GPN3

protein-coding

GPN-loop GTPase 3, the group of GPN-loop GTPases

Gene summary

Predicted to enable GTPase activity. Involved in protein import into nucleus. Located in cytoplasm and nucleus. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ATPBD1C

MANE transcript

NM_016301.4

Inheritance

—

ClinVar variants

U:27

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr12:110,452,486-110,469,268

External References & Databases

Ensembl (ENSG00000111231)

Transcript & Mutation Effects

hg38 • Region Span ~16.8 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 GPN3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 24

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016301.4. 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			24 clinvar			24
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	27	0	0	27

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016301.4	RefSeq	NP_057385.3	8	MANE Select
ENST00000228827.8	Ensembl	ENSP00000228827.3	8	MANE Select
NM_001164372.2	RefSeq	NP_001157844.1	8	Standard
NM_001164373.2	RefSeq	NP_001157845.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

GTPase activity
protein binding
GTP binding

Cellular Component

protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000543199
Coding exons: 8
Length: 16785
Individuals with no LoFs: 125640
Homozygous LoFs: 0
Heterozygous LoFs: 108
Defined: 125748
p: 0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.989	141	178	0.791	0.00000907	2156
Missense (PolyPhen)		32	50.229	0.63708		650
Synonymous	0.700	59	66.2	0.891	0.00000365	562
Loss of Function	1.33	13	19.3	0.672	0.00000106	213

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0.0074	0.0075	notable
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.000036	0.000033	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Small GTPase required for proper localization of RNA polymerase II (RNAPII). May act at an RNAP assembly step prior to nuclear import. {ECO:0000269|PubMed:21768307}.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.885
RVIS EVS: -0.38
RVIS percentile EVS: 27.69

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.955

Gene Damage Prediction

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