STK19

serine/threonine kinase 19

Basic information

Region (hg38): 6:31971090-31982821

Links

ENSG00000204344 ∙ NCBI:8859 ∙ OMIM:604977 ∙ HGNC:11398 ∙ Uniprot:P49842 ∙ 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 STK19 gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK19 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	1		5
Total	0	0	16	1	0

Variants in STK19

This is a list of pathogenic ClinVar variants found in the STK19 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31971368-A-G		not specified	Uncertain significance (Jan 18, 2023)
6-31971440-C-T		not specified	Uncertain significance (Jan 24, 2023)
6-31971485-G-T		not specified	Uncertain significance (Apr 25, 2022)
6-31971511-A-C		not specified	Uncertain significance (Aug 12, 2022)
6-31971617-T-C		not specified	Uncertain significance (Aug 02, 2022)
6-31972108-G-A		not specified	Uncertain significance (Oct 26, 2022)
6-31972121-C-T			Likely benign (Feb 01, 2023)
6-31972162-T-G		not specified	Uncertain significance (Dec 26, 2023)
6-31972319-A-T		not specified	Uncertain significance (Dec 02, 2021)
6-31972346-G-A		Squamous cell carcinoma of the skin • Malignant melanoma of skin	Likely pathogenic (May 31, 2016)
6-31972382-C-G		not specified	Uncertain significance (Dec 07, 2023)
6-31972407-G-T		not specified	Uncertain significance (Jun 09, 2022)
6-31972409-G-A		not specified	Uncertain significance (Mar 02, 2023)
6-31972415-A-G		not specified	Uncertain significance (Jan 26, 2022)
6-31972449-T-C		not specified	Uncertain significance (May 18, 2022)
6-31972492-T-G		not specified	Uncertain significance (Jan 17, 2024)
6-31972494-C-T		not specified	Uncertain significance (Jan 03, 2024)
6-31972624-C-G		not specified	Uncertain significance (Feb 28, 2023)
6-31972626-G-T		not specified	Uncertain significance (Dec 31, 2023)
6-31972627-C-T		not specified	Uncertain significance (Dec 31, 2023)
6-31978936-G-A		not specified	Likely benign (Oct 20, 2023)
6-31978951-G-A		not specified	Uncertain significance (Dec 17, 2023)
6-31978982-A-G		not specified	Uncertain significance (Jun 18, 2021)
6-31978988-A-G		not specified	Uncertain significance (Aug 02, 2023)
6-31979423-G-T		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STK19	protein_coding	protein_coding	ENST00000375333	8	11731

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.74e-9	0.444	125622	0	67	125689	0.000267

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.236	206	216	0.955	0.0000114	2323
Missense in Polyphen		41	52.86	0.77564		603
Synonymous	1.54	71	89.5	0.793	0.00000464	807
Loss of Function	0.955	15	19.6	0.767	0.00000111	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000575	0.000565
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000218	0.000218
Finnish	0.00	0.00
European (Non-Finnish)	0.000371	0.000361
Middle Eastern	0.000218	0.000218
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to be a protein kinase. In vitro it can phosphorylate casein-alpha on serine and threonine residues and histones on serine residues.

Recessive Scores

• pRec: 0.0938

Intolerance Scores

• loftool: 0.891
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• pHI: 0.229
• hipred: N
• hipred_score: 0.403
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.910

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stk19

Gene ontology

• Biological process: protein phosphorylation
• Cellular component: nucleus;nuclear speck
• Molecular function: protein serine/threonine kinase activity;ATP binding