RGPD6

protein-coding

RANBP2 like and GRIP domain containing 6, 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 located in cytoplasm. Predicted to be part of nuclear pore. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001123363.4

Inheritance

—

ClinVar variants

U:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr2:110,513,802-110,610,840

External References & Databases

Ensembl (ENSG00000183054)

Transcript & Mutation Effects

hg38 • Region Span ~97.0 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 RGPD6 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001123363.4. 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						0
missense			5 clinvar			5
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	5	0	0	5

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001123363.4	RefSeq	NP_001116835.1	23	MANE Select
ENST00000329516.8	Ensembl	ENSP00000330842.3	23	MANE Select
NM_001037866.2	RefSeq	NP_001032955.1	19	Standard
NM_001384362.1	RefSeq	NP_001371291.1	17	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000329516
Coding exons: 23
Length: 63374
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.541	3	7.03	0.426	3.21e-7	11598
Missense (PolyPhen)		0	2.3317	0		3549
Synonymous	1.53	0	3.78	0.00	1.77e-7	3362
Loss of Function	0.924	0	0.995	0.00	4.47e-8	1080

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): E
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.143

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low