STK38L

protein-coding

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

Gene summary

Enables ATP binding activity; magnesium ion binding activity; and protein serine/threonine kinase activity. Involved in intracellular signal transduction and negative regulation of autophagy. Acts upstream of or within protein phosphorylation. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015000.4

Inheritance

—

ClinVar variants

U:38B:2

Top phenotype

STK38L-related disorder

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr12:27,243,968-27,325,959

External References & Databases

Ensembl (ENSG00000211455)

Transcript & Mutation Effects

hg38 • Region Span ~82.0 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 STK38L variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 4

STK38L-related disorderTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015000.4. 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 clinvar	1 clinvar	3
missense			31 clinvar			31
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	38	1	1	40

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015000.4	RefSeq	NP_055815.1	13	MANE Select
ENST00000389032.8	Ensembl	ENSP00000373684.3	13	MANE Select
ENST00000407753.2	Ensembl	ENSP00000385174.2	4	Standard
ENST00000536093.5	Ensembl	ENSP00000443961.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
peptidyl-serine phosphorylation
intracellular signal transduction
regulation of cellular component organization

Molecular Function

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

Cellular Component

cytoplasm
cytosol
actin cytoskeleton
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389032
Coding exons: 13
Length: 81992
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125735
p: 0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.94	117	247	0.473	0.0000124	3085
Missense (PolyPhen)		31	103.26	0.30021		1287
Synonymous	1.74	60	79.8	0.752	0.00000395	795
Loss of Function	4.03	4	26.3	0.152	0.00000126	345

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000060	0.000058	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0	0.0	absent
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the regulation of structural processes in differentiating and mature neuronal cells. {ECO:0000250, ECO:0000269|PubMed:15037617, ECO:0000269|PubMed:15067004}.;

Recessive Scores

pRec: 0.126

Intolerance Scores

LoFtool: 0.562
RVIS EVS: -0.36
RVIS percentile EVS: 28.63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.983

Gene Damage Prediction

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