TSSK1B

testis specific serine kinase 1B

Basic information

Region (hg38): 5:113432553-113434989

Previous symbols: [ "STK22D", "TSSK1" ]

Links

ENSG00000212122 ∙ NCBI:83942 ∙ OMIM:610709 ∙ HGNC:14968 ∙ Uniprot:Q9BXA7 ∙ 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 TSSK1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSSK1B 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			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	0	0

Variants in TSSK1B

This is a list of pathogenic ClinVar variants found in the TSSK1B region.

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

Position	Type	Phenotype	Significance	ClinVar
5-113433771-G-A		not specified	Uncertain significance (Feb 14, 2023)
5-113433824-G-A		not specified	Uncertain significance (Jul 12, 2022)
5-113433828-G-C		not specified	Uncertain significance (Aug 17, 2022)
5-113433840-G-T		not specified	Uncertain significance (Dec 07, 2023)
5-113433851-C-A		not specified	Uncertain significance (Jan 24, 2024)
5-113433909-T-C		not specified	Uncertain significance (May 20, 2024)
5-113433944-G-T		not specified	Uncertain significance (Jun 16, 2023)
5-113433949-C-A		not specified	Uncertain significance (Jul 05, 2023)
5-113433965-C-T		not specified	Uncertain significance (Apr 07, 2022)
5-113433966-G-A		not specified	Uncertain significance (Feb 16, 2023)
5-113434010-C-T		not specified	Uncertain significance (Nov 17, 2022)
5-113434064-C-A		not specified	Uncertain significance (Apr 01, 2024)
5-113434071-C-T		not specified	Uncertain significance (Jan 24, 2024)
5-113434101-C-T		not specified	Uncertain significance (Jan 10, 2023)
5-113434115-G-A		not specified	Uncertain significance (Jun 03, 2022)
5-113434143-C-T		not specified	Uncertain significance (Dec 09, 2023)
5-113434191-C-T		not specified	Uncertain significance (Nov 18, 2022)
5-113434215-T-C		not specified	Uncertain significance (Mar 03, 2022)
5-113434248-C-T		not specified	Uncertain significance (Dec 01, 2022)
5-113434254-C-T		not specified	Uncertain significance (Jul 12, 2022)
5-113434295-G-A		not specified	Uncertain significance (Jun 27, 2022)
5-113434340-C-T		not specified	Uncertain significance (May 11, 2022)
5-113434352-C-T		not specified	Uncertain significance (Sep 15, 2021)
5-113434443-C-T		not specified	Uncertain significance (Aug 12, 2021)
5-113434527-G-A		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSSK1B	protein_coding	protein_coding	ENST00000390666	1	2478

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000134	0.421	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.344	260	245	1.06	0.0000161	2408
Missense in Polyphen		50	71.264	0.70162		727
Synonymous	-0.701	113	104	1.09	0.00000726	731
Loss of Function	0.174	6	6.48	0.926	5.19e-7	71

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 'Ser-288' of TSKS. 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:15733851, ECO:0000269|PubMed:19530700}.

Intolerance Scores

• loftool: 0.711
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.57

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.170
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.519

Gene Damage Prediction

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

Gene ontology

• Biological process: protein phosphorylation;multicellular organism development;spermatid development;peptidyl-serine phosphorylation;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;protein-containing complex binding