TSSK2

testis specific serine kinase 2

Basic information

Region (hg38): 22:19131308-19132622

Previous symbols: [ "STK22B" ]

Links

ENSG00000206203 ∙ NCBI:23617 ∙ OMIM:610710 ∙ HGNC:11401 ∙ Uniprot:Q96PF2 ∙ 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 TSSK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSSK2 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	1		28
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	1	0

Variants in TSSK2

This is a list of pathogenic ClinVar variants found in the TSSK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-19131439-G-A		not specified	Uncertain significance (Feb 01, 2023)
22-19131497-G-A		not specified	Uncertain significance (Dec 12, 2023)
22-19131508-A-G		not specified	Uncertain significance (May 24, 2024)
22-19131529-G-A		not specified	Uncertain significance (Mar 25, 2022)
22-19131532-C-A		not specified	Uncertain significance (Nov 18, 2023)
22-19131532-C-T		not specified	Uncertain significance (Apr 08, 2024)
22-19131571-C-A		not specified	Uncertain significance (Apr 25, 2022)
22-19131580-A-G		not specified	Uncertain significance (Dec 16, 2023)
22-19131586-A-G		not specified	Uncertain significance (Oct 26, 2022)
22-19131596-C-A		not specified	Uncertain significance (Apr 25, 2022)
22-19131679-G-A		not specified	Uncertain significance (Apr 25, 2022)
22-19131823-C-G		not specified	Uncertain significance (Sep 27, 2021)
22-19131878-G-A		not specified	Uncertain significance (Jan 04, 2022)
22-19131940-T-C		not specified	Uncertain significance (Jan 26, 2022)
22-19131974-A-C		not specified	Uncertain significance (Aug 10, 2023)
22-19132009-G-A		not specified	Uncertain significance (Jul 14, 2021)
22-19132031-G-A		not specified	Uncertain significance (Aug 15, 2023)
22-19132057-G-A		not specified	Uncertain significance (May 17, 2023)
22-19132141-C-T		not specified	Uncertain significance (Feb 22, 2023)
22-19132208-C-T		not specified	Uncertain significance (Jun 09, 2022)
22-19132263-G-C		not specified	Uncertain significance (Feb 13, 2024)
22-19132265-G-C		not specified	Uncertain significance (Sep 01, 2021)
22-19132280-G-A		not specified	Uncertain significance (Oct 04, 2022)
22-19132292-A-G		not specified	Uncertain significance (Dec 28, 2023)
22-19132323-C-A		not specified	Likely benign (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSSK2	protein_coding	protein_coding	ENST00000399635	1	1814

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00386	0.864	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.807	205	240	0.853	0.0000163	2369
Missense in Polyphen		52	69.315	0.75019		723
Synonymous	-0.294	108	104	1.04	0.00000772	712
Loss of Function	1.27	5	9.13	0.548	4.76e-7	106

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Testis-specific serine/threonine-protein kinase required during spermatid development. Phosphorylates TSKS at 'Ser-288' and SPAG16. Involved in the late stages of spermatogenesis, during the reconstruction of the cytoplasm. During spermatogenesis, required for the transformation of a ring-shaped structure around the base of the flagellum originating from the chromatoid body. {ECO:0000269|PubMed:15044604, ECO:0000269|PubMed:18533145, ECO:0000269|PubMed:20729278}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.269
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.93

Haploinsufficiency Scores

• pHI: 0.214
• hipred: N
• hipred_score: 0.208
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.932

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tssk2

Gene ontology

• Biological process: protein phosphorylation;multicellular organism development;spermatid development;peptidyl-serine phosphorylation;intracellular signal transduction;protein autophosphorylation
• Cellular component: acrosomal vesicle;nucleus;cytoplasm;centriole
• Molecular function: magnesium ion binding;protein serine/threonine kinase activity;protein binding;ATP binding;protein-containing complex binding