STK38

protein-coding

serine/threonine kinase 38, the group of AGC family kinases

Gene summary

This gene encodes a member of the AGC serine/threonine kinase family of proteins. The kinase activity of this protein is regulated by autophosphorylation and phosphorylation by other upstream kinases. This protein has been shown to function in the cell cycle and apoptosis. This protein has also been found to regulate the protein stability and transcriptional activity of the MYC oncogene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]

MANE transcript

NM_007271.4

Inheritance

—

ClinVar variants

U:46B:2

Top phenotype

Primary dilated cardiomyopathy

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr6:36,493,892-36,547,479

External References & Databases

Ensembl (ENSG00000112079)

Transcript & Mutation Effects

hg38 • Region Span ~53.6 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 STK38 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 2

Primary dilated cardiomyopathyTotal: 1

Bladder exstrophy-epispadias-cloacal exstrophy complexTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007271.4. 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			2 clinvar		2 clinvar	4
missense			41 clinvar			41
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	46	0	2	48

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007271.4	RefSeq	NP_009202.1	13	MANE Select
ENST00000229812.8	Ensembl	ENSP00000229812.7	13	MANE Select
NM_001305102.2	RefSeq	NP_001292031.1	13	Standard
ENST00000850860.1	Ensembl	ENSP00000520947.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Interactome of polycomb repressive complex 2 (PRC2)

Biological Process

cellular protein modification process
protein phosphorylation
peptidyl-serine phosphorylation
intracellular signal transduction
negative regulation of MAP kinase activity

Molecular Function

magnesium ion binding
protein serine/threonine kinase activity
protein binding
ATP binding
mitogen-activated protein kinase kinase kinase binding

Cellular Component

nucleus
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000229812
Coding exons: 13
Length: 53579
Individuals with no LoFs: 125701
Homozygous LoFs: 0
Heterozygous LoFs: 46
Defined: 125747
p: 0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.12	161	257	0.627	0.0000132	3110
Missense (PolyPhen)		47	107.99	0.43523		1245
Synonymous	0.346	78	82.0	0.951	0.00000409	809
Loss of Function	2.97	10	26.5	0.378	0.00000131	333

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00069	0.00068	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.000071	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Negative regulator of MAP3K1/2 signaling. Converts MAP3K2 from its phosphorylated form to its non-phosphorylated form and inhibits autophosphorylation of MAP3K2. {ECO:0000269|PubMed:12493777, ECO:0000269|PubMed:15197186, ECO:0000269|PubMed:17906693, ECO:0000269|PubMed:7761441}.;

Recessive Scores

pRec: 0.338

Intolerance Scores

LoFtool: 0.489
RVIS EVS: -0.3
RVIS percentile EVS: 32.62

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.944

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High