STYXL2

serine/threonine/tyrosine interacting like 2

Basic information

Region (hg38): 1:167094075-167129165

Previous symbols: [ "DUSP27" ]

Links

ENSG00000198842 ∙ NCBI:92235 ∙ ∙ HGNC:25034 ∙ Uniprot:Q5VZP5 ∙ 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 STYXL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STYXL2 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				1	4	5
missense			125	8	1	134
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	126	9	6

Variants in STYXL2

This is a list of pathogenic ClinVar variants found in the STYXL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-167094854-C-T		not specified	Uncertain significance (Mar 29, 2023)
1-167094895-G-C		not specified	Uncertain significance (Dec 01, 2022)
1-167094907-G-A		not specified	Uncertain significance (Aug 27, 2024)
1-167094912-C-A		not specified	Uncertain significance (Mar 18, 2024)
1-167094920-C-T		not specified	Uncertain significance (Jul 16, 2021)
1-167094928-G-A		not specified	Uncertain significance (Oct 06, 2024)
1-167094935-A-G		not specified	Uncertain significance (Nov 27, 2023)
1-167094937-C-A		not specified	Uncertain significance (Sep 30, 2024)
1-167094941-G-A		not specified	Uncertain significance (Jun 03, 2022)
1-167113751-T-C		not specified	Uncertain significance (Oct 19, 2024)
1-167113790-A-G		not specified	Uncertain significance (Jul 12, 2022)
1-167117340-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-167117353-A-T			Benign (Apr 30, 2018)
1-167117357-G-A		not specified	Likely benign (Nov 07, 2022)
1-167117385-C-G		not specified	Uncertain significance (Oct 12, 2024)
1-167117396-C-A		not specified	Uncertain significance (Apr 26, 2024)
1-167117480-C-T		not specified	Uncertain significance (Jun 18, 2021)
1-167117481-G-A			Likely benign (Apr 01, 2023)
1-167117484-C-A		not specified	Uncertain significance (Jul 22, 2024)
1-167117492-C-G		not specified	Uncertain significance (Mar 20, 2023)
1-167117522-G-T		not specified	Uncertain significance (May 08, 2023)
1-167117528-G-C		not specified	Uncertain significance (Apr 09, 2024)
1-167117532-T-C		not specified	Uncertain significance (Apr 25, 2022)
1-167119239-C-T			Benign (Apr 10, 2018)
1-167119270-G-C			Benign (Apr 05, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STYXL2	protein_coding	protein_coding	ENST00000361200	5	35121

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.23e-19	0.0424	125430	0	318	125748	0.00127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.604	708	664	1.07	0.0000396	7584
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00350	0.00350
Ashkenazi Jewish	0.000302	0.000298
East Asian	0.00107	0.00103
Finnish	0.000508	0.000508
European (Non-Finnish)	0.00156	0.00156
Middle Eastern	0.00107	0.00103
South Asian	0.000723	0.000719
Other	0.00130	0.00130

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.251
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.135

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dusp27

Gene ontology

• Biological process: protein dephosphorylation
• Cellular component: sarcomere
• Molecular function: protein tyrosine/serine/threonine phosphatase activity