TSSK2

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	1 clinvar		5
missense			66 clinvar	2 clinvar		68
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	71	3	0	74

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_053006.5	RefSeq	NP_443732.3	1	MANE Select
ENST00000399635.4	Ensembl	ENSP00000382544.2	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
multicellular organism development
spermatid development
peptidyl-serine phosphorylation
intracellular signal transduction

Molecular Function

magnesium ion binding
protein serine/threonine kinase activity
protein binding
ATP binding
protein-containing complex binding

Cellular Component

acrosomal vesicle
nucleus
cytoplasm
centriole

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399635
Coding exons: 1
Length: 1814
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.807	205	240	0.853	0.0000163	2369
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.932

Gene Damage Prediction

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