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.

ClinVar

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

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.

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				1		1
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in PSKH1

This is a list of pathogenic ClinVar variants found in the PSKH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67908770-G-C		not specified	Uncertain significance (Jun 21, 2023)
16-67908790-A-G		not specified	Uncertain significance (Aug 17, 2022)
16-67908795-G-A		not specified	Uncertain significance (Jan 16, 2024)
16-67908849-G-A		not specified	Uncertain significance (May 23, 2023)
16-67908922-A-G		not specified	Uncertain significance (Nov 10, 2022)
16-67908939-G-A		not specified	Likely benign (Jun 11, 2021)
16-67908943-C-T		not specified	Uncertain significance (May 06, 2022)
16-67908978-C-T		not specified	Uncertain significance (Mar 19, 2024)
16-67908984-C-T		not specified	Uncertain significance (May 24, 2023)
16-67909006-A-G		not specified	Uncertain significance (Dec 01, 2023)
16-67909110-C-T		CHOLESTASIS, PROGRESSIVE FAMILIAL INTRAHEPATIC, 13	Pathogenic (Dec 19, 2024)
16-67909125-A-G		CHOLESTASIS, PROGRESSIVE FAMILIAL INTRAHEPATIC, 13	Pathogenic (Sep 27, 2024)
16-67909150-G-C		not specified	Uncertain significance (Nov 07, 2024)
16-67909158-C-T		not specified	Uncertain significance (Oct 02, 2023)
16-67909245-G-A		not specified	Uncertain significance (Feb 28, 2024)
16-67909257-A-G		not specified	Uncertain significance (Sep 09, 2024)
16-67909296-C-T		CHOLESTASIS, PROGRESSIVE FAMILIAL INTRAHEPATIC, 13	Pathogenic (Sep 27, 2024)
16-67909322-C-T			Likely benign (May 01, 2022)
16-67909338-C-T		not specified	Uncertain significance (Sep 10, 2024)
16-67909369-G-A		not specified	Uncertain significance (Oct 20, 2023)
16-67909485-C-G		not specified	Uncertain significance (Sep 30, 2021)
16-67909560-C-T		not specified	Uncertain significance (Feb 16, 2023)
16-67909651-A-G		not specified	Uncertain significance (Mar 28, 2022)
16-67909657-C-T		not specified	Uncertain significance (Nov 10, 2024)
16-67909660-G-A		not specified	Uncertain significance (Sep 27, 2022)

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