WLS

Wnt ligand secretion mediator, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:68098472-68233120

Previous symbols: [ "C1orf139", "GPR177" ]

Links

ENSG00000116729 ∙ NCBI:79971 ∙ OMIM:611514 ∙ HGNC:30238 ∙ Uniprot:Q5T9L3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Zaki syndrome (Strong), mode of inheritance: AR
• Zaki syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WLS gene.

• Inborn genetic diseases (23 variants)
• Zaki syndrome (7 variants)
• WLS syndrome (4 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WLS 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	1
missense	2	2	25			29
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	2	2	25	0	2

Highest pathogenic variant AF is 0.0000460

Variants in WLS

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

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

Position	Type	Phenotype	Significance	ClinVar
1-68098709-CA-C		WLS-related disorder	Benign/Likely benign (Jul 15, 2023)
1-68126246-G-A		WLS syndrome • Zaki syndrome	Likely pathogenic (Apr 21, 2021)
1-68126260-A-G		WLS syndrome • Zaki syndrome	Likely pathogenic (Apr 21, 2021)
1-68137782-T-C		not specified	Uncertain significance (Dec 15, 2022)
1-68137795-C-G		not specified	Uncertain significance (Jun 28, 2022)
1-68137800-T-C		not specified	Uncertain significance (Jul 28, 2021)
1-68137829-C-T		not specified	Uncertain significance (Jan 03, 2022)
1-68137846-A-G		not specified	Uncertain significance (Jul 20, 2022)
1-68137863-T-C		WLS syndrome • Zaki syndrome	Pathogenic (Apr 21, 2021)
1-68137882-C-A		not specified	Uncertain significance (Aug 21, 2023)
1-68137929-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-68141212-G-T		WLS-related disorder	Uncertain significance (Dec 21, 2023)
1-68144577-C-T		not specified	Uncertain significance (Apr 22, 2022)
1-68144633-T-C		not specified	Uncertain significance (Jan 04, 2024)
1-68145933-C-T		not specified	Uncertain significance (Aug 28, 2023)
1-68145972-T-C		WLS syndrome • Zaki syndrome	Pathogenic (Apr 21, 2021)
1-68145979-A-C		not specified	Uncertain significance (Jan 27, 2022)
1-68150199-C-T		not specified	Uncertain significance (Mar 17, 2023)
1-68150241-A-G		Zaki syndrome	Uncertain significance (Dec 16, 2022)
1-68150244-T-C		not specified	Uncertain significance (Jan 25, 2023)
1-68153518-T-G		not specified	Uncertain significance (Dec 17, 2023)
1-68153595-G-A		not specified	Uncertain significance (Apr 13, 2022)
1-68153602-A-G		not specified	Uncertain significance (Feb 28, 2023)
1-68153618-C-G		Zaki syndrome	Uncertain significance (-)
1-68155106-C-T		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WLS	protein_coding	protein_coding	ENST00000354777	12	134662

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0205	0.979	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.603	295	326	0.906	0.0000181	3652
Missense in Polyphen		86	121.47	0.70797		1390
Synonymous	0.0102	119	119	0.999	0.00000717	991
Loss of Function	3.33	8	26.5	0.302	0.00000142	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.0000984	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates Wnt proteins sorting and secretion in a feedback regulatory mechanism. This reciprocal interaction plays a key role in the regulation of expression, subcellular location, binding and organelle-specific association of Wnt proteins. Plays also an important role in establishment of the anterior-posterior body axis formation during development (By similarity). {ECO:0000250, ECO:0000269|PubMed:16678095, ECO:0000269|PubMed:16678096}.
• Pathway: Signaling by WNT;Signal Transduction;WNT ligand biogenesis and trafficking (Consensus)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.443
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.06

Haploinsufficiency Scores

• pHI: 0.193
• hipred: Y
• hipred_score: 0.605
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wls
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; muscle phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype

Zebrafish Information Network

• Gene name: wls
• Affected structure: chondrocyte
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: mesoderm formation;intracellular protein transport;anterior/posterior axis specification;Wnt signaling pathway;positive regulation of Wnt signaling pathway;midbrain development;hindbrain development;exocrine pancreas development;positive regulation of I-kappaB kinase/NF-kappaB signaling;Wnt protein secretion;positive regulation of Wnt protein secretion;positive regulation of canonical Wnt signaling pathway
• Cellular component: Golgi membrane;early endosome;endoplasmic reticulum membrane;Golgi apparatus;trans-Golgi network;plasma membrane;integral component of membrane;endocytic vesicle membrane;cytoplasmic vesicle;early endosome membrane;dendrite membrane;dendrite cytoplasm;extracellular exosome
• Molecular function: protein binding;Wnt-protein binding;mu-type opioid receptor binding