RGPD3

protein-coding

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

Gene summary

This gene is located in a cluster of Ran-binding protein related genes on chromosome 2 which arose through duplication in primates. The encoded protein contains an N-terminal TPR (tetratricopeptide repeat) domain, two Ran-binding domains, and a C-terminal GRIP domain (golgin-97, RanBP2alpha, Imh1p and p230/golgin-245) domain. [provided by RefSeq, Sep 2011]

MANE transcript

NM_001144013.2

Inheritance

—

ClinVar variants

U:364B:25

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.4

Max pathogenic AF

—

Genomic locus

chr2:106,391,290-106,468,413

External References & Databases

Ensembl (ENSG00000153165)

Transcript & Mutation Effects

hg38 • Region Span ~77.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RGPD3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 376

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001144013.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	5 clinvar		6
missense			360 clinvar	20 clinvar		380
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	364	25	0	389

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001144013.2	RefSeq	NP_001137485.1	23	MANE Select
ENST00000409886.4	Ensembl	ENSP00000386588.4	23	MANE Select
ENST00000304514.11	Ensembl	ENSP00000303659.8	23	Standard
ENST00000304514.12	Ensembl	ENSP00000303659.8	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

RNA transport - Homo sapiens (human)

Biological Process

NLS-bearing protein import into nucleus
positive regulation of GTPase activity

Molecular Function

GTPase activator activity
Ran GTPase binding

Cellular Component

nucleus
nuclear pore
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409886
Coding exons: 23
Length: 63387
Individuals with no LoFs: 123389
Homozygous LoFs: 72
Heterozygous LoFs: 2250
Defined: 125711
p: 0.00928

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-3.42	772	547	1.41	0.0000274	11240
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.013	0.011	notable
Latino/Admixed American	0.030	0.025	notable
Ashkenazi Jewish	0.00071	0.00069	rare
East Asian	0.0045	0.0044	notable
Finnish	0.0026	0.0025	notable
European (Non-Finnish)	0.0075	0.0073	notable
South Asian	0.010	0.0086	notable
Other	0.0083	0.0079	notable

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0269

Gene Damage Prediction

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