RGPD2

RANBP2 like and GRIP domain containing 2, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 2:87755960-87825796

Links

ENSG00000185304 ∙ NCBI:729857 ∙ OMIM:612705 ∙ HGNC:32415 ∙ Uniprot:P0DJD1 ∙ 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 RGPD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGPD2 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				1		1
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	2	0

Variants in RGPD2

This is a list of pathogenic ClinVar variants found in the RGPD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-87772192-C-T		not specified	Uncertain significance (Jun 22, 2021)
2-87772232-C-T		not specified	Uncertain significance (May 13, 2024)
2-87772238-G-A		not specified	Uncertain significance (Oct 29, 2021)
2-87782504-T-A		not specified	Uncertain significance (Mar 01, 2023)
2-87782520-C-T		not specified	Uncertain significance (Jun 29, 2022)
2-87782525-A-G		not specified	Uncertain significance (Jun 29, 2022)
2-87782669-A-T		not specified	Uncertain significance (Jun 06, 2023)
2-87782703-T-C		not specified	Likely benign (Sep 25, 2023)
2-87782738-C-T		not specified	Uncertain significance (Jun 11, 2021)
2-87782867-C-T		not specified	Uncertain significance (May 16, 2022)
2-87782868-G-A		not specified	Uncertain significance (Aug 11, 2022)
2-87782888-T-C		not specified	Uncertain significance (Jun 07, 2023)
2-87782907-C-G		not specified	Uncertain significance (Oct 10, 2023)
2-87782913-T-C		not specified	Uncertain significance (Apr 09, 2024)
2-87782915-C-T		not specified	Uncertain significance (Feb 28, 2023)
2-87782945-T-A		not specified	Uncertain significance (Jan 17, 2024)
2-87782967-T-C		not specified	Uncertain significance (Dec 26, 2023)
2-87783002-C-G		not specified	Uncertain significance (Aug 12, 2021)
2-87783036-C-A		not specified	Uncertain significance (Nov 17, 2022)
2-87783128-G-A		not specified	Uncertain significance (Mar 16, 2022)
2-87783146-C-T		not specified	Uncertain significance (May 02, 2024)
2-87783197-C-T		not specified	Uncertain significance (Feb 15, 2023)
2-87783225-T-C		not specified	Uncertain significance (Feb 23, 2023)
2-87784158-C-G		not specified	Uncertain significance (Mar 31, 2023)
2-87784203-C-T		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGPD2	protein_coding	protein_coding	ENST00000398146	23	229836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00138	0.678	125245	0	12	125257	0.0000479

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0279	98	97.2	1.01	0.00000517	11468
Missense in Polyphen		20	17.243	1.1599		2495
Synonymous	0.725	31	36.6	0.847	0.00000211	3266
Loss of Function	0.709	5	7.03	0.711	2.96e-7	1062

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000634	0.0000618
Middle Eastern	0.000168	0.000163
South Asian	0.00	0.00
Other	0.000180	0.000164

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.143

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0629

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;positive regulation of GTPase activity
• Cellular component: nucleus;nuclear pore;cytoplasm
• Molecular function: GTPase activator activity;Ran GTPase binding