STYK1

serine/threonine/tyrosine kinase 1, the group of Receptor tyrosine kinases

Basic information

Region (hg38): 12:10618922-10674318

Links

ENSG00000060140 ∙ NCBI:55359 ∙ OMIM:611433 ∙ HGNC:18889 ∙ Uniprot:Q6J9G0 ∙ 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 STYK1 gene.

• Inborn genetic diseases (16 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STYK1 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					1	1
missense			16		1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	2

Variants in STYK1

This is a list of pathogenic ClinVar variants found in the STYK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10620263-T-C		not specified	Uncertain significance (Feb 05, 2024)
12-10620316-C-T		not specified	Uncertain significance (Jun 24, 2022)
12-10620341-T-C		not specified	Uncertain significance (Jan 31, 2024)
12-10621906-A-G		not specified	Uncertain significance (Jan 03, 2024)
12-10622655-T-C		not specified	Uncertain significance (Jan 18, 2023)
12-10624678-A-G		not specified	Uncertain significance (Nov 12, 2021)
12-10624742-G-C		not specified	Uncertain significance (Feb 15, 2023)
12-10624798-T-C		not specified	Uncertain significance (Sep 12, 2023)
12-10624801-A-G		not specified	Uncertain significance (Feb 13, 2023)
12-10624811-T-C		not specified	Uncertain significance (Jul 22, 2022)
12-10624856-A-G		not specified	Uncertain significance (Jul 09, 2021)
12-10627684-T-C		not specified	Uncertain significance (Aug 02, 2021)
12-10629494-C-T		not specified	Uncertain significance (Jul 09, 2021)
12-10629497-C-T		not specified	Uncertain significance (Jun 12, 2023)
12-10629593-A-G		not specified	Uncertain significance (Dec 18, 2023)
12-10631058-G-C			Benign (May 21, 2018)
12-10631083-G-T		not specified	Uncertain significance (Apr 07, 2022)
12-10631123-A-C		not specified	Uncertain significance (Dec 27, 2022)
12-10631263-C-T		not specified	Uncertain significance (Sep 14, 2023)
12-10631285-T-C			Benign (May 21, 2018)
12-10634059-G-A		not specified	Uncertain significance (Apr 12, 2022)
12-10634116-C-T		not specified	Uncertain significance (Mar 07, 2024)
12-10634605-C-T		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STYK1	protein_coding	protein_coding	ENST00000075503	9	55380

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.10e-11	0.279	125651	0	97	125748	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0302	236	237	0.994	0.0000130	2729
Missense in Polyphen		95	95.919	0.99042		1098
Synonymous	0.738	78	86.7	0.899	0.00000447	848
Loss of Function	0.881	18	22.5	0.800	0.00000119	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000410	0.000410
Ashkenazi Jewish	0.00301	0.00298
East Asian	0.000109	0.000109
Finnish	0.000601	0.000601
European (Non-Finnish)	0.000264	0.000264
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable tyrosine protein-kinase, which has strong transforming capabilities on a variety of cell lines. When overexpressed, it can also induce tumor cell invasion as well as metastasis in distant organs. May act by activating both MAP kinase and phosphatidylinositol 3'-kinases (PI3K) pathways (By similarity). {ECO:0000250}.
• Pathway: Focal Adhesion (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.466
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.07

Haploinsufficiency Scores

• pHI: 0.300
• hipred: N
• hipred_score: 0.150
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.744

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Styk1

Gene ontology

• Biological process: peptidyl-tyrosine phosphorylation;regulation of cell population proliferation
• Cellular component: plasma membrane;integral component of membrane;extrinsic component of cytoplasmic side of plasma membrane
• Molecular function: non-membrane spanning protein tyrosine kinase activity;protein binding;ATP binding