PSTK

phosphoseryl-tRNA kinase

Basic information

Region (hg38): 10:122954381-122997513

Previous symbols: [ "C10orf89" ]

Links

ENSG00000179988 ∙ NCBI:118672 ∙ OMIM:611310 ∙ HGNC:28578 ∙ Uniprot:Q8IV42 ∙ 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 PSTK gene.

Variants pathogenicity by type

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

Variants in PSTK

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

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

Position	Type	Phenotype	Significance	ClinVar
10-122980490-C-T		not specified	Uncertain significance (May 07, 2024)
10-122980500-C-G		not specified	Uncertain significance (May 17, 2023)
10-122980519-G-A		not specified	Uncertain significance (Jun 16, 2023)
10-122980523-C-T		not specified	Uncertain significance (Apr 08, 2024)
10-122980550-G-A		not specified	Uncertain significance (Mar 13, 2023)
10-122980600-C-T		not specified	Uncertain significance (May 10, 2022)
10-122980684-G-C		not specified	Uncertain significance (Apr 13, 2022)
10-122982733-C-T		not specified	Uncertain significance (May 18, 2023)
10-122982740-A-T		not specified	Uncertain significance (Nov 09, 2023)
10-122982775-C-G		not specified	Uncertain significance (Nov 17, 2023)
10-122982859-A-G		not specified	Uncertain significance (Aug 13, 2021)
10-122982890-T-A		not specified	Uncertain significance (Jan 23, 2024)
10-122983391-G-A		not specified	Uncertain significance (Feb 01, 2023)
10-122983452-C-T		not specified	Uncertain significance (Feb 14, 2023)
10-122983454-T-C		not specified	Uncertain significance (Feb 07, 2023)
10-122986901-T-G		not specified	Uncertain significance (Dec 18, 2023)
10-122993890-C-T			Uncertain significance (Sep 22, 2022)
10-122993928-A-G			Likely benign (Jun 01, 2022)
10-122993968-G-T		Thrombocytopenia 7	Uncertain significance (-)
10-122994026-C-T			Likely benign (Jul 01, 2024)
10-122994143-G-A			Likely benign (Oct 01, 2022)
10-122994157-C-T		not specified	Uncertain significance (Apr 09, 2024)
10-122994577-G-A		Thrombocytopenia 7	Pathogenic (Dec 23, 2020)
10-122994581-C-G		Thrombocytopenia 7	Uncertain significance (Feb 23, 2023)
10-122994622-A-G		Thrombocytopenia 7	Pathogenic (Dec 23, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSTK	protein_coding	protein_coding	ENST00000368887	6	43133

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000740	0.916	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.138	193	188	1.03	0.00000895	2270
Missense in Polyphen		47	51.69	0.90927		695
Synonymous	0.133	71	72.4	0.980	0.00000371	652
Loss of Function	1.65	11	18.7	0.588	9.52e-7	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000735	0.000735
Ashkenazi Jewish	0.00	0.00
East Asian	0.00104	0.00103
Finnish	0.00	0.00
European (Non-Finnish)	0.000232	0.000229
Middle Eastern	0.00104	0.00103
South Asian	0.0000656	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically phosphorylates seryl-tRNA(Sec) to O- phosphoseryl-tRNA(Sec), an activated intermediate for selenocysteine biosynthesis. {ECO:0000250}.
• Pathway: Selenocompound metabolism - Homo sapiens (human);Aminoacyl-tRNA biosynthesis - Homo sapiens (human);Selenocysteine synthesis;Metabolism of amino acids and derivatives;selenocysteine biosynthesis;Metabolism;Selenoamino acid metabolism (Consensus)

Recessive Scores

• pRec: 0.0959

Intolerance Scores

• loftool: 0.804
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• pHI: 0.254
• hipred: N
• hipred_score: 0.172
• ghis: 0.446

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00651

Mouse Genome Informatics

• Gene name: Pstk

Gene ontology

• Biological process: selenocysteine incorporation;phosphorylation;selenocysteinyl-tRNA(Sec) biosynthetic process
• Molecular function: tRNA binding;ATP binding;kinase activity