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.

not_specified (33 variants)

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. These statistics are base on transcript: NM_001184739.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			30 clinvar	3 clinvar		33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	3	0

Loading clinvar variants...

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