TSSK3

testis specific serine kinase 3

Basic information

Region (hg38): 1:32351521-32364312

Previous symbols: [ "STK22C" ]

Links

ENSG00000162526 ∙ NCBI:81629 ∙ OMIM:607660 ∙ HGNC:15473 ∙ Uniprot:Q96PN8 ∙ 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 TSSK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSSK3 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in TSSK3

This is a list of pathogenic ClinVar variants found in the TSSK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-32361483-T-C		not specified	Uncertain significance (Aug 13, 2021)
1-32361764-G-A		not specified	Uncertain significance (May 10, 2024)
1-32361784-G-A		not specified	Uncertain significance (Aug 06, 2021)
1-32361788-C-T		not specified	Uncertain significance (Jun 07, 2024)
1-32361855-C-G		not specified	Uncertain significance (Jul 13, 2022)
1-32361872-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-32362003-G-T		not specified	Uncertain significance (Mar 18, 2024)
1-32362029-T-G			Likely benign (Oct 01, 2022)
1-32362058-C-T		not specified	Uncertain significance (Oct 10, 2023)
1-32362070-C-G		not specified	Uncertain significance (Dec 09, 2023)
1-32362070-C-T		not specified	Uncertain significance (May 23, 2023)
1-32362084-G-A		not specified	Uncertain significance (Dec 14, 2022)
1-32362720-T-G		not specified	Uncertain significance (Jan 09, 2024)
1-32362748-T-C		not specified	Uncertain significance (Jan 30, 2024)
1-32362778-A-C		not specified	Uncertain significance (May 13, 2024)
1-32362802-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-32363651-A-G		not specified	Uncertain significance (Jul 14, 2022)
1-32363666-G-A		not specified	Uncertain significance (Nov 10, 2021)
1-32363669-T-C		not specified	Uncertain significance (Oct 20, 2023)
1-32363693-G-A		not specified	Uncertain significance (Sep 29, 2023)
1-32363720-G-A		not specified	Uncertain significance (Jun 22, 2021)
1-32363729-G-T		not specified	Uncertain significance (Sep 22, 2022)
1-32363777-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-32363795-C-T		not specified	Uncertain significance (Dec 13, 2023)
1-32363796-G-A		not specified	Uncertain significance (Jun 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSSK3	protein_coding	protein_coding	ENST00000373534	2	12792

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0570	0.873	125657	0	91	125748	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0102	156	156	0.998	0.00000928	1769
Missense in Polyphen		56	56.561	0.99008		646
Synonymous	0.288	61	63.9	0.954	0.00000392	532
Loss of Function	1.52	3	7.48	0.401	3.22e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000864	0.000865
Ashkenazi Jewish	0.00180	0.00179
East Asian	0.000707	0.000707
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000317	0.000316
Middle Eastern	0.000707	0.000707
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in a signaling pathway during male germ cell development or mature sperm function.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.766
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.194
• hipred: N
• hipred_score: 0.383
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.792

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tssk3

Gene ontology

• Biological process: protein phosphorylation;multicellular organism development;spermatogenesis;cell differentiation;intracellular signal transduction
• Cellular component: nucleus;cytoplasm
• Molecular function: magnesium ion binding;protein serine/threonine kinase activity;protein binding;ATP binding