STYXL2

protein-coding

serine/threonine/tyrosine interacting like 2

Gene summary

Predicted to enable MAP kinase phosphatase activity and protein tyrosine/serine/threonine phosphatase activity. Predicted to be involved in negative regulation of MAPK cascade. Predicted to be located in sarcomere. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

DUSP27

MANE transcript

NM_001080426.3

Inheritance

—

ClinVar variants

U:243B:21

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr1:167,094,075-167,129,165

External References & Databases

Ensembl (ENSG00000198842)

Transcript & Mutation Effects

hg38 • Region Span ~35.1 kb

Loading mutation effect viewer...

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 STYXL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 248

not providedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080426.3. 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			2 clinvar	2 clinvar	4 clinvar	8
missense			240 clinvar	14 clinvar	1 clinvar	255
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	243	16	5	264

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080426.3	RefSeq	NP_001073895.1	5	MANE Select
ENST00000361200.7	Ensembl	ENSP00000354483.2	5	MANE Select
ENST00000271385.9	Ensembl	ENSP00000271385.5	5	Standard
ENST00000443333.1	Ensembl	ENSP00000404874.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein dephosphorylation

Molecular Function

protein tyrosine/serine/threonine phosphatase activity

Cellular Component

sarcomere

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361200
Coding exons: 5
Length: 35121
Individuals with no LoFs: 125430
Homozygous LoFs: 0
Heterozygous LoFs: 318
Defined: 125748
p: 0.00127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.604	708	664	1.07	0.0000396	7584
Missense (PolyPhen)		202	187.23	1.0789		2267
Synonymous	-0.302	286	280	1.02	0.0000181	2233
Loss of Function	0.977	32	38.5	0.830	0.00000196	487

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0023	0.0023	notable
Latino/Admixed American	0.0012	0.0012	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.0011	0.0010	notable
Finnish	0.00051	0.00051	rare
European (Non-Finnish)	0.0016	0.0016	notable
South Asian	0.00072	0.00072	rare
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be required for myofiber maturation. {ECO:0000250|UniProtKB:F1QWM2}.;

Intolerance Scores

LoFtool: 0.863
RVIS EVS: 0.97
RVIS percentile EVS: 90.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.135

Gene Damage Prediction

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