STK10

serine/threonine kinase 10

Basic information

Region (hg38): 5:172042078-172188224

Links

ENSG00000072786 ∙ NCBI:6793 ∙ OMIM:603919 ∙ HGNC:11388 ∙ Uniprot:O94804 ∙ 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 STK10 gene.

• Inborn genetic diseases (42 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK10 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	4
missense			41	1	2	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	41	3	4

Variants in STK10

This is a list of pathogenic ClinVar variants found in the STK10 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-172044944-T-C		not specified	Uncertain significance (Dec 08, 2023)
5-172044949-C-T		not specified	Uncertain significance (Oct 26, 2021)
5-172052937-G-A		not specified	Uncertain significance (May 11, 2022)
5-172052938-C-T			Likely benign (Aug 01, 2018)
5-172053000-G-C		not specified	Uncertain significance (Aug 26, 2022)
5-172054563-C-G			Benign (Oct 03, 2017)
5-172054603-C-A		not specified	Uncertain significance (Jul 26, 2021)
5-172054658-G-A		not specified	Uncertain significance (Sep 22, 2023)
5-172055605-G-A		not specified	Uncertain significance (Jul 27, 2021)
5-172055635-T-C		not specified	Uncertain significance (Nov 19, 2022)
5-172055656-T-G		not specified	Uncertain significance (Nov 30, 2022)
5-172055679-C-T		not specified	Uncertain significance (Jun 29, 2023)
5-172055701-G-A		not specified	Uncertain significance (Dec 20, 2021)
5-172057437-T-G		not specified	Uncertain significance (Jan 22, 2024)
5-172057471-G-A		not specified	Uncertain significance (May 25, 2022)
5-172061141-C-A		not specified	Uncertain significance (Nov 03, 2023)
5-172061141-C-T		not specified	Uncertain significance (May 08, 2023)
5-172061195-C-T		not specified	Uncertain significance (May 11, 2022)
5-172061265-G-A		not specified	Uncertain significance (Feb 22, 2023)
5-172064733-T-C		not specified	Uncertain significance (Jul 27, 2022)
5-172064752-T-C		not specified	Uncertain significance (Dec 20, 2021)
5-172064788-G-A		not specified	Uncertain significance (Feb 03, 2022)
5-172064803-C-T		not specified	Uncertain significance (Feb 05, 2024)
5-172082337-T-C		not specified	Uncertain significance (Jan 16, 2024)
5-172082425-G-C		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STK10	protein_coding	protein_coding	ENST00000176763	19	146314

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.28e-14	0.995	125567	1	180	125748	0.000720

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	495	596	0.831	0.0000373	6405
Missense in Polyphen		172	236.84	0.72624		2491
Synonymous	-0.108	241	239	1.01	0.0000152	1788
Loss of Function	2.77	31	52.7	0.588	0.00000303	564

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00118
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000449	0.000435
Finnish	0.00394	0.00389
European (Non-Finnish)	0.000353	0.000343
Middle Eastern	0.000449	0.000435
South Asian	0.000744	0.000686
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine-protein kinase involved in regulation of lymphocyte migration. Phosphorylates MSN, and possibly PLK1. Involved in regulation of lymphocyte migration by mediating phosphorylation of ERM proteins such as MSN. Acts as a negative regulator of MAP3K1/MEKK1. May also act as a cell cycle regulator by acting as a polo kinase kinase: mediates phosphorylation of PLK1 in vitro; however such data require additional evidences in vivo. {ECO:0000269|PubMed:11903060, ECO:0000269|PubMed:12639966, ECO:0000269|PubMed:19255442}.
• Disease: DISEASE: Testicular germ cell tumor (TGCT) [MIM:273300]: A common malignancy in males representing 95% of all testicular neoplasms. TGCTs have various pathologic subtypes including: unclassified intratubular germ cell neoplasia, seminoma (including cases with syncytiotrophoblastic cells), spermatocytic seminoma, embryonal carcinoma, yolk sac tumor, choriocarcinoma, and teratoma. {ECO:0000269|PubMed:16175573}. Note=The disease may be caused by mutations affecting the gene represented in this entry.
• Pathway: Progesterone-mediated oocyte maturation - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.868
• rvis_EVS: -0.92
• rvis_percentile_EVS: 9.78

Haploinsufficiency Scores

• pHI: 0.492
• hipred: Y
• hipred_score: 0.639
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.785

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stk10
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: protein phosphorylation;cell cycle;signal transduction by protein phosphorylation;stress-activated protein kinase signaling cascade;activation of protein kinase activity;neutrophil degranulation;protein autophosphorylation;lymphocyte aggregation;regulation of lymphocyte migration
• Cellular component: cytoplasm;plasma membrane;specific granule membrane;extracellular exosome
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;identical protein binding;protein homodimerization activity