PSKH2

protein serine kinase H2

Basic information

Region (hg38): 8:86047109-86088621

Links

ENSG00000147613 ∙ NCBI:85481 ∙ ∙ HGNC:18997 ∙ Uniprot:Q96QS6 ∙ 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 PSKH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSKH2 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in PSKH2

This is a list of pathogenic ClinVar variants found in the PSKH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-86048472-G-A		not specified	Uncertain significance (Mar 29, 2024)
8-86048492-T-C		not specified	Uncertain significance (Oct 21, 2024)
8-86048554-A-T		not specified	Uncertain significance (May 23, 2024)
8-86048608-G-C		not specified	Uncertain significance (Nov 11, 2024)
8-86048652-A-G		not specified	Uncertain significance (Nov 28, 2023)
8-86048689-C-A		not specified	Uncertain significance (Feb 01, 2023)
8-86048693-C-T		not specified	Uncertain significance (Aug 04, 2024)
8-86048697-C-T		not specified	Uncertain significance (Jul 31, 2024)
8-86048698-G-A		not specified	Uncertain significance (Feb 15, 2023)
8-86048737-C-T		not specified	Uncertain significance (Oct 14, 2023)
8-86048742-G-A		not specified	Uncertain significance (Nov 23, 2024)
8-86063987-C-T		not specified	Uncertain significance (May 13, 2024)
8-86064029-T-C		not specified	Uncertain significance (May 18, 2022)
8-86064156-T-C		not specified	Uncertain significance (Jun 02, 2023)
8-86064224-G-A		not specified	Uncertain significance (Jan 09, 2024)
8-86064301-C-G		not specified	Uncertain significance (Aug 28, 2024)
8-86064393-C-T		not specified	Uncertain significance (Sep 14, 2022)
8-86064395-G-A		not specified	Uncertain significance (Jun 11, 2024)
8-86064408-T-C		not specified	Uncertain significance (Aug 27, 2024)
8-86064423-G-C		not specified	Uncertain significance (Oct 10, 2023)
8-86064447-T-G		not specified	Uncertain significance (Aug 26, 2024)
8-86064465-G-C		not specified	Uncertain significance (May 13, 2022)
8-86064476-C-T		not specified	Uncertain significance (Nov 21, 2023)
8-86064479-C-T		not specified	Uncertain significance (Nov 10, 2022)
8-86064480-G-A		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSKH2	protein_coding	protein_coding	ENST00000276616	3	40249

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.21e-9	0.0794	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.110	226	221	1.02	0.0000117	2500
Missense in Polyphen		55	64.688	0.85024		794
Synonymous	0.709	78	86.4	0.903	0.00000499	775
Loss of Function	-0.248	12	11.1	1.08	5.33e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000155
Ashkenazi Jewish	0.00	0.00
East Asian	0.000383	0.000381
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000265	0.000255
Middle Eastern	0.000383	0.000381
South Asian	0.00111	0.00105
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0974

Intolerance Scores

• loftool: 0.810
• rvis_EVS: 1.13
• rvis_percentile_EVS: 92.26

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.142

Gene Damage Prediction

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

Gene ontology

• Biological process: protein phosphorylation
• Molecular function: protein serine/threonine kinase activity;ATP binding