RGPD2

protein-coding

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

Gene summary

Predicted to enable SUMO transferase activity. Predicted to be involved in NLS-bearing protein import into nucleus and nuclear export. Predicted to be part of nuclear pore. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001078170.3

Inheritance

—

ClinVar variants

U:65B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr2:87,755,960-87,825,796

External References & Databases

Ensembl (ENSG00000185304)

Transcript & Mutation Effects

hg38 • Region Span ~69.8 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 RGPD2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 66

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001078170.3. 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				2 clinvar		2
missense			65 clinvar	1 clinvar		66
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	3	0	68

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001078170.3	RefSeq	NP_001071638.2	23	MANE Select
ENST00000398146.5	Ensembl	ENSP00000381214.3	23	MANE Select
NM_001393613.1	RefSeq	NP_001380542.1	23	Standard
ENST00000971290.1	Ensembl	ENSP00000641349.1	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: ENST00000398146
Coding exons: 23
Length: 229836
Individuals with no LoFs: 125245
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125257
p: 0.0000479

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0279	98	97.2	1.01	0.00000517	11468
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000063	0.000062	rare
South Asian	0	0.0	absent
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0629

Gene Damage Prediction

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