1-38859391-T-C			Benign (Jan 25, 2021)
1-38859423-G-T		Long-Olsen-Distelmaier syndrome	Pathogenic (Mar 07, 2025)
1-38859480-C-T		Inborn genetic diseases	Uncertain significance (Sep 26, 2024)
1-38859483-C-G		Inborn genetic diseases	Uncertain significance (Dec 20, 2022)
1-38859484-C-G		Inborn genetic diseases	Uncertain significance (Dec 09, 2024)
1-38859487-G-A		Inborn genetic diseases	Uncertain significance (Aug 30, 2022)
1-38859516-A-G		Inborn genetic diseases	Uncertain significance (Apr 25, 2023)
1-38859519-C-A		Inborn genetic diseases	Uncertain significance (Apr 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RRAGC	protein_coding	protein_coding	ENST00000373001	7	21626

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.975	0.0246	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.46	113	215	0.527	0.00000996	2660
Missense in Polyphen		15	44.978	0.3335		595
Synonymous	0.623	76	83.2	0.913	0.00000440	736
Loss of Function	3.45	1	15.8	0.0633	7.48e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000163	0.000163
South Asian	0.0000364	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide-binding protein forming heterodimeric Rag complexes required for the amino acid-induced relocalization of mTORC1 to the lysosomes and its subsequent activation by the GTPase RHEB. This is a crucial step in the activation of the TOR signaling cascade by amino acids. {ECO:0000269|PubMed:20381137, ECO:0000269|PubMed:27234373}.
• Disease: DISEASE: Note=RRAGC mutations have been found in a patient with idiopathic dilated cardiomyopathy with ventricular dilation and systolic dysfunction, bilateral cataracts, and mild facial dysmorphisms. {ECO:0000269|PubMed:27234373}.
• Pathway: mTOR signaling pathway - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Target Of Rapamycin (TOR) Signaling;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;mTORC1-mediated signalling;Energy dependent regulation of mTOR by LKB1-AMPK;mTOR signalling;TP53 Regulates Metabolic Genes;Macroautophagy;Cellular responses to external stimuli;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Transcriptional Regulation by TP53;Intracellular signaling by second messengers;mTOR signaling pathway (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.175
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.372
• hipred: Y
• hipred_score: 0.765
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rragc

Gene ontology

• Biological process: transcription, DNA-templated;apoptotic process;cell cycle arrest;small GTPase mediated signal transduction;RNA splicing;cellular response to starvation;regulation of autophagy;regulation of macroautophagy;regulation of TOR signaling;positive regulation of TOR signaling;cellular response to amino acid starvation;cellular protein localization;response to amino acid;cellular response to amino acid stimulus;regulation of TORC1 signaling
• Cellular component: nucleus;cytoplasm;lysosome;cytosol;EGO complex;intracellular membrane-bounded organelle;Gtr1-Gtr2 GTPase complex
• Molecular function: magnesium ion binding;GTPase activity;protein binding;GTP binding;GDP binding;protein heterodimerization activity;GTPase binding