TSKS

testis specific serine kinase substrate, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 19:49739753-49763306

Links

ENSG00000126467 ∙ NCBI:60385 ∙ OMIM:608253 ∙ HGNC:30719 ∙ Uniprot:Q9UJT2 ∙ 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 TSKS gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSKS 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			42	1		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	1	0

Variants in TSKS

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

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

Position	Type	Phenotype	Significance	ClinVar
19-49739824-G-T		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
19-49739831-C-T		not specified	Uncertain significance (Apr 11, 2023)
19-49739846-G-A		not specified	Uncertain significance (May 24, 2023)
19-49739921-G-T		not specified	Uncertain significance (Apr 09, 2024)
19-49739931-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-49740098-C-T		not specified	Uncertain significance (Apr 13, 2023)
19-49741899-G-A		not specified	Uncertain significance (Dec 05, 2022)
19-49741936-C-G		not specified	Uncertain significance (Oct 10, 2023)
19-49741973-C-T		not specified	Uncertain significance (May 23, 2023)
19-49744235-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-49744265-G-A		not specified	Uncertain significance (Nov 09, 2023)
19-49744267-T-C		not specified	Uncertain significance (Jun 01, 2023)
19-49744276-A-G		not specified	Uncertain significance (May 21, 2024)
19-49745263-G-C		not specified	Uncertain significance (Apr 20, 2023)
19-49745313-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-49745389-C-A		not specified	Uncertain significance (May 04, 2023)
19-49746514-G-T		not specified	Uncertain significance (Feb 11, 2022)
19-49746573-C-T		not specified	Likely benign (May 05, 2023)
19-49746609-G-A		not specified	Uncertain significance (Jun 01, 2023)
19-49746656-G-C		not specified	Uncertain significance (Jun 01, 2023)
19-49746672-G-A		not specified	Uncertain significance (May 08, 2024)
19-49746675-T-C		not specified	Uncertain significance (Nov 15, 2021)
19-49746705-C-T		not specified	Uncertain significance (Feb 05, 2024)
19-49746712-C-G		not specified	Uncertain significance (Jan 17, 2024)
19-49746729-C-T		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSKS	protein_coding	protein_coding	ENST00000246801	11	23578

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00348	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.283	355	370	0.959	0.0000239	3769
Missense in Polyphen		145	159.87	0.90698		1693
Synonymous	0.491	165	173	0.953	0.0000120	1246
Loss of Function	4.56	3	29.9	0.100	0.00000159	316

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000840	0.0000527
Middle Eastern	0.000113	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in testicular physiology, most probably in the process of spermatogenesis or spermatid development.

Intolerance Scores

• loftool: 0.326
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.86

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.423
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.447

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tsks

Gene ontology

• Biological process: negative regulation of phosphatase activity
• Cellular component: centriole
• Molecular function: protein binding;protein kinase binding