STK16

serine/threonine kinase 16

Basic information

Region (hg38): 2:219245454-219250337

Links

ENSG00000115661 ∙ NCBI:8576 ∙ OMIM:604719 ∙ HGNC:11394 ∙ Uniprot:O75716 ∙ 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 STK16 gene.

• Inborn genetic diseases (14 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK16 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	14	0	1

Variants in STK16

This is a list of pathogenic ClinVar variants found in the STK16 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-219246076-T-G		not specified	Uncertain significance (Nov 17, 2022)
2-219246685-G-T		not specified	Uncertain significance (Aug 17, 2022)
2-219246761-G-A		not specified	Uncertain significance (Feb 17, 2024)
2-219246775-C-T		not specified	Uncertain significance (May 09, 2023)
2-219246799-A-G		not specified	Uncertain significance (Sep 29, 2023)
2-219246805-C-T		not specified	Uncertain significance (Apr 19, 2023)
2-219246806-G-A		not specified	Uncertain significance (Aug 09, 2021)
2-219246836-G-T		not specified	Uncertain significance (Mar 21, 2023)
2-219247144-T-A		not specified	Uncertain significance (Jul 13, 2021)
2-219247165-T-C		not specified	Uncertain significance (Jan 10, 2022)
2-219247185-T-C		not specified	Uncertain significance (Mar 04, 2024)
2-219247441-T-C		not specified	Uncertain significance (Jan 03, 2024)
2-219247677-C-T		not specified	Uncertain significance (Aug 12, 2021)
2-219247696-G-A		not specified	Uncertain significance (Jun 26, 2023)
2-219247743-C-T		not specified	Uncertain significance (Dec 27, 2023)
2-219248217-A-G		not specified	Uncertain significance (Jan 30, 2024)
2-219248244-A-G		not specified	Uncertain significance (Nov 22, 2022)
2-219248247-G-C		not specified	Uncertain significance (Aug 28, 2023)
2-219248307-A-G		not specified	Uncertain significance (Apr 18, 2023)
2-219248429-C-T		not specified	Uncertain significance (Aug 19, 2023)
2-219248464-G-A		not specified	Uncertain significance (Aug 30, 2022)
2-219250304-C-T			Benign (Sep 18, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STK16	protein_coding	protein_coding	ENST00000409638	7	4883

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000118	0.957	124752	0	52	124804	0.000208

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	147	186	0.789	0.0000108	1990
Missense in Polyphen		44	66.541	0.66125		715
Synonymous	2.02	53	75.3	0.704	0.00000437	603
Loss of Function	1.83	9	17.2	0.524	9.83e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000643	0.000642
Ashkenazi Jewish	0.00	0.00
East Asian	0.000222	0.000223
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.000222	0.000223
South Asian	0.000233	0.000229
Other	0.000169	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Membrane-associated protein kinase that phosphorylates on serine and threonine residues. In vitro substrates include DRG1, ENO1 and EIF4EBP1. Also autophosphorylates. May be involved in secretory vesicle trafficking or intracellular signaling. May have a role in regulating stromal-epithelial interactions that occur during ductal morphogenesis in the mammary gland. May be involved in TGF-beta signaling. Able to autophosphorylate on Tyr residue; it is however unclear whether it has tyrosine-protein kinase toward other proteins. {ECO:0000269|PubMed:10364453}.

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.714
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.409
• hipred: N
• hipred_score: 0.408
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stk16
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: peptidyl-tyrosine phosphorylation;positive regulation of transcription by RNA polymerase II;protein autophosphorylation;cellular response to transforming growth factor beta stimulus
• Cellular component: Golgi-associated vesicle;cytosol;membrane;perinuclear region of cytoplasm
• Molecular function: protein serine/threonine kinase activity;non-membrane spanning protein tyrosine kinase activity;protein binding;ATP binding