TSSK3

protein-coding

testis specific serine kinase 3

Gene summary

This gene encodes a kinase expressed exclusively in the testis that is thought to play a role in either germ cell differentiation or mature sperm function. [provided by RefSeq, Jul 2008]

Previous symbols:

STK22C

MANE transcript

NM_052841.4

Inheritance

—

ClinVar variants

U:48

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr1:32,351,521-32,364,312

External References & Databases

Ensembl (ENSG00000162526)

Transcript & Mutation Effects

hg38 • Region Span ~12.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TSSK3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 46

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052841.4. Only rare variants are included.

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						0
missense			48 clinvar			48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	0	0	48

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052841.4	RefSeq	NP_443073.1	2	MANE Select
ENST00000373534.4	Ensembl	ENSP00000362634.3	2	MANE Select
ENST00000574315.1	Ensembl	ENSP00000459187.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
multicellular organism development
spermatogenesis
cell differentiation
intracellular signal transduction

Molecular Function

magnesium ion binding
protein serine/threonine kinase activity
protein binding
ATP binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373534
Coding exons: 2
Length: 12792
Individuals with no LoFs: 125657
Homozygous LoFs: 0
Heterozygous LoFs: 91
Defined: 125748
p: 0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0102	156	156	0.998	0.00000928	1769
Missense (PolyPhen)		56	56.561	0.99008		646
Synonymous	0.288	61	63.9	0.954	0.00000392	532
Loss of Function	1.52	3	7.48	0.401	3.22e-7	100

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0.0018	0.0018	notable
East Asian	0.00071	0.00071	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00032	0.00032	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in a signaling pathway during male germ cell development or mature sperm function.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.766
RVIS EVS: -0.27
RVIS percentile EVS: 34.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.792

Gene Damage Prediction

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