RGPD4

RANBP2 like and GRIP domain containing 4, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 2:107826892-107892544

Links

ENSG00000196862 ∙ NCBI:285190 ∙ OMIM:612707 ∙ HGNC:32417 ∙ Uniprot:Q7Z3J3 ∙ 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 RGPD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGPD4 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				5	1	6
missense			131	13		144
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	131	18	1

Variants in RGPD4

This is a list of pathogenic ClinVar variants found in the RGPD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-107827032-T-C		not specified	Uncertain significance (Feb 01, 2023)
2-107827035-G-C		not specified	Uncertain significance (Nov 07, 2022)
2-107827042-G-A		not specified	Uncertain significance (Oct 05, 2023)
2-107827042-G-C		not specified	Uncertain significance (May 31, 2023)
2-107827053-T-C		not specified	Uncertain significance (Jul 26, 2022)
2-107827081-G-C		not specified	Uncertain significance (Jul 20, 2021)
2-107836609-C-T		not specified	Likely benign (Jul 19, 2023)
2-107838834-C-T		not specified	Uncertain significance (Mar 07, 2024)
2-107838861-C-A		not specified	Uncertain significance (Jul 05, 2023)
2-107838947-G-A		not specified	Uncertain significance (Nov 23, 2021)
2-107843163-G-A		not specified	Likely benign (Nov 29, 2021)
2-107843195-C-T		not specified	Uncertain significance (Feb 27, 2023)
2-107843222-G-T		not specified	Uncertain significance (Jul 06, 2021)
2-107843625-G-C		not specified	Uncertain significance (Oct 26, 2021)
2-107843660-G-A		not specified	Likely benign (Jun 21, 2021)
2-107854577-T-G		not specified	Uncertain significance (Aug 04, 2023)
2-107854602-A-G		not specified	Uncertain significance (Apr 12, 2022)
2-107854629-G-A		not specified	Uncertain significance (Sep 23, 2023)
2-107859114-G-A		not specified	Uncertain significance (Apr 26, 2023)
2-107859134-G-T		not specified	Uncertain significance (May 08, 2024)
2-107859153-C-G		not specified	Likely benign (Apr 25, 2022)
2-107859172-G-A			not provided (-)
2-107859201-G-A		not specified	Uncertain significance (Jun 03, 2024)
2-107859210-T-C		not specified	Uncertain significance (Feb 27, 2023)
2-107859250-G-C		not specified	Uncertain significance (Mar 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGPD4	protein_coding	protein_coding	ENST00000408999	23	63910

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.53e-62	8.87e-15	124398	20	1270	125688	0.00515

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.75	822	570	1.44	0.0000281	11352
Missense in Polyphen		256	172.31	1.4857		2910
Synonymous	-1.81	240	207	1.16	0.0000110	3249
Loss of Function	-3.89	76	47.2	1.61	0.00000240	1061

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0606	0.0502
Ashkenazi Jewish	0.000301	0.000198
East Asian	0.00464	0.00414
Finnish	0.00124	0.00116
European (Non-Finnish)	0.00190	0.00184
Middle Eastern	0.00464	0.00414
South Asian	0.00239	0.00226
Other	0.00310	0.00294

dbNSFP

Source: dbNSFP

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

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.225

Gene Damage Prediction

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

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