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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			15			15
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	2

Variants in STK38

This is a list of pathogenic ClinVar variants found in the STK38 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-36495878-T-C		not specified	Uncertain significance (Apr 07, 2022)
6-36496783-T-C		not specified	Uncertain significance (Apr 25, 2022)
6-36497788-T-C			Benign (Dec 09, 2017)
6-36497799-C-T		not specified	Uncertain significance (May 13, 2022)
6-36498400-C-T		not specified	Uncertain significance (Jan 24, 2023)
6-36498408-G-A		not specified	Uncertain significance (Feb 17, 2022)
6-36499957-C-A		not specified	Uncertain significance (Mar 07, 2024)
6-36499987-A-G		not specified	Uncertain significance (Jun 19, 2024)
6-36507509-T-A		not specified	Uncertain significance (Aug 28, 2024)
6-36507530-T-A		not specified	Uncertain significance (Jan 29, 2024)
6-36515370-T-C		not specified	Uncertain significance (May 01, 2023)
6-36515375-CTG-C		Bladder exstrophy-epispadias-cloacal extrophy complex	Uncertain significance (-)
6-36515391-G-C		not specified	Uncertain significance (Mar 07, 2023)
6-36515402-G-C		not specified	Uncertain significance (Mar 23, 2022)
6-36515430-T-C		not specified	Uncertain significance (Apr 22, 2022)
6-36515476-C-A		not specified	Uncertain significance (Nov 28, 2023)
6-36517770-T-C		not specified	Uncertain significance (Jul 20, 2021)
6-36517794-C-T		not specified	Uncertain significance (Nov 24, 2024)
6-36521757-C-T		not specified	Uncertain significance (Aug 12, 2024)
6-36521763-G-A		not specified	Uncertain significance (Aug 24, 2023)
6-36521808-C-G		not specified	Uncertain significance (Aug 07, 2023)
6-36524406-T-G			Benign (Apr 10, 2018)
6-36524424-C-CT		Primary dilated cardiomyopathy	Uncertain significance (-)
6-36525598-T-A		not specified	Uncertain significance (Oct 07, 2024)

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