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

intellectual disability (Strong), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GSPT2 gene.

not_specified (30 variants)
not_provided (6 variants)
Autism (1 variants)
Seizure (1 variants)
Delayed_speech_and_language_development (1 variants)
GSPT2-related_disorder (1 variants)

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. These statistics are base on transcript: NM_000018094.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar	1 clinvar	4
missense	1 clinvar		31 clinvar		1 clinvar	33
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	1	0	33	2	2

Highest pathogenic variant AF is 0.00000182285

Loading clinvar variants...

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

loftool
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
Phenotype

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