TSSK6

testis specific serine kinase 6

Basic information

Region (hg38): 19:19512418-19515548

Links

ENSG00000178093 ∙ NCBI:83983 ∙ OMIM:610712 ∙ HGNC:30410 ∙ Uniprot:Q9BXA6 ∙ 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 TSSK6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSSK6 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				1		1
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in TSSK6

This is a list of pathogenic ClinVar variants found in the TSSK6 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19514674-G-C		not specified	Uncertain significance (Jan 12, 2024)
19-19514692-C-T		not specified	Uncertain significance (Mar 01, 2023)
19-19514749-C-T		not specified	Uncertain significance (Mar 01, 2023)
19-19514822-G-A			Likely benign (Apr 01, 2022)
19-19514962-C-T		not specified	Uncertain significance (Mar 07, 2024)
19-19514994-G-C		not specified	Uncertain significance (Jun 24, 2022)
19-19515178-C-T		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSSK6	protein_coding	protein_coding	ENST00000360913	1	3612

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.741	0.257	125709	0	15	125724	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.25	122	215	0.568	0.0000167	1717
Missense in Polyphen		32	68.136	0.46965		603
Synonymous	1.00	97	110	0.878	0.00000963	593
Loss of Function	2.44	1	8.79	0.114	6.28e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000914	0.0000905
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00	0.00
Finnish	0.0000577	0.0000462
European (Non-Finnish)	0.0000896	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for sperm production and function. Plays a role in DNA condensation during postmeiotic chromatin remodeling (By similarity). {ECO:0000250|UniProtKB:Q925K9, ECO:0000269|PubMed:15870294}.

Intolerance Scores

• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.0952
• hipred: N
• hipred_score: 0.399
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.845

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tssk6
• Phenotype: reproductive system phenotype

Gene ontology

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