PSKH1

protein serine kinase H1

Basic information

Region (hg38): 16:67893254-67929676

Links

ENSG00000159792

∙ NCBI:5681 ∙ OMIM:177015 ∙ HGNC:9529 ∙ Uniprot:P11801 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cholestasis, progressive familial intrahepatic, 13	AR	Gastrointestinal; Renal	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	Gastrointestinal; Renal	39132680

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PSKH1 gene.

not_specified (52 variants)
Cholestasis,_progressive_familial_intrahepatic,_13 (4 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSKH1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006742.3. 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		1
missense	3 clinvar		52 clinvar	1 clinvar		56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	3	0	52	2	0

Highest pathogenic variant AF is 0.0000055762566

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSKH1	protein_coding	protein_coding	ENST00000291041	2	36407

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.260	0.735	125724	0	4	125728	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.28	188	299	0.629	0.0000209	2726
Missense in Polyphen		96	171.51	0.55973		1568
Synonymous	0.214	112	115	0.975	0.00000697	928
Loss of Function	2.41	3	12.0	0.250	7.76e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.;
Pathway: mRNA Processing (Consensus)

Recessive Scores

pRec: 0.141

Intolerance Scores

loftool: 0.283
rvis_EVS: -0.74
rvis_percentile_EVS: 13.94

Haploinsufficiency Scores

pHI: 0.468
hipred: Y
hipred_score: 0.600
ghis: 0.589

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pskh1
Phenotype: respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); renal/urinary system phenotype; growth/size/body region phenotype;

Gene ontology

Biological process: protein phosphorylation;determination of left/right symmetry;heart development
Cellular component: cellular_component;nucleoplasm;endoplasmic reticulum membrane;Golgi apparatus;microtubule organizing center;plasma membrane;nuclear speck
Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding