WNT2B

Wnt family member 2B, the group of Wnt family

Basic information

Region (hg38): 1:112466541-112530165

Previous symbols: [ "WNT13" ]

Links

ENSG00000134245 ∙ NCBI:7482 ∙ OMIM:601968 ∙ HGNC:12781 ∙ Uniprot:Q93097 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• diarrhea 9 (Strong), mode of inheritance: AR
• diarrhea 9 (Limited), mode of inheritance: AR
• diarrhea 9 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diarrhea 9	AR	Gastrointestinal	The condition can involve severe and early-onset diarrhea, and awareness may help with management (eg, via parenteral nutrition, which has been described as necessary)	Gastrointestinal	29909964

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WNT2B gene.

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WNT2B 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				48	4	52
missense			60	1	2	63
nonsense	2		1			3
start loss						0
frameshift			1			1
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region				5		5
non coding				8	1	9
Total	2	0	63	57	7

Variants in WNT2B

This is a list of pathogenic ClinVar variants found in the WNT2B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-112509271-A-G			Likely benign (Nov 18, 2023)
1-112509273-C-T			Uncertain significance (Apr 01, 2022)
1-112509274-G-A			Likely benign (Jan 14, 2023)
1-112509274-G-C			Likely benign (Nov 29, 2022)
1-112509275-G-C		not specified	Uncertain significance (Aug 14, 2023)
1-112509285-A-C			Uncertain significance (Jul 01, 2022)
1-112509287-G-A			Benign (Feb 01, 2024)
1-112509297-A-G			Uncertain significance (Aug 06, 2022)
1-112509299-C-T		not specified	Uncertain significance (May 26, 2024)
1-112509309-G-C			Uncertain significance (Jun 22, 2022)
1-112509311-C-T			Uncertain significance (Oct 05, 2022)
1-112509314-G-A		not specified	Uncertain significance (Jul 11, 2023)
1-112509316-C-G			Likely benign (Nov 30, 2022)
1-112509324-C-G			Uncertain significance (Jun 26, 2022)
1-112509327-T-C		not specified	Uncertain significance (Aug 29, 2022)
1-112509329-C-T		not specified	Uncertain significance (Oct 17, 2023)
1-112509331-T-C			Likely benign (Feb 22, 2023)
1-112509335-C-A			Uncertain significance (Mar 22, 2022)
1-112509340-G-A			Likely benign (Apr 06, 2022)
1-112509341-C-T		not specified	Uncertain significance (May 05, 2023)
1-112509344-G-A			Likely benign (Jan 30, 2024)
1-112509352-C-T			Likely benign (Jul 27, 2023)
1-112509356-G-C		not specified	Uncertain significance (Dec 28, 2023)
1-112509364-G-A			Likely benign (Oct 04, 2023)
1-112509388-C-G			Likely benign (Sep 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WNT2B	protein_coding	protein_coding	ENST00000369684	5	63625

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0383	0.960	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	198	267	0.741	0.0000185	2492
Missense in Polyphen		60	115.19	0.52087		1074
Synonymous	-0.0268	98	97.7	1.00	0.00000529	836
Loss of Function	2.82	6	19.4	0.309	0.00000154	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.000210	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors. Functions in the canonical Wnt/beta- catenin signaling pathway. Plays a redundant role in embryonic lung development. {ECO:0000250|UniProtKB:O70283}.
• 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);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 Canonical;Wnt Mammals (Consensus)

Recessive Scores

• pRec: 0.223

Intolerance Scores

• loftool: 0.851
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.0424
• hipred: Y
• hipred_score: 0.735
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.379

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wnt2b
• Phenotype: respiratory system phenotype; normal phenotype

Zebrafish Information Network

• Gene name: wnt2bb
• Affected structure: extrahepatic duct
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: chondrocyte differentiation;lens development in camera-type eye;male gonad development;cellular response to starvation;Wnt signaling pathway;forebrain regionalization;neuron differentiation;cell fate commitment;canonical Wnt signaling pathway;lung induction;mesenchymal-epithelial cell signaling;iris morphogenesis;cornea development in camera-type eye;hematopoietic stem cell proliferation;positive regulation of branching involved in ureteric bud morphogenesis
• Cellular component: extracellular region;extracellular space;intracellular membrane-bounded organelle
• Molecular function: frizzled binding