TSSK4

testis specific serine kinase 4

Basic information

Region (hg38): 14:24205696-24208362

Previous symbols: [ "C14orf20", "STK22E" ]

Links

ENSG00000139908 ∙ NCBI:283629 ∙ OMIM:610711 ∙ HGNC:19825 ∙ Uniprot:Q6SA08 ∙ 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 TSSK4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSSK4 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in TSSK4

This is a list of pathogenic ClinVar variants found in the TSSK4 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24205979-T-G		not specified	Uncertain significance (May 11, 2022)
14-24206002-G-T		not specified	Uncertain significance (Aug 19, 2024)
14-24206021-A-G		not specified	Uncertain significance (Dec 20, 2023)
14-24206036-C-T		not specified	Uncertain significance (Feb 01, 2023)
14-24206525-G-A		not specified	Uncertain significance (Dec 30, 2024)
14-24206533-T-A		not specified	Uncertain significance (Sep 16, 2021)
14-24206552-G-A		not specified	Likely benign (Sep 24, 2024)
14-24206591-A-G		not specified	Uncertain significance (Aug 16, 2021)
14-24206722-C-T		not specified	Uncertain significance (Oct 12, 2021)
14-24207162-A-C		not specified	Uncertain significance (Feb 22, 2023)
14-24207175-A-C		not specified	Uncertain significance (Aug 20, 2024)
14-24207193-A-G		not specified	Uncertain significance (Nov 26, 2024)
14-24207261-C-G		not specified	Uncertain significance (Oct 02, 2023)
14-24207329-G-C		not specified	Uncertain significance (Oct 11, 2024)
14-24207363-T-G		not specified	Uncertain significance (Aug 08, 2022)
14-24207364-C-G		not specified	Uncertain significance (Apr 20, 2024)
14-24207370-C-T		not specified	Uncertain significance (Jul 26, 2024)
14-24207394-A-G		not specified	Uncertain significance (Mar 15, 2024)
14-24207985-C-T		not specified	Uncertain significance (Mar 25, 2024)
14-24207986-G-A		not specified	Likely benign (Jan 23, 2025)
14-24208031-C-T		not specified	Uncertain significance (Sep 14, 2022)
14-24208043-A-G		not specified	Uncertain significance (Nov 21, 2023)
14-24208057-C-G		not specified	Uncertain significance (Aug 26, 2024)
14-24208139-C-T		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSSK4	protein_coding	protein_coding	ENST00000339917	4	2666

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.46e-9	0.127	125565	1	182	125748	0.000728

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	148	189	0.782	0.0000102	2211
Missense in Polyphen		60	81.157	0.73931		999
Synonymous	0.954	63	73.4	0.858	0.00000378	670
Loss of Function	0.131	13	13.5	0.962	7.45e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00187	0.00187
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000381	0.000381
Finnish	0.000558	0.000416
European (Non-Finnish)	0.000572	0.000571
Middle Eastern	0.000381	0.000381
South Asian	0.000980	0.000980
Other	0.00179	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine kinase which is involved in male germ cell development and in mature sperm function (By similarity). May be involved in the Cre/Creb signaling pathway (By similarity). Phosphorylates CREB1 on 'Ser-133' in vitro and can stimulate Cre/Creb pathway in cells (PubMed:15964553). Phosphorylates CREM on 'Ser-116' in vitro (By similarity). Phosphorylates ODF2 on 'Ser-95' (By similarity). {ECO:0000250|UniProtKB:Q9D411, ECO:0000269|PubMed:15964553}.

Recessive Scores

• pRec: 0.0929

Intolerance Scores

• loftool: 0.912
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.7

Haploinsufficiency Scores

• pHI: 0.218
• hipred: N
• hipred_score: 0.147
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.218

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tssk4
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: protein phosphorylation;multicellular organism development;spermatogenesis;cell differentiation;positive regulation of CREB transcription factor activity;intracellular signal transduction
• Cellular component: acrosomal vesicle;nucleus;cytoplasm;motile cilium
• Molecular function: magnesium ion binding;protein serine/threonine kinase activity;protein binding;ATP binding