GPN2

GPN-loop GTPase 2, the group of GPN-loop GTPases

Basic information

Region (hg38): 1:26876132-26890283

Previous symbols: [ "ATPBD1B" ]

Links

ENSG00000142751 ∙ NCBI:54707 ∙ ∙ HGNC:25513 ∙ Uniprot:Q9H9Y4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GPN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPN2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in GPN2

This is a list of pathogenic ClinVar variants found in the GPN2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-26884185-T-C		not specified	Likely benign (Apr 23, 2024)
1-26884188-C-T		not specified	Uncertain significance (Aug 02, 2021)
1-26884196-A-G		not specified	Uncertain significance (Aug 04, 2021)
1-26884236-A-G		not specified	Uncertain significance (Jan 19, 2024)
1-26885981-T-C		not specified	Uncertain significance (Mar 10, 2025)
1-26886007-T-C		not specified	Uncertain significance (Mar 14, 2023)
1-26886035-C-T		not specified	Uncertain significance (Dec 23, 2024)
1-26886037-T-C		not specified	Uncertain significance (Oct 04, 2022)
1-26886038-T-C		Perrault syndrome 1	Uncertain significance (Apr 10, 2025)
1-26886049-T-C		not specified	Uncertain significance (Dec 21, 2022)
1-26886056-G-A		not specified	Uncertain significance (Aug 04, 2023)
1-26886060-G-C		not specified	Uncertain significance (Dec 12, 2023)
1-26886077-G-C		not specified	Uncertain significance (Jul 26, 2024)
1-26888987-C-T		not specified	Uncertain significance (Feb 09, 2025)
1-26888989-A-G		not specified	Uncertain significance (Feb 06, 2025)
1-26888998-A-G		not specified	Uncertain significance (Feb 13, 2023)
1-26889018-G-T		not specified	Uncertain significance (Dec 29, 2024)
1-26889047-C-T		not specified	Uncertain significance (Apr 26, 2023)
1-26889098-G-A		not specified	Uncertain significance (Jun 24, 2022)
1-26889703-C-T		not specified	Uncertain significance (Jul 13, 2021)
1-26889734-G-T		Perrault syndrome 1	Likely pathogenic (Apr 10, 2025)
1-26889787-C-T		not specified	Uncertain significance (Feb 10, 2023)
1-26889807-G-C		not specified	Uncertain significance (May 24, 2023)
1-26889808-C-A		not specified	Uncertain significance (May 24, 2023)
1-26889811-G-A		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPN2	protein_coding	protein_coding	ENST00000374135	5	14165

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0142	0.960	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.171	175	181	0.964	0.00000919	2007
Missense in Polyphen		44	58.057	0.75788		704
Synonymous	-1.02	92	80.3	1.15	0.00000423	633
Loss of Function	1.94	5	12.3	0.405	6.89e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000240	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.000165	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Small GTPase required for proper localization of RNA polymerase II and III (RNAPII and RNAPIII). May act at an RNAP assembly step prior to nuclear import. {ECO:0000250|UniProtKB:Q08726}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.567
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.141
• hipred: Y
• hipred_score: 0.507
• ghis: 0.591

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.235

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpn2

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function;GTPase activity;GTP binding