STK24

serine/threonine kinase 24, the group of STRIPAK complex

Basic information

Region (hg38): 13:98445184-98577940

Links

ENSG00000102572 ∙ NCBI:8428 ∙ OMIM:604984 ∙ HGNC:11403 ∙ Uniprot:Q9Y6E0 ∙ 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 STK24 gene.

• Inborn genetic diseases (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK24 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5			5
Total	0	0	16	0	0

Variants in STK24

This is a list of pathogenic ClinVar variants found in the STK24 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-98446138-G-A		not specified	Uncertain significance (Apr 22, 2022)
13-98446171-C-G		not specified	Uncertain significance (Sep 30, 2021)
13-98446191-T-C		not specified	Uncertain significance (Jan 16, 2024)
13-98446198-C-T		not specified	Uncertain significance (Mar 22, 2023)
13-98446706-C-T		not specified	Uncertain significance (Feb 17, 2022)
13-98448268-C-T		not specified	Uncertain significance (Feb 23, 2023)
13-98448290-G-C		not specified	Uncertain significance (Jan 04, 2024)
13-98453184-A-C		not specified	Uncertain significance (Jun 29, 2022)
13-98457184-C-T		not specified	Uncertain significance (Feb 15, 2023)
13-98457285-G-A		not specified	Uncertain significance (Oct 03, 2022)
13-98460409-T-C		not specified	Uncertain significance (Jul 06, 2022)
13-98463731-C-T		not specified	Uncertain significance (Sep 22, 2023)
13-98463760-A-G		not specified	Uncertain significance (Jan 22, 2024)
13-98463793-C-T		not specified	Uncertain significance (Nov 05, 2021)
13-98463800-T-C		not specified	Uncertain significance (Jan 26, 2023)
13-98466384-G-C		not specified	Uncertain significance (May 17, 2023)
13-98466446-G-A		not specified	Uncertain significance (Jul 11, 2023)
13-98474952-C-T		not specified	Uncertain significance (Jan 30, 2024)
13-98474970-C-A		not specified	Uncertain significance (Jan 09, 2024)
13-98475333-G-A		not specified	Uncertain significance (Apr 08, 2023)
13-98519337-G-T		not specified	Uncertain significance (Jun 30, 2022)
13-98519362-T-C		not specified	Uncertain significance (Sep 29, 2023)
13-98519387-G-C		not specified	Uncertain significance (Dec 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STK24	protein_coding	protein_coding	ENST00000376547	11	127740

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0113	0.988	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	164	253	0.647	0.0000142	2897
Missense in Polyphen		33	91.08	0.36232		1091
Synonymous	0.502	102	109	0.939	0.00000723	848
Loss of Function	3.13	8	24.9	0.322	0.00000132	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.000120	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine-protein kinase that acts on both serine and threonine residues and promotes apoptosis in response to stress stimuli and caspase activation. Mediates oxidative-stress- induced cell death by modulating phosphorylation of JNK1-JNK2 (MAPK8 and MAPK9), p38 (MAPK11, MAPK12, MAPK13 and MAPK14) during oxidative stress. Plays a role in a staurosporine-induced caspase- independent apoptotic pathway by regulating the nuclear translocation of AIFM1 and ENDOG and the DNase activity associated with ENDOG. Phosphorylates STK38L on 'Thr-442' and stimulates its kinase activity. In association with STK26 negatively regulates Golgi reorientation in polarized cell migration upon RHO activation (PubMed:27807006). Regulates also cellular migration with alteration of PTPN12 activity and PXN phosphorylation: phosphorylates PTPN12 and inhibits its activity and may regulate PXN phosphorylation through PTPN12. May act as a key regulator of axon regeneration in the optic nerve and radial nerve. {ECO:0000269|PubMed:16314523, ECO:0000269|PubMed:17046825, ECO:0000269|PubMed:19604147, ECO:0000269|PubMed:19782762, ECO:0000269|PubMed:19855390, ECO:0000269|PubMed:27807006}.
• Pathway: Apoptotic cleavage of cellular proteins;Apoptotic execution phase;Apoptosis;Programmed Cell Death (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.303
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.588
• hipred: Y
• hipred_score: 0.851
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stk24
• Phenotype: hematopoietic system phenotype; renal/urinary system phenotype; immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: MAPK cascade;protein phosphorylation;signal transduction;intrinsic apoptotic signaling pathway in response to oxidative stress;cellular response to starvation;signal transduction by protein phosphorylation;negative regulation of cell migration;stress-activated protein kinase signaling cascade;activation of protein kinase activity;response to hydrogen peroxide;protein autophosphorylation;regulation of axon regeneration;neuron projection morphogenesis;execution phase of apoptosis
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;Golgi apparatus;cytosol;membrane;extracellular exosome
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;cadherin binding;metal ion binding