GSPT2

G1 to S phase transition 2, the group of SURF complex

Basic information

Region (hg38): X:51743442-51746232

Links

ENSG00000189369 ∙ NCBI:23708 ∙ OMIM:300418 ∙ HGNC:4622 ∙ Uniprot:Q8IYD1 ∙ 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 GSPT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSPT2 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			1	2	1	4
missense			12		1	13
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	2

Variants in GSPT2

This is a list of pathogenic ClinVar variants found in the GSPT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-51743672-G-A		not specified	Uncertain significance (Jun 27, 2022)
X-51743694-C-T			Benign (Dec 31, 2019)
X-51743814-T-C		not specified	Uncertain significance (Jan 24, 2023)
X-51743853-C-T		not specified	Uncertain significance (Mar 18, 2024)
X-51743886-G-A		not specified	Uncertain significance (Jan 23, 2023)
X-51743896-T-G		not specified	Uncertain significance (Apr 07, 2022)
X-51743916-G-T		not specified	Uncertain significance (Feb 06, 2023)
X-51743942-C-CG			Uncertain significance (Oct 22, 2013)
X-51744014-A-G		GSPT2-related disorder	Uncertain significance (May 27, 2023)
X-51744049-G-A			Benign (Dec 31, 2019)
X-51744104-G-A		not specified	Uncertain significance (Aug 11, 2022)
X-51744293-A-G		not specified	Uncertain significance (Dec 03, 2021)
X-51744647-G-A		Delayed speech and language development;Autism;Seizure	Pathogenic (-)
X-51744714-A-T		not specified	Uncertain significance (Aug 08, 2022)
X-51744784-C-T			Uncertain significance (Mar 14, 2014)
X-51744836-T-G		not specified	Uncertain significance (Feb 22, 2023)
X-51745085-C-T		not specified	Uncertain significance (Aug 15, 2023)
X-51745147-C-T			Likely benign (Sep 01, 2022)
X-51745186-C-T			Likely benign (Dec 01, 2022)
X-51745367-G-A		not specified	Uncertain significance (Jun 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSPT2	protein_coding	protein_coding	ENST00000340438	1	2844

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0168	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.49	133	242	0.550	0.0000174	4121
Missense in Polyphen		16	79.538	0.20116		1382
Synonymous	0.637	86	93.9	0.916	0.00000709	1247
Loss of Function	3.27	0	12.4	0.00	9.30e-7	248

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)	0.00	0.00
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. May play a role as a potent stimulator of the release factor activity of ETF1. Exhibits GTPase activity, which is ribosome- and ETF1-dependent. May play a role in cell cycle progression. 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. {ECO:0000269|PubMed:11524954, ECO:0000269|PubMed:15987998, ECO:0000269|PubMed:17562865}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);Translation Factors;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: 0.116

Intolerance Scores

• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.464
• hipred: Y
• hipred_score: 0.771
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gspt2

Gene ontology

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