WNT2

Wnt family member 2, the group of Wnt family

Basic information

Region (hg38): 7:117275450-117323152

Previous symbols: [ "INT1L1" ]

Links

ENSG00000105989 ∙ NCBI:7472 ∙ OMIM:147870 ∙ HGNC:12780 ∙ Uniprot:P09544 ∙ 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 WNT2 gene.

• Inborn genetic diseases (7 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WNT2 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			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	2

Variants in WNT2

This is a list of pathogenic ClinVar variants found in the WNT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-117278181-T-C			Benign (Jun 06, 2018)
7-117278241-C-T		not specified	Uncertain significance (May 10, 2022)
7-117278279-C-T		not specified	Uncertain significance (Jan 02, 2024)
7-117278283-T-C		not specified	Uncertain significance (Oct 05, 2023)
7-117278325-C-T		not specified	Uncertain significance (Mar 22, 2022)
7-117297673-C-T			Benign (Jun 13, 2018)
7-117297734-A-G		not specified	Uncertain significance (Nov 03, 2022)
7-117297776-G-A		not specified	Uncertain significance (Feb 28, 2024)
7-117315142-C-A		not specified	Uncertain significance (Oct 25, 2023)
7-117315153-C-T		not specified	Uncertain significance (Jul 12, 2022)
7-117315241-T-C		not specified	Uncertain significance (Aug 17, 2021)
7-117315342-C-T		not specified	Uncertain significance (Dec 19, 2022)
7-117320674-C-G		not specified	Uncertain significance (Aug 12, 2022)
7-117320690-G-A		not specified	Uncertain significance (May 30, 2023)
7-117320789-T-C		not specified	Uncertain significance (Oct 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WNT2	protein_coding	protein_coding	ENST00000265441	5	46659

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0178	0.978	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	172	222	0.776	0.0000130	2389
Missense in Polyphen		67	99.119	0.67595		1097
Synonymous	-0.00704	85	84.9	1.00	0.00000514	687
Loss of Function	2.52	6	17.3	0.347	9.97e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000563	0.0000462
European (Non-Finnish)	0.0000534	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors. Functions in the canonical Wnt signaling pathway that results in activation of transcription factors of the TCF/LEF family (PubMed:20018874). Functions as upstream regulator of FGF10 expression. Plays an important role in embryonic lung development. May contribute to embryonic brain development by regulating the proliferation of dopaminergic precursors and neurons (By similarity). {ECO:0000250|UniProtKB:P21552, ECO:0000269|PubMed:20018874}.
• Pathway: Gastric cancer - Homo sapiens (human);mTOR signaling pathway - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Breast cancer - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Basal cell carcinoma - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Melanogenesis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);WNT-Core;Differentiation Pathway;ESC Pluripotency Pathways;Wnt Signaling Pathway and Pluripotency;Wnt Signaling in Kidney Disease;EMT transition in Colorectal Cancer;Wnt Signaling Pathway;DNA Damage Response (only ATM dependent);Signaling by GPCR;Signaling by WNT;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Class B/2 (Secretin family receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;WNT ligand biogenesis and trafficking;GPCR signaling-G alpha i;Wnt;Wnt Canonical;Wnt signaling network;Wnt Mammals (Consensus)

Recessive Scores

• pRec: 0.435

Intolerance Scores

• loftool: 0.577
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.140
• hipred: Y
• hipred_score: 0.792
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wnt2
• Phenotype: respiratory system phenotype; embryo phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); homeostasis/metabolism phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: wnt2
• Affected structure: pancreatic B cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: positive regulation of endothelial cell proliferation;positive regulation of mesenchymal cell proliferation;lens development in camera-type eye;cell-cell signaling;positive regulation of cell population proliferation;regulation of signaling receptor activity;Wnt signaling pathway;neurogenesis;neuron differentiation;lung development;cell proliferation in midbrain;cell fate commitment;positive regulation of transcription by RNA polymerase II;positive regulation of fibroblast proliferation;positive regulation of DNA-binding transcription factor activity;atrial cardiac muscle tissue morphogenesis;positive regulation of cardiac muscle cell proliferation;canonical Wnt signaling pathway;cardiac epithelial to mesenchymal transition;lung induction;positive regulation of epithelial cell proliferation involved in lung morphogenesis;labyrinthine layer blood vessel development;iris morphogenesis;mammary gland epithelium development;cellular response to retinoic acid;cellular response to transforming growth factor beta stimulus;midbrain dopaminergic neuron differentiation;canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation
• Cellular component: extracellular region;extracellular space;cytoplasm;extrinsic component of external side of plasma membrane;collagen-containing extracellular matrix;Wnt signalosome
• Molecular function: frizzled binding;cytokine activity;protein binding;receptor ligand activity