GPN3

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

Basic information

Region (hg38): 12:110452485-110469268

Previous symbols: [ "ATPBD1C" ]

Links

ENSG00000111231 ∙ NCBI:51184 ∙ ∙ HGNC:30186 ∙ Uniprot:Q9UHW5 ∙ 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 GPN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPN3 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in GPN3

This is a list of pathogenic ClinVar variants found in the GPN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-110453796-G-A		not specified	Uncertain significance (Sep 30, 2021)
12-110453825-T-C		not specified	Uncertain significance (Dec 19, 2022)
12-110455848-A-G		not specified	Uncertain significance (May 27, 2022)
12-110455860-G-A		not specified	Uncertain significance (Aug 28, 2023)
12-110455918-T-C		not specified	Uncertain significance (Aug 28, 2023)
12-110457525-C-T		not specified	Uncertain significance (Dec 26, 2023)
12-110457595-T-C		not specified	Uncertain significance (Sep 17, 2021)
12-110457605-C-G		not specified	Uncertain significance (Mar 11, 2024)
12-110459811-C-T		not specified	Uncertain significance (Feb 17, 2022)
12-110465199-T-C		not specified	Uncertain significance (Apr 07, 2023)
12-110468885-C-G		not specified	Uncertain significance (Oct 21, 2021)
12-110468906-C-G		not specified	Uncertain significance (Oct 06, 2021)
12-110468909-G-A		not specified	Uncertain significance (Mar 25, 2024)
12-110468934-G-T		not specified	Uncertain significance (Feb 22, 2024)
12-110468988-C-G		not specified	Uncertain significance (Dec 26, 2023)
12-110469000-C-T		not specified	Uncertain significance (Jul 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPN3	protein_coding	protein_coding	ENST00000543199	8	16785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.90e-7	0.768	125640	0	108	125748	0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.989	141	178	0.791	0.00000907	2156
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000238	0.000238
Ashkenazi Jewish	0.00744	0.00747
East Asian	0.000164	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000164	0.000163
South Asian	0.0000359	0.0000327
Other	0.000818	0.000815

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.510
• hipred: N
• hipred_score: 0.352
• ghis: 0.637

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpn3

Gene ontology

• Cellular component: protein-containing complex
• Molecular function: GTPase activity;protein binding;GTP binding