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.

• not_specified (54 variants)
• not_provided (2 variants)

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. These statistics are base on transcript: NM_001078170.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			53	1		54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	3	0

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