TSSK6

protein-coding

testis specific serine kinase 6

Gene summary

This intronless gene encodes a member of the CAMK (calcium/calmodulin-dependent) serine/threonine protein kinase family. The encoded kinase has a broad expression pattern but is described as testis-specific due to effects on fertility. Male mice which lack the gene encoding a highly similar protein are sterile and have morphologically abnormal sperm. [provided by RefSeq, Jan 2012]

MANE transcript

NM_032037.4

Inheritance

—

ClinVar variants

U:21B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr19:19,512,418-19,515,548

External References & Databases

Ensembl (ENSG00000178093)

Transcript & Mutation Effects

hg38 • Region Span ~3.1 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 TSSK6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 21

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032037.4. 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				1 clinvar		1
missense			21 clinvar			21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	1	0	22

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032037.4	RefSeq	NP_114426.1	1	MANE Select
ENST00000585580.4	Ensembl	ENSP00000466477.1	1	MANE Select
ENST00000587522.3	Ensembl	ENSP00000466056.1	1	Standard
ENST00000602623.1	Ensembl	ENSP00000473413.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
multicellular organism development
peptidyl-serine phosphorylation
sperm chromatin condensation
intracellular signal transduction

Molecular Function

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

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360913
Coding exons: 1
Length: 3612
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125724
p: 0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.25	122	215	0.568	0.0000167	1717
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000058	0.000046	rare
European (Non-Finnish)	0.000090	0.000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.845

Gene Damage Prediction

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