GPN1

GPN-loop GTPase 1, the group of GPN-loop GTPases

Basic information

Region (hg38): 2:27628247-27651511

Previous symbols: [ "XAB1" ]

Links

ENSG00000198522 ∙ NCBI:11321 ∙ OMIM:611479 ∙ HGNC:17030 ∙ Uniprot:Q9HCN4 ∙ 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 GPN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPN1 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	27	0	0

Variants in GPN1

This is a list of pathogenic ClinVar variants found in the GPN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27628454-C-T		not specified	Likely benign (May 28, 2024)
2-27628474-G-C		not specified	Uncertain significance (Dec 05, 2024)
2-27628487-G-C		not specified	Uncertain significance (Nov 18, 2022)
2-27628526-G-C		not specified	Uncertain significance (Nov 07, 2024)
2-27628529-C-T		not specified	Likely benign (Jun 27, 2022)
2-27628565-G-C		not specified	Uncertain significance (Jan 22, 2024)
2-27628613-G-T		not specified	Uncertain significance (Nov 25, 2024)
2-27628627-T-G		not specified	Likely benign (May 25, 2022)
2-27628658-G-C		not specified	Uncertain significance (Dec 14, 2023)
2-27628663-G-A		not specified	Uncertain significance (Apr 29, 2024)
2-27628693-C-T		not specified	Uncertain significance (Sep 22, 2023)
2-27629042-G-A		not specified	Uncertain significance (Dec 15, 2023)
2-27629081-C-T		not specified	Uncertain significance (Aug 04, 2023)
2-27629086-C-T		not specified	Uncertain significance (Nov 14, 2024)
2-27629104-C-T		not specified	Uncertain significance (Sep 18, 2024)
2-27629108-G-T		not specified	Uncertain significance (Nov 14, 2023)
2-27629865-A-G		not specified	Uncertain significance (Feb 22, 2023)
2-27629877-C-T		not specified	Uncertain significance (Dec 02, 2024)
2-27629878-A-G		not specified	Uncertain significance (Dec 04, 2024)
2-27629944-C-T		not specified	Uncertain significance (Aug 01, 2022)
2-27631033-G-A		not specified	Uncertain significance (Mar 01, 2023)
2-27632633-G-T		not specified	Uncertain significance (Nov 13, 2024)
2-27635198-C-T		not specified	Uncertain significance (Apr 04, 2024)
2-27638239-T-C		not specified	Uncertain significance (Aug 27, 2024)
2-27638976-G-A		not specified	Uncertain significance (May 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPN1	protein_coding	protein_coding	ENST00000264718	14	23262

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000558	0.994	125723	0	24	125747	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.436	201	219	0.917	0.0000110	2544
Missense in Polyphen		50	68.256	0.73253		815
Synonymous	-1.06	92	79.9	1.15	0.00000418	730
Loss of Function	2.44	11	23.9	0.461	0.00000114	285

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000793	0.0000791
Middle Eastern	0.000273	0.000272
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Small GTPase required for proper nuclear import of RNA polymerase II (RNAPII) (PubMed:20855544, PubMed:21768307). May act at an RNAP assembly step prior to nuclear import (PubMed:21768307). Forms an interface between the RNA polymerase II enzyme and chaperone/scaffolding proteins, suggesting that it is required to connect RNA polymerase II to regulators of protein complex formation (PubMed:17643375). May be involved in nuclear localization of XPA (PubMed:11058119). {ECO:0000269|PubMed:17643375, ECO:0000269|PubMed:20855544, ECO:0000269|PubMed:21768307, ECO:0000305|PubMed:11058119}.

Recessive Scores

• pRec: 0.0938

Intolerance Scores

• loftool: 0.488
• rvis_EVS: 0
• rvis_percentile_EVS: 53.85

Haploinsufficiency Scores

• pHI: 0.0809
• hipred: Y
• hipred_score: 0.651
• ghis: 0.593

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.358

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpn1

Gene ontology

• Cellular component: nucleoplasm;mitochondrion;cytosol
• Molecular function: GTPase activity;protein binding;GTP binding