STYXL1

serine/threonine/tyrosine interacting like 1, the group of MAP kinase phosphatases

Basic information

Region (hg38): 7:75996338-76048004

Previous symbols: [ "DUSP24" ]

Links

ENSG00000127952 ∙ NCBI:51657 ∙ OMIM:616695 ∙ HGNC:18165 ∙ Uniprot:Q9Y6J8 ∙ 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 STYXL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STYXL1 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			20	3		23
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	21	3	1

Variants in STYXL1

This is a list of pathogenic ClinVar variants found in the STYXL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-75996478-G-A		not specified	Uncertain significance (Nov 25, 2024)
7-75996479-G-C		STYXL1-related disorder	Benign (Feb 21, 2019)
7-75996496-A-G		not specified	Uncertain significance (Jan 10, 2023)
7-75996505-C-T		not specified	Uncertain significance (Feb 11, 2025)
7-75996522-C-G		not specified	Uncertain significance (Mar 06, 2023)
7-75996534-C-CT		not specified	Uncertain significance (Jan 01, 2019)
7-75996542-C-T		not specified	Uncertain significance (Dec 08, 2023)
7-76000934-C-T		not specified	Likely benign (Mar 31, 2023)
7-76000936-G-T		not specified	Uncertain significance (Mar 11, 2022)
7-76000946-G-A		not specified	Uncertain significance (Aug 18, 2023)
7-76000948-C-G		not specified	Uncertain significance (May 04, 2023)
7-76003778-C-T		not specified	Uncertain significance (Aug 14, 2023)
7-76003779-G-A		not specified	Uncertain significance (Jul 05, 2024)
7-76003796-T-C		not specified	Uncertain significance (Nov 19, 2022)
7-76003821-G-A		not specified	Uncertain significance (Feb 28, 2025)
7-76005346-C-A		not specified	Uncertain significance (Apr 12, 2024)
7-76005369-G-A		STYXL1-related disorder	Benign (Oct 30, 2019)
7-76013744-G-C		not specified	Uncertain significance (Oct 06, 2021)
7-76013785-G-A		not specified	Likely benign (Apr 06, 2022)
7-76013786-T-C		not specified	Uncertain significance (Jan 23, 2025)
7-76013860-T-C		not specified	Likely benign (Sep 09, 2024)
7-76013867-T-C			Uncertain significance (Dec 10, 2021)
7-76013879-G-A		not specified	Uncertain significance (Dec 11, 2023)
7-76021886-T-A		not specified	Uncertain significance (Mar 29, 2023)
7-76021887-C-T		not specified	Uncertain significance (Aug 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STYXL1	protein_coding	protein_coding	ENST00000248600	8	51667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.32e-8	0.206	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.604	162	185	0.875	0.0000104	2080
Missense in Polyphen		50	48.437	1.0323		574
Synonymous	0.588	64	70.3	0.911	0.00000400	580
Loss of Function	0.387	13	14.6	0.891	6.81e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000539	0.000539
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.000410	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytically inactive phosphatase (PubMed:20180778, PubMed:23163895). By binding to G3BP1, inhibits the formation of G3BP1-induced stress granules (PubMed:20180778, PubMed:23163895). Does not act by protecting the dephosphorylation of G3BP1 at 'Ser- 149' (PubMed:23163895). Inhibits PTPMT1 phosphatase activity (PubMed:24709986). By inhibiting PTPMT1, positively regulates intrinsic apoptosis (PubMed:21262771). May play a role in the formation of neurites during neuronal development (PubMed:29250526). {ECO:0000269|PubMed:20180778, ECO:0000269|PubMed:21262771, ECO:0000269|PubMed:23163895, ECO:0000269|PubMed:24709986, ECO:0000269|PubMed:29250526}.

Recessive Scores

• pRec: 0.0884

Intolerance Scores

• loftool: 0.558
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.0470
• hipred: N
• hipred_score: 0.145
• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.638

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Styxl1

Gene ontology

• Biological process: protein dephosphorylation;positive regulation of neuron projection development;negative regulation of phosphoprotein phosphatase activity;intracellular signal transduction;negative regulation of stress granule assembly;regulation of intrinsic apoptotic signaling pathway;positive regulation of intrinsic apoptotic signaling pathway
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: pseudophosphatase activity;protein phosphatase inhibitor activity;protein binding;protein tyrosine/serine/threonine phosphatase activity;protein phosphatase binding