GTSE1

protein-coding

G2 and S-phase expressed 1

Gene summary

The protein encoded by this gene is only expressed in the S and G2 phases of the cell cycle, where it colocalizes with cytoplasmic tubulin and microtubules. In response to DNA damage, the encoded protein accumulates in the nucleus and binds the tumor suppressor protein p53, shuttling it out of the nucleus and repressing its ability to induce apoptosis. [provided by RefSeq, Jul 2008]

MANE transcript

NM_016426.7

Inheritance

—

ClinVar variants

U:125B:33

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr22:46,296,870-46,330,810

External References & Databases

Ensembl (ENSG00000075218)

Transcript & Mutation Effects

hg38 • Region Span ~33.9 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 GTSE1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 141

not providedTotal: 13

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016426.7. 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			2 clinvar	3 clinvar	2 clinvar	7
missense			122 clinvar	22 clinvar	6 clinvar	150
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	125	25	8	158

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016426.7	RefSeq	NP_057510.5	11	MANE Select
ENST00000454366.2	Ensembl	ENSP00000415430.1	11	MANE Select
ENST00000905433.1	Ensembl	ENSP00000575492.1	10	Standard
ENST00000905433.2	Ensembl	ENSP00000575492.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

Molecular Function

molecular_function
protein binding

Cellular Component

nucleoplasm
cytosol
cytoplasmic microtubule
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000454366
Coding exons: 11
Length: 34070
Individuals with no LoFs: 125692
Homozygous LoFs: 0
Heterozygous LoFs: 56
Defined: 125748
p: 0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0586	444	447	0.992	0.0000280	4737
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00065	0.00065	rare
Finnish	0.00032	0.00032	rare
European (Non-Finnish)	0.00021	0.00020	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.0686

Intolerance Scores

RVIS EVS: 0.85
RVIS percentile EVS: 88.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.148

Gene Damage Prediction

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