RGPD3

RANBP2 like and GRIP domain containing 3, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 2:106391290-106468413

Links

ENSG00000153165 ∙ NCBI:653489 ∙ OMIM:612706 ∙ HGNC:32416 ∙ Uniprot:A6NKT7 ∙ 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 RGPD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGPD3 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				4		4
missense			146	15		161
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	146	19	0

Variants in RGPD3

This is a list of pathogenic ClinVar variants found in the RGPD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-106413095-G-A		not specified	Uncertain significance (Jun 18, 2021)
2-106413119-A-G		not specified	Likely benign (Nov 16, 2021)
2-106413137-G-A		not specified	Uncertain significance (Feb 22, 2023)
2-106413143-A-G		not specified	Uncertain significance (Nov 18, 2023)
2-106413270-T-C		not specified	Uncertain significance (May 10, 2024)
2-106415860-T-C		not specified	Uncertain significance (Aug 28, 2021)
2-106415863-A-G		not specified	Uncertain significance (Jan 06, 2023)
2-106415878-G-A		not specified	Uncertain significance (Nov 09, 2021)
2-106415894-G-A		not specified	Uncertain significance (Jan 23, 2023)
2-106415903-C-T		not specified	Uncertain significance (Apr 09, 2024)
2-106415971-G-A		not specified	Uncertain significance (Aug 09, 2021)
2-106415974-T-C		not specified	Uncertain significance (Jan 23, 2024)
2-106415975-A-T		not specified	Uncertain significance (Oct 22, 2021)
2-106415978-A-G		not specified	Uncertain significance (Sep 29, 2022)
2-106423081-T-G		not specified	Uncertain significance (Nov 09, 2022)
2-106423087-G-A		not specified	Uncertain significance (Jun 02, 2024)
2-106423130-A-C		not specified	Uncertain significance (Feb 28, 2024)
2-106423139-T-C		not specified	Uncertain significance (Jun 22, 2021)
2-106423140-A-T		not specified	Uncertain significance (Dec 19, 2023)
2-106423153-G-A		not specified	Uncertain significance (May 02, 2024)
2-106423154-A-G		not specified	Uncertain significance (Dec 02, 2022)
2-106423208-A-C		not specified	Uncertain significance (Dec 21, 2023)
2-106423209-A-T		not specified	Uncertain significance (Feb 14, 2023)
2-106423210-C-G		not specified	Uncertain significance (Jan 31, 2023)
2-106423289-A-G		not specified	Uncertain significance (Mar 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGPD3	protein_coding	protein_coding	ENST00000409886	23	63387

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.46e-50	2.73e-11	123389	72	2250	125711	0.00928

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.42	772	547	1.41	0.0000274	11240
Missense in Polyphen		166	117.88	1.4082		2380
Synonymous	-2.65	254	206	1.23	0.0000115	3245
Loss of Function	-2.53	65	46.4	1.40	0.00000235	1057

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0428	0.0416
Ashkenazi Jewish	0.000715	0.000695
East Asian	0.00447	0.00436
Finnish	0.00265	0.00254
European (Non-Finnish)	0.00748	0.00726
Middle Eastern	0.00447	0.00436
South Asian	0.0100	0.00856
Other	0.00830	0.00785

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: 0.0269

Gene Damage Prediction

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

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