STK25

serine/threonine kinase 25, the group of STRIPAK complex

Basic information

Region (hg38): 2:241492670-241509730

Links

ENSG00000115694 ∙ NCBI:10494 ∙ OMIM:602255 ∙ HGNC:11404 ∙ Uniprot:O00506 ∙ 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 STK25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK25 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15	3		18
Total	0	0	44	4	0

Variants in STK25

This is a list of pathogenic ClinVar variants found in the STK25 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-241492995-G-A		not specified	Uncertain significance (Mar 14, 2023)
2-241493023-A-G		not specified	Uncertain significance (Aug 17, 2022)
2-241493032-A-G		not specified	Uncertain significance (Jul 17, 2024)
2-241493327-G-A		not specified	Uncertain significance (Nov 22, 2022)
2-241493333-G-A		not specified	Uncertain significance (Sep 02, 2024)
2-241493339-G-A		not specified	Uncertain significance (Dec 03, 2024)
2-241493353-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-241493365-C-A		not specified	Uncertain significance (Aug 02, 2022)
2-241493408-A-G		not specified	Uncertain significance (Nov 09, 2024)
2-241493416-C-T		not specified	Uncertain significance (Feb 20, 2025)
2-241493417-G-A		not specified	Uncertain significance (Dec 07, 2024)
2-241493420-C-T		not specified	Uncertain significance (Mar 04, 2024)
2-241493424-G-A			Likely benign (Mar 28, 2018)
2-241493441-A-G		not specified	Uncertain significance (Oct 04, 2022)
2-241493443-A-G		not specified	Uncertain significance (Feb 24, 2025)
2-241494013-T-C		not specified	Uncertain significance (Feb 04, 2025)
2-241494016-A-T		not specified	Uncertain significance (Dec 23, 2024)
2-241494030-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-241494057-A-G		not specified	Uncertain significance (Oct 05, 2021)
2-241494098-G-A			Likely benign (Jan 30, 2018)
2-241494100-G-A		not specified	Uncertain significance (Oct 01, 2024)
2-241494119-G-A			Likely benign (Mar 01, 2023)
2-241495666-C-T		not specified	Uncertain significance (Nov 13, 2024)
2-241495667-G-A		not specified	Uncertain significance (Jun 03, 2022)
2-241495667-G-T		not specified	Uncertain significance (Jul 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STK25	protein_coding	protein_coding	ENST00000316586	11	17057

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0519	0.948	125725	0	17	125742	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	171	275	0.621	0.0000179	2780
Missense in Polyphen		49	103.81	0.47202		1053
Synonymous	-0.308	129	125	1.04	0.00000921	839
Loss of Function	3.29	7	24.6	0.284	0.00000139	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000178
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000532	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Oxidant stress-activated serine/threonine kinase that may play a role in the response to environmental stress. Targets to the Golgi apparatus where it appears to regulate protein transport events, cell adhesion, and polarity complexes important for cell migration. {ECO:0000269|PubMed:15037601}.

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.654
• rvis_EVS: -1.05
• rvis_percentile_EVS: 7.66

Haploinsufficiency Scores

• pHI: 0.179
• hipred: Y
• hipred_score: 0.756
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stk25
• Phenotype: cellular 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)

Zebrafish Information Network

• Gene name: stk25a
• Affected structure: cranial vasculature
• Phenotype tag: abnormal
• Phenotype quality: spatial pattern

Gene ontology

• Biological process: protein phosphorylation;response to oxidative stress;establishment or maintenance of cell polarity;signal transduction;signal transduction by protein phosphorylation;stress-activated protein kinase signaling cascade;activation of protein kinase activity;positive regulation of stress-activated MAPK cascade;intrinsic apoptotic signaling pathway in response to hydrogen peroxide;response to hydrogen peroxide;protein autophosphorylation;positive regulation of axonogenesis;Golgi localization;establishment of Golgi localization;Golgi reassembly
• Cellular component: Golgi membrane;cytoplasm;Golgi apparatus;extracellular exosome
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;protein homodimerization activity;metal ion binding