STYK1

protein-coding

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

Gene summary

Receptor protein tyrosine kinases, like STYK1, play important roles in diverse cellular and developmental processes, such as cell proliferation, differentiation, and survival (Liu et al., 2004 [PubMed 15150103]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_018423.3

Inheritance

—

ClinVar variants

U:65B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr12:10,618,923-10,674,318

External References & Databases

Ensembl (ENSG00000060140)

Transcript & Mutation Effects

hg38 • Region Span ~55.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to STYK1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018423.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			63 clinvar	3 clinvar	1 clinvar	67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	65	4	2	71

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018423.3	RefSeq	NP_060893.2	9	MANE Select
ENST00000075503.8	Ensembl	ENSP00000075503.3	9	MANE Select
ENST00000535345.5	Ensembl	ENSP00000444488.1	2	Standard
ENST00000538867.5	Ensembl	ENSP00000445391.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Focal Adhesion

Biological Process

peptidyl-tyrosine phosphorylation
regulation of cell population proliferation

Molecular Function

non-membrane spanning protein tyrosine kinase activity
protein binding
ATP binding

Cellular Component

plasma membrane
integral component of membrane
extrinsic component of cytoplasmic side of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000075503
Coding exons: 9
Length: 55380
Individuals with no LoFs: 125651
Homozygous LoFs: 0
Heterozygous LoFs: 97
Defined: 125748
p: 0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0302	236	237	0.994	0.0000130	2729
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0.0030	0.0030	notable
East Asian	0.00011	0.00011	rare
Finnish	0.00060	0.00060	rare
European (Non-Finnish)	0.00026	0.00026	rare
South Asian	0.00020	0.00020	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.466
RVIS EVS: 0.18
RVIS percentile EVS: 66.07

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.744

Gene Damage Prediction

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