RGPD8

RANBP2 like and GRIP domain containing 8, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 2:112368369-112434488

Previous symbols: [ "RANBP2L1" ]

Links

ENSG00000169629 ∙ NCBI:727851 ∙ OMIM:602752 ∙ HGNC:9849 ∙ Uniprot:O14715 ∙ 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 RGPD8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGPD8 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				3		3
missense			73	10	1	84
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	73	13	1

Variants in RGPD8

This is a list of pathogenic ClinVar variants found in the RGPD8 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-112370196-A-G			Likely benign (Jan 01, 2023)
2-112378125-G-A		not specified	Uncertain significance (Feb 14, 2023)
2-112378218-G-C		not specified	Uncertain significance (Feb 15, 2023)
2-112378247-T-C		not specified	Uncertain significance (Apr 07, 2022)
2-112380827-A-C		not specified	Uncertain significance (Dec 21, 2023)
2-112380828-A-G		not specified	Uncertain significance (May 23, 2024)
2-112380867-C-T		not specified	Uncertain significance (Jul 14, 2021)
2-112380948-T-C		not specified	Uncertain significance (Sep 14, 2023)
2-112388039-T-C		not specified	Uncertain significance (Oct 26, 2022)
2-112388078-A-C		not specified	Uncertain significance (Jun 11, 2024)
2-112388083-G-A		not specified	Likely benign (Oct 12, 2021)
2-112388101-C-T		not specified	Uncertain significance (Nov 16, 2022)
2-112388104-T-A		not specified	Uncertain significance (May 24, 2023)
2-112388152-G-C		not specified	Uncertain significance (May 01, 2023)
2-112388201-T-C		not specified	Uncertain significance (Jun 05, 2023)
2-112388219-G-A		not specified	Uncertain significance (Jan 08, 2024)
2-112388229-A-C		not specified	Uncertain significance (Nov 28, 2023)
2-112388315-A-C		not specified	Uncertain significance (Apr 28, 2022)
2-112388401-G-A		not specified	Uncertain significance (Feb 07, 2023)
2-112388429-C-G		not specified	Likely benign (Aug 18, 2023)
2-112388509-C-T		not specified	Uncertain significance (Feb 07, 2023)
2-112388533-G-T		not specified	Uncertain significance (Aug 08, 2023)
2-112388539-T-A		not specified	Uncertain significance (Jun 24, 2022)
2-112388555-T-C		not specified	Uncertain significance (Oct 20, 2023)
2-112388581-G-A		not specified	Uncertain significance (Aug 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGPD8	protein_coding	protein_coding	ENST00000302558	23	64397

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.93e-7	0.770	125366	25	179	125570	0.000813

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.466	247	227	1.09	0.0000113	11391
Missense in Polyphen		53	49.5	1.0707		3832
Synonymous	-0.528	93	86.7	1.07	0.00000439	3295
Loss of Function	1.34	13	19.4	0.672	9.91e-7	1070

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000345	0.000338
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00469	0.00412
European (Non-Finnish)	0.000702	0.000591
Middle Eastern	0.000110	0.000109
South Asian	0.00140	0.00108
Other	0.000706	0.000489

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0426

Gene Damage Prediction

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

Gene ontology

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