STK38

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

Basic information

Region (hg38): 6:36493892-36547479

Links

ENSG00000112079

∙ NCBI:11329 ∙ OMIM:606964 ∙ HGNC:17847 ∙ Uniprot:Q15208 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STK38 gene.

not_specified (37 variants)
not_provided (2 variants)
Primary_dilated_cardiomyopathy (1 variants)
Bladder_exstrophy-epispadias-cloacal_extrophy_complex (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK38 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007271.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					2 clinvar	2
missense			37 clinvar			37
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	0	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STK38	protein_coding	protein_coding	ENST00000229812	13	53579

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000767	0.999	125701	0	46	125747	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	161	257	0.627	0.0000132	3110
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000809	0.000799
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000111	0.000109
Finnish	0.000372	0.000370
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.000111	0.000109
South Asian	0.0000711	0.0000653
Other	0.000166	0.000163

dbNSFP

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}.;
Pathway: Interactome of polycomb repressive complex 2 (PRC2) (Consensus)

Recessive Scores

pRec: 0.338

Intolerance Scores

loftool: 0.489
rvis_EVS: -0.3
rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

pHI: 0.670
hipred: Y
hipred_score: 0.749
ghis: 0.671

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.944

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Stk38
Phenotype: neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process: cellular protein modification process;protein phosphorylation;peptidyl-serine phosphorylation;intracellular signal transduction;negative regulation of MAP kinase activity
Cellular component: nucleus;cytoplasm;cytosol
Molecular function: magnesium ion binding;protein serine/threonine kinase activity;protein binding;ATP binding;mitogen-activated protein kinase kinase kinase binding;cadherin binding