GeneBe

PSKH1

protein-coding

protein serine kinase H1

Gene summary

Enables protein serine/threonine kinase activity. Predicted to act upstream of or within determination of left/right symmetry; heart development; and protein phosphorylation. Located in cytosol; nuclear speck; and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_006742.3

Inheritance

AR

ClinVar variants

P:4U:62B:10

Top phenotype

Cholestasis, progressive familial intrahepatic, 13

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr16:67,893,254-67,929,676

External References & Databases

Ensembl (ENSG00000159792)NCBI Gene (5681)OMIM (177015)HGNC:9529GenCCUniProt (P11801)AlphaFoldClinVar (PSKH1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~36.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

cholestasis, progressive familial intrahepatic, 13STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0975807

Submitter: PanelApp Australia

cholestasis, progressive familial intrahepatic, 13MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0975807

Submitter: G2P

Clinical Genomic Database (CGD)

Cholestasis, progressive familial intrahepatic, 13AR

Manifestation: Gastrointestinal; Renal

Intervention: Gastrointestinal; Renal

Rationale: The condition can involve cholestasis and hepatic disease, and awareness may allow early diagnosis and medical management of hepatic sequelae; Liver transplant has been described; The conditoin can involve reanl disease, and renal failure, and awareness may allow early diagnosis and management of renal sequelae

Refs: 39132680Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PSKH1 variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 54
PSKH1-related conditionTotal: 16
Cholestasis, progressive familial intrahepatic, 13Total: 5
not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006742.3. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
6
clinvar
 8
missense
3
clinvar
1
clinvar
60
clinvar
4
clinvar
 68
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total316210076

Highest pathogenic variant AF is 0.0000055762566

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006742.3RefSeqNP_006733.12MANE Select
ENST00000291041.6EnsemblENSP00000291041.42MANE Select
ENST00000570631.5EnsemblENSP00000482880.11Standard
ENST00000570631.6EnsemblENSP00000482880.11Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • mRNA Processing

Biological Process

  • protein phosphorylation
  • determination of left/right symmetry
  • heart development

Molecular Function

  • protein serine/threonine kinase activity
  • protein binding
  • ATP binding

Cellular Component

  • cellular_component
  • nucleoplasm
  • endoplasmic reticulum membrane
  • Golgi apparatus
  • microtubule organizing center

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000291041
Coding exons
2
Length
36407
Individuals with no LoFs
125724
Homozygous LoFs
0
Heterozygous LoFs
4
Defined
125728
p
0.0000159
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.281882990.6290.00002092726
Missense (PolyPhen)96171.510.559731568
Synonymous0.2141121150.9750.00000697928
Loss of Function2.41312.00.2507.76e-7133

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000260.000026rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: May be a SFC-associated serine kinase (splicing factor compartment-associated serine kinase) with a role in intranuclear SR protein (non-snRNP splicing factors containing a serine/arginine-rich domain) trafficking and pre-mRNA processing. {ECO:0000269|PubMed:12466556}.;

Recessive Scores

pRec
0.141

Intolerance Scores

LoFtool
0.283
RVIS EVS
-0.74
RVIS percentile EVS
13.94

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.982

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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