RANBP6

protein-coding

RAN binding protein 6, the group of Armadillo like helical domain containing

Gene summary

Predicted to enable nuclear import signal receptor activity and nuclear localization sequence binding activity. Predicted to be involved in protein import into nucleus. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_012416.4

Inheritance

—

ClinVar variants

U:144B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr9:6,011,025-6,015,625

External References & Databases

Ensembl (ENSG00000137040)

Transcript & Mutation Effects

hg38 • Region Span ~4.6 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 RANBP6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 141

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012416.4. 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			2 clinvar	2 clinvar		4
missense			141 clinvar	2 clinvar		143
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	144	4	0	148

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_012416.4	RefSeq	NP_036548.1	1	MANE Select
ENST00000259569.6	Ensembl	ENSP00000259569.5	1	MANE Select
NM_001243202.2	RefSeq	NP_001230131.1	2	Standard
NM_001243203.2	RefSeq	NP_001230132.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

NLS-bearing protein import into nucleus
ribosomal protein import into nucleus

Molecular Function

protein binding
nuclear localization sequence binding
protein transporter activity

Cellular Component

cytoplasm
nuclear membrane
nuclear periphery

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000259569
Coding exons: 1
Length: 4576
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	-0.333	594	572	1.04	0.0000274	7295
Missense (PolyPhen)		131	152.87	0.85693		1969
Synonymous	-2.85	260	208	1.25	0.00000990	2136
Loss of Function	3.40	13	34.6	0.376	0.00000171	461

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

Function: FUNCTION: May function in nuclear protein import as nuclear transport receptor.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.455
RVIS EVS: -1
RVIS percentile EVS: 8.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.471

Gene Damage Prediction

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