GSPT1

G1 to S phase transition 1, the group of SURF complex

Basic information

Region (hg38): 16:11868128-11916082

Links

ENSG00000103342 ∙ NCBI:2935 ∙ OMIM:139259 ∙ HGNC:4621 ∙ Uniprot:P15170 ∙ 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 GSPT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSPT1 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			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	1	0

Variants in GSPT1

This is a list of pathogenic ClinVar variants found in the GSPT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-11873124-C-T		not specified	Uncertain significance (Aug 01, 2024)
16-11873133-G-A		not specified	Uncertain significance (Dec 20, 2023)
16-11875857-G-C		not specified	Uncertain significance (Aug 20, 2023)
16-11875880-C-T		not specified	Uncertain significance (Aug 01, 2024)
16-11876132-T-C		not specified	Uncertain significance (Sep 07, 2022)
16-11876174-A-G		not specified	Uncertain significance (Jul 22, 2024)
16-11877414-T-C		not specified	Uncertain significance (Nov 21, 2022)
16-11883080-C-T		not specified	Uncertain significance (Sep 04, 2024)
16-11886558-T-C		not specified	Uncertain significance (Mar 31, 2024)
16-11886782-A-T		not specified	Uncertain significance (Aug 21, 2024)
16-11886832-G-T		not specified	Uncertain significance (Aug 28, 2024)
16-11887682-C-T		not specified	Uncertain significance (Apr 25, 2023)
16-11891110-G-A		not specified	Uncertain significance (Sep 28, 2022)
16-11891126-T-C		not specified	Uncertain significance (Mar 07, 2024)
16-11896591-C-G		not specified	Uncertain significance (Dec 15, 2023)
16-11896611-G-A		not specified	Uncertain significance (Jan 16, 2024)
16-11896620-A-G		not specified	Uncertain significance (Jan 04, 2022)
16-11896639-T-C		not specified	Uncertain significance (May 08, 2024)
16-11896676-C-G		not specified	Uncertain significance (May 28, 2024)
16-11896677-T-C		not specified	Uncertain significance (May 25, 2022)
16-11896699-A-T		not specified	Uncertain significance (Oct 25, 2022)
16-11896705-C-G		not specified	Uncertain significance (Jul 06, 2022)
16-11896708-C-A		not specified	Uncertain significance (Feb 15, 2023)
16-11896759-G-T		not specified	Uncertain significance (Apr 06, 2023)
16-11897876-T-C		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSPT1	protein_coding	protein_coding	ENST00000434724	15	47955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000142	118715	0	1	118716	0.00000421

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.32	152	319	0.477	0.0000157	4117
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000932	0.00000932
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);Eukaryotic Translation Termination;Translation;Metabolism of proteins;Metabolism of RNA;Nonsense-Mediated Decay (NMD);Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC);Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) (Consensus)

Recessive Scores

• pRec: 0.148

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.617
• hipred: Y
• hipred_score: 0.701
• ghis: 0.419

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gspt1

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translational termination;translation;protein methylation
• Cellular component: cytosol;translation release factor complex
• Molecular function: RNA binding;translation release factor activity;GTPase activity;protein binding;GTP binding