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.

not_specified (43 variants)

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. These statistics are base on transcript: NM_001271977.2. 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						0
missense			42 clinvar	1 clinvar		43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	1	0

Loading clinvar variants...

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