GSPT1
protein-codingG1 to S phase transition 1, the group of SURF complex
Gene summary
Enables GTPase activity and translation release factor activity. Involved in regulation of translational termination and translational termination. Acts upstream of or within protein methylation. Part of translation release factor complex. Is active in cytosolic ribosome. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~48.0 kbGenCC 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 GSPT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002094.4. 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 | 1 | 1 | ||||
| missense | 74 | 1 | 75 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 79 | 1 | 0 | 80 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002085.3 | 15 | MANE Select | |
| Ensembl | ENSP00000398131.2 | 15 | MANE Select | |
| RefSeq | NP_001123478.2 | 15 | Standard | |
| RefSeq | NP_001123479.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- mRNA surveillance pathway - Homo sapiens (human)
- Eukaryotic Translation Termination
- Translation
- Metabolism of proteins
- Metabolism of RNA
Biological Process
- G1/S transition of mitotic cell cycle
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
- cytoplasmic translational termination
- translation
- protein methylation
Molecular Function
- RNA binding
- translation release factor activity
- GTPase activity
- protein binding
- GTP binding
Cellular Component
- cytosol
- translation release factor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000434724
- Coding exons
- 15
- Length
- 47955
- Individuals with no LoFs
- 118715
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 118716
- p
- 0.00000421
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.32 | 152 | 319 | 0.477 | 0.0000157 | 4117 |
| Missense (PolyPhen) | 18 | 99.638 | 0.18065 | 1317 | ||
| Synonymous | -0.246 | 115 | 112 | 1.03 | 0.00000586 | 1194 |
| Loss of Function | 4.88 | 1 | 29.7 | 0.0337 | 0.00000144 | 404 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000093 | 0.0000093 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in translation termination in response to the termination codons UAA, UAG and UGA. Stimulates the activity of ERF1. Involved in regulation of mammalian cell growth. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.;
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- RVIS EVS
- -0.03
- RVIS percentile EVS
- 51.4
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.989
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |