RGPD1

RANBP2 like and GRIP domain containing 1, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 2:86913783-87013976

Links

ENSG00000187627 ∙ NCBI:400966 ∙ OMIM:612704 ∙ HGNC:32414 ∙ Uniprot:P0DJD0 ∙ 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 RGPD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGPD1 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				2		2
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	0

Variants in RGPD1

This is a list of pathogenic ClinVar variants found in the RGPD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-86913883-C-G			Likely benign (Jun 01, 2024)
2-86942269-C-T			Likely benign (Jul 01, 2023)
2-86951349-T-A		not specified	Uncertain significance (Oct 03, 2023)
2-86974160-G-A		not specified	Uncertain significance (Dec 07, 2021)
2-86974204-T-G		not specified	Uncertain significance (Jun 07, 2024)
2-86974217-C-T		not specified	Uncertain significance (Jul 05, 2022)
2-86974366-G-A		not specified	Uncertain significance (Feb 08, 2022)
2-86977863-C-G		not specified	Uncertain significance (Sep 27, 2022)
2-86984812-T-C			Likely benign (Mar 01, 2023)
2-86985576-G-T		not specified	Uncertain significance (Jul 05, 2023)
2-86985637-A-G		not specified	Uncertain significance (Feb 28, 2023)
2-86986541-G-C		not specified	Uncertain significance (Sep 01, 2021)
2-86986628-C-G		not specified	Uncertain significance (Sep 15, 2021)
2-86986725-C-T		not specified	Uncertain significance (Nov 08, 2022)
2-86986735-A-C		not specified	Uncertain significance (Aug 08, 2023)
2-86986771-C-T		not specified	Uncertain significance (Apr 28, 2022)
2-86986791-C-A		not specified	Uncertain significance (Dec 13, 2022)
2-86986828-C-T		not specified	Uncertain significance (Jul 12, 2022)
2-86986834-A-G		not specified	Uncertain significance (Mar 25, 2024)
2-86986926-G-C		not specified	Uncertain significance (Nov 18, 2022)
2-86986983-G-T		not specified	Uncertain significance (Jan 03, 2024)
2-86986990-G-A		not specified	Uncertain significance (Jan 30, 2024)
2-86987040-G-T		not specified	Likely benign (Jul 06, 2021)
2-86987055-C-T		not specified	Uncertain significance (Dec 27, 2022)
2-86987062-T-A		not specified	Uncertain significance (Dec 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGPD1	protein_coding	protein_coding	ENST00000559485	23	106029

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00701	0.778	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	22	52.2	0.421	0.00000231	11424
Missense in Polyphen		4	6.3055	0.63437		2049
Synonymous	1.23	11	17.6	0.626	7.54e-7	3244
Loss of Function	0.937	4	6.60	0.606	3.14e-7	1048

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	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: RNA transport - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• pHI: 0.252
• hipred: N
• hipred_score: 0.394

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.211

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: NLS-bearing protein import into nucleus;positive regulation of GTPase activity
• Cellular component: nucleus;nuclear pore;cytoplasm
• Molecular function: GTPase activator activity;Ran GTPase binding