RGP1

RGP1 homolog, RAB6A GEF complex partner 1

Basic information

Region (hg38): 9:35749287-35758585

Previous symbols: [ "KIAA0258" ]

Links

ENSG00000107185 ∙ NCBI:9827 ∙ OMIM:615742 ∙ HGNC:21965 ∙ Uniprot:Q92546 ∙ 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 RGP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGP1 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			5	1	1	7
Total	0	0	27	1	1

Variants in RGP1

This is a list of pathogenic ClinVar variants found in the RGP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-35749311-A-ACGC			Likely benign (Oct 29, 2019)
9-35749406-G-C			Benign (Apr 07, 2019)
9-35749547-T-C			Benign (Sep 18, 2018)
9-35749780-A-C		not specified	Uncertain significance (Nov 18, 2022)
9-35749868-C-G		not specified	Uncertain significance (Dec 27, 2023)
9-35750244-G-A		not specified	Uncertain significance (Aug 20, 2024)
9-35750316-C-T		not specified	Uncertain significance (Sep 14, 2022)
9-35750322-G-C		not specified	Uncertain significance (Jan 12, 2024)
9-35750374-A-G		not specified	Uncertain significance (Oct 25, 2024)
9-35750376-C-G		not specified	Uncertain significance (Nov 21, 2024)
9-35750843-C-G		not specified	Uncertain significance (Sep 27, 2021)
9-35750932-C-T		not specified	Uncertain significance (Jan 06, 2023)
9-35750933-G-A		not specified	Uncertain significance (Dec 03, 2021)
9-35751274-G-T		not specified	Uncertain significance (Mar 16, 2022)
9-35751277-G-A		not specified	Uncertain significance (Mar 08, 2024)
9-35751280-C-T		not specified	Uncertain significance (Dec 21, 2023)
9-35751347-A-G		not specified	Uncertain significance (Aug 04, 2024)
9-35751380-G-A		not specified	Uncertain significance (Dec 03, 2024)
9-35751395-C-T		not specified	Uncertain significance (Aug 20, 2024)
9-35751401-G-T		not specified	Uncertain significance (Jan 22, 2024)
9-35751404-G-A		not specified	Uncertain significance (Jan 17, 2024)
9-35751666-C-T		not specified	Uncertain significance (Jul 31, 2024)
9-35751977-G-A		not specified	Uncertain significance (Mar 12, 2024)
9-35751983-C-T		not specified	Uncertain significance (Sep 23, 2023)
9-35752002-A-G		not specified	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGP1	protein_coding	protein_coding	ENST00000378078	8	9370

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.30e-9	0.526	124601	0	39	124640	0.000156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.718	196	226	0.866	0.0000126	2477
Missense in Polyphen		39	59.999	0.65001		717
Synonymous	0.0815	91	92.0	0.989	0.00000501	854
Loss of Function	1.12	16	21.6	0.741	0.00000140	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000309	0.000309
Ashkenazi Jewish	0.000110	0.0000994
East Asian	0.000501	0.000501
Finnish	0.0000929	0.0000464
European (Non-Finnish)	0.000134	0.000133
Middle Eastern	0.000501	0.000501
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The RIC1-RGP1 complex acts as a guanine nucleotide exchange factor (GEF), which activates RAB6A by exchanging bound GDP for free GTP and may thereby required for efficient fusion of endosome-derived vesicles with the Golgi compartment. The RIC1- RGP1 complex participates in the recycling of mannose-6-phosphate receptors. {ECO:0000269|PubMed:23091056}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;Intra-Golgi traffic;RAB GEFs exchange GTP for GDP on RABs;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Intolerance Scores

• loftool: 0.459
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.195
• hipred: N
• hipred_score: 0.394
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.410

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rgp1
• 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)

Gene ontology

• Biological process: retrograde transport, endosome to Golgi;positive regulation of GTPase activity;negative regulation of cellular protein catabolic process
• Cellular component: Golgi membrane;cytosol;plasma membrane;membrane;trans-Golgi network membrane;protein-containing complex;RIC1-RGP1 guanyl-nucleotide exchange factor complex
• Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity;Rab GTPase binding