GTSE1

G2 and S-phase expressed 1

Basic information

Region (hg38): 22:46296870-46330810

Links

ENSG00000075218 ∙ NCBI:51512 ∙ OMIM:607477 ∙ HGNC:13698 ∙ Uniprot:Q9NYZ3 ∙ 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 GTSE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTSE1 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				2	2	4
missense			48	10	6	64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	48	12	8

Variants in GTSE1

This is a list of pathogenic ClinVar variants found in the GTSE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-46297419-C-T		not specified	Uncertain significance (Nov 29, 2021)
22-46297434-G-A		not specified	Uncertain significance (Nov 22, 2023)
22-46297440-C-G			Benign (Aug 11, 2018)
22-46297458-A-G		not specified	Uncertain significance (May 10, 2022)
22-46297467-C-G		not specified	Uncertain significance (Aug 28, 2023)
22-46308142-C-T			Benign (Jul 15, 2018)
22-46308470-A-G		not specified	Uncertain significance (Dec 20, 2023)
22-46308482-G-A		not specified	Uncertain significance (Mar 15, 2024)
22-46308502-A-C		not specified	Uncertain significance (Dec 17, 2023)
22-46308504-T-C		not specified	Uncertain significance (Oct 26, 2022)
22-46308521-A-G		not specified	Uncertain significance (May 30, 2023)
22-46308529-C-G		not specified	Uncertain significance (Dec 22, 2023)
22-46308531-G-A		not specified	Uncertain significance (Jul 19, 2022)
22-46308569-C-T		not specified	Uncertain significance (Apr 16, 2024)
22-46308644-A-G		not specified	Uncertain significance (May 16, 2023)
22-46308658-G-A			Benign (Jul 23, 2018)
22-46308675-C-T		not specified	Uncertain significance (Jul 26, 2022)
22-46308683-C-T			Benign (Jul 15, 2018)
22-46308713-G-A		not specified	Uncertain significance (May 14, 2024)
22-46308713-G-T			Benign (Oct 17, 2017)
22-46308717-G-A		not specified	Uncertain significance (Jun 11, 2024)
22-46308720-A-T		not specified	Uncertain significance (Dec 27, 2023)
22-46308730-C-G			Benign/Likely benign (Nov 01, 2022)
22-46308744-C-T		not specified	Uncertain significance (Nov 10, 2022)
22-46308764-G-T		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTSE1	protein_coding	protein_coding	ENST00000454366	11	34070

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000270	0.997	125692	0	56	125748	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0586	444	447	0.992	0.0000280	4737
Missense in Polyphen		120	119.78	1.0019		1366
Synonymous	-0.624	195	184	1.06	0.0000124	1599
Loss of Function	2.59	12	26.3	0.455	0.00000127	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000452	0.000447
Ashkenazi Jewish	0.00	0.00
East Asian	0.000653	0.000653
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000206	0.000202
Middle Eastern	0.000653	0.000653
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in p53-induced cell cycle arrest in G2/M phase by interfering with microtubule rearrangements that are required to enter mitosis. Overexpression delays G2/M phase progression.
• Pathway: p53 signaling pathway - Homo sapiens (human);G2/M Checkpoints;Cell Cycle Checkpoints;The role of GTSE1 in G2/M progression after G2 checkpoint;G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.0686

Intolerance Scores

• rvis_EVS: 0.85
• rvis_percentile_EVS: 88.51

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.145
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtse1

Gene ontology

• Biological process: DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;microtubule-based process;positive regulation of cell migration;positive regulation of protein export from nucleus;protein stabilization;positive regulation of protein localization to nucleus;regulation of cell cycle G2/M phase transition
• Cellular component: nucleoplasm;cytosol;cytoplasmic microtubule;membrane
• Molecular function: molecular_function;protein binding