STYK1

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

Basic information

Region (hg38): 12:10618923-10674318

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.

• not_specified (56 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. These statistics are base on transcript: NM_000018423.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			52	3	1	56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	4	2

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