STYX

serine/threonine/tyrosine interacting protein, the group of Atypical dual specificity phosphatases

Basic information

Region (hg38): 14:52730165-52774989

Links

ENSG00000198252 ∙ NCBI:6815 ∙ OMIM:615814 ∙ HGNC:11447 ∙ Uniprot:Q8WUJ0 ∙ 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 STYX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STYX 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	8	0	0

Variants in STYX

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

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

Position	Type	Phenotype	Significance	ClinVar
14-52730513-G-T		not specified	Uncertain significance (Aug 15, 2023)
14-52730517-A-G		not specified	Uncertain significance (Mar 05, 2024)
14-52730529-G-A		not specified	Uncertain significance (Sep 29, 2023)
14-52744844-C-A			Benign (May 08, 2018)
14-52746475-G-A		not specified	Uncertain significance (Dec 13, 2022)
14-52746477-A-G		not specified	Uncertain significance (Jul 14, 2021)
14-52750725-A-G		not specified	Uncertain significance (Jul 15, 2021)
14-52756597-C-T		not specified	Uncertain significance (Dec 27, 2023)
14-52757320-C-T		not specified	Uncertain significance (May 20, 2024)
14-52768915-G-A		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STYX	protein_coding	protein_coding	ENST00000354586	11	44819

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.377	0.622	125706	0	6	125712	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	72	117	0.616	0.00000538	1472
Missense in Polyphen		13	31.239	0.41615		422
Synonymous	0.113	35	35.9	0.976	0.00000163	376
Loss of Function	3.04	4	17.9	0.224	8.58e-7	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000666	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000288	0.0000264
Middle Eastern	0.0000666	0.0000544
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytically inactive phosphatase (PubMed:23847209). Acts as a nuclear anchor for MAPK1/MAPK3 (ERK1/ERK2) (PubMed:23847209). Modulates cell-fate decisions and cell migration by spatiotemporal regulation of MAPK1/MAPK3 (ERK1/ERK2) (PubMed:23847209). By binding to the F-box of FBXW7, prevents the assembly of FBXW7 into the SCF E3 ubiquitin-protein ligase complex, and thereby inhibits degradation of its substrates (PubMed:28007894). Plays a role in spermatogenesis (By similarity). {ECO:0000250|UniProtKB:Q60969, ECO:0000269|PubMed:23847209, ECO:0000269|PubMed:28007894}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.307
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.343
• hipred: N
• hipred_score: 0.475
• ghis: 0.675

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Styx
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: protein dephosphorylation;negative regulation of protein binding;negative regulation of catalytic activity;MAPK export from nucleus;negative regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process;regulation of ERK1 and ERK2 cascade
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: pseudophosphatase activity;protein binding;protein tyrosine/serine/threonine phosphatase activity;F-box domain binding