STK40

protein-coding

serine/threonine kinase 40

Gene summary

Predicted to enable ATP binding activity; protein serine kinase activity; and protein serine/threonine kinase activity. Predicted to be involved in regulation of MAPK cascade. Predicted to act upstream of or within several processes, including glycogen metabolic process; lung development; and respiratory system process. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001282547.2

Inheritance

—

ClinVar variants

U:60B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr1:36,339,624-36,385,924

External References & Databases

Ensembl (ENSG00000196182)

Transcript & Mutation Effects

hg38 • Region Span ~46.3 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 STK40 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 59

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001282547.2. 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			2 clinvar	2 clinvar	2 clinvar	6
missense			56 clinvar	3 clinvar		59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	60	5	2	67

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 65 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001282547.2	RefSeq	NP_001269476.1	10	MANE Select
ENST00000373132.4	Ensembl	ENSP00000362224.4	10	MANE Select
NM_001282546.2	RefSeq	NP_001269475.1	10	Standard
NM_032017.3	RefSeq	NP_114406.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

respiratory system process
glycogen metabolic process
protein phosphorylation
regulation of gene expression
multicellular organism growth

Molecular Function

protein serine/threonine kinase activity
protein binding
ATP binding

Cellular Component

nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373129
Coding exons: 10
Length: 46273
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125736
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.46	218	288	0.757	0.0000193	2833
Missense (PolyPhen)		59	106.23	0.5554		1087
Synonymous	1.18	107	124	0.865	0.00000910	862
Loss of Function	4.03	1	20.9	0.0479	9.72e-7	242

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be a negative regulator of NF-kappa-B and p53- mediated gene transcription. {ECO:0000269|PubMed:13679039}.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.171
RVIS EVS: -0.96
RVIS percentile EVS: 9.17

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.999

Gene Damage Prediction

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