RGPD4

protein-coding

RANBP2 like and GRIP domain containing 4, 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_182588.3

Inheritance

—

ClinVar variants

U:331B:37

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.61

Max pathogenic AF

—

Genomic locus

chr2:107,826,892-107,892,544

External References & Databases

Ensembl (ENSG00000196862)

Transcript & Mutation Effects

hg38 • Region Span ~65.7 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 RGPD4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 355

not providedTotal: 13

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182588.3. 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			1 clinvar	10 clinvar		11
missense			329 clinvar	27 clinvar		356
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	331	37	0	368

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182588.3	RefSeq	NP_872394.2	23	MANE Select
ENST00000408999.4	Ensembl	ENSP00000386810.4	23	MANE Select
XM_011511017.4	RefSeq	XP_011509319.1	22	Standard
XM_011511018.4	RefSeq	XP_011509320.1	22	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: ENST00000408999
Coding exons: 23
Length: 63910
Individuals with no LoFs: 124398
Homozygous LoFs: 20
Heterozygous LoFs: 1270
Defined: 125688
p: 0.00515

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-3.75	822	570	1.44	0.0000281	11352
Missense (PolyPhen)		256	172.31	1.4857		2910
Synonymous	-1.81	240	207	1.16	0.0000110	3249
Loss of Function	-3.89	76	47.2	1.61	0.00000240	1061

Population LoF Frequency

Population	CAF	p-value	Status
African	0.055	0.045	notable
Latino/Admixed American	0.0055	0.0052	notable
Ashkenazi Jewish	0.00030	0.00020	rare
East Asian	0.0046	0.0041	notable
Finnish	0.0012	0.0012	notable
European (Non-Finnish)	0.0019	0.0018	notable
South Asian	0.0024	0.0023	notable
Other	0.0031	0.0029	notable

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.225

Gene Damage Prediction

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