STK39

serine/threonine kinase 39

Basic information

Region (hg38): 2:167954019-168247595

Links

ENSG00000198648 ∙ NCBI:27347 ∙ OMIM:607648 ∙ HGNC:17717 ∙ Uniprot:Q9UEW8 ∙ 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 STK39 gene.

• Inborn genetic diseases (13 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK39 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				1		1
missense			13			13
nonsense						0
start loss						0
frameshift			1			1
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	1

Variants in STK39

This is a list of pathogenic ClinVar variants found in the STK39 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-167955560-C-T		not specified	Uncertain significance (Sep 16, 2021)
2-168063549-C-A		not specified	Uncertain significance (Dec 06, 2022)
2-168065344-T-G		not specified	Uncertain significance (Jun 26, 2023)
2-168129599-T-C		not specified	Uncertain significance (Nov 01, 2022)
2-168140368-G-A		not specified	Uncertain significance (Jun 30, 2022)
2-168163797-T-C		not specified	Uncertain significance (May 11, 2022)
2-168163812-C-T		not specified	Uncertain significance (Jun 22, 2021)
2-168163844-C-T		not specified	Uncertain significance (Jun 22, 2023)
2-168247273-C-T		not specified	Uncertain significance (Aug 08, 2023)
2-168247276-C-T		not specified	Uncertain significance (Feb 17, 2022)
2-168247278-G-A		not specified	Uncertain significance (May 18, 2022)
2-168247286-C-CGCCGGG			Benign (Aug 21, 2018)
2-168247349-C-G			Likely benign (Apr 24, 2018)
2-168247354-G-C		not specified	Uncertain significance (Jun 05, 2023)
2-168247357-C-A		not specified	Uncertain significance (Jan 23, 2024)
2-168247366-CCGCCGCTGTCACCGGG-C			Uncertain significance (Jan 13, 2016)
2-168247374-G-C		not specified	Uncertain significance (Jan 24, 2024)
2-168247400-C-G		not specified	Uncertain significance (Feb 08, 2023)
2-168247420-C-G		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STK39	protein_coding	protein_coding	ENST00000355999	18	294122

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000839	125123	0	10	125133	0.0000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	166	262	0.633	0.0000129	3542
Missense in Polyphen		25	86.989	0.28739		1104
Synonymous	-0.0852	96	94.9	1.01	0.00000568	1022
Loss of Function	4.90	3	33.7	0.0890	0.00000178	416

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000644
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000546
Finnish	0.0000465	0.0000463
European (Non-Finnish)	0.0000532	0.0000529
Middle Eastern	0.0000557	0.0000546
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a mediator of stress-activated signals. Mediates the inhibition of SLC4A4, SLC26A6 as well as CFTR activities by the WNK scaffolds, probably through phosphorylation. Phosphorylates RELT. {ECO:0000250|UniProtKB:Q9Z1W9}.
• Pathway: Diuretics Pathway, Pharmacodynamics;TCR;TCR signaling in naïve CD4+ T cells (Consensus)

Recessive Scores

• pRec: 0.220

Intolerance Scores

• loftool: 0.341
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.355
• hipred: Y
• hipred_score: 0.786
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.832

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stk39
• Phenotype: reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: activation of MAPK activity;protein phosphorylation;regulation of blood pressure;positive regulation of T cell chemotaxis;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;signal transduction by protein phosphorylation;signal transduction by trans-phosphorylation;stress-activated protein kinase signaling cascade;activation of protein kinase activity;positive regulation of ion transmembrane transporter activity;intracellular signal transduction;maintenance of lens transparency;chemokine (C-X-C motif) ligand 12 signaling pathway;positive regulation of potassium ion transport;protein autophosphorylation;regulation of inflammatory response;ion homeostasis;cellular hypotonic response;negative regulation of pancreatic juice secretion;negative regulation of potassium ion transmembrane transporter activity;negative regulation of potassium ion transmembrane transport;negative regulation of creatine transmembrane transporter activity;cellular response to chemokine;negative regulation of sodium ion transmembrane transporter activity
• Cellular component: nucleoplasm;cytoplasm;cytosol;cytoskeleton;basolateral plasma membrane;apical plasma membrane;extrinsic component of membrane;intracellular membrane-bounded organelle
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;kinase activity;protein kinase binding