PSTK

protein-coding

phosphoseryl-tRNA kinase

Gene summary

Predicted to enable kinase activity and tRNA binding activity. Predicted to be involved in translation. Predicted to act upstream of or within selenocysteine incorporation. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C10orf89

MANE transcript

NM_001363531.2

Inheritance

—

ClinVar variants

U:46

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr10:122,954,381-122,997,513

External References & Databases

Ensembl (ENSG00000179988)

Transcript & Mutation Effects

hg38 • Region Span ~43.1 kb

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GenCC 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 PSTK variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 42

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001363531.2. 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						0
missense			44 clinvar			44
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	46	0	0	46

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001363531.2	RefSeq	NP_001350460.1	6	MANE Select
ENST00000406217.8	Ensembl	ENSP00000384653.3	6	MANE Select
NM_153336.3	RefSeq	NP_699167.2	6	Standard
ENST00000368887.7	Ensembl	ENSP00000357882.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Selenocompound metabolism - Homo sapiens (human)
Aminoacyl-tRNA biosynthesis - Homo sapiens (human)
Selenocysteine synthesis
Metabolism of amino acids and derivatives
selenocysteine biosynthesis

Biological Process

selenocysteine incorporation
phosphorylation
selenocysteinyl-tRNA(Sec) biosynthetic process

Molecular Function

tRNA binding
ATP binding
kinase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368887
Coding exons: 6
Length: 43133
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 70
Defined: 125748
p: 0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.138	193	188	1.03	0.00000895	2270
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0010	0.0010	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00023	0.00023	rare
South Asian	0.000066	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Specifically phosphorylates seryl-tRNA(Sec) to O- phosphoseryl-tRNA(Sec), an activated intermediate for selenocysteine biosynthesis. {ECO:0000250}.;

Recessive Scores

pRec: 0.0959

Intolerance Scores

LoFtool: 0.804
RVIS EVS: 0.53
RVIS percentile EVS: 80.73

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.00651