WNT8B

Wnt family member 8B, the group of Wnt family

Basic information

Region (hg38): 10:100463009-100483744

Links

ENSG00000075290

∙ NCBI:7479 ∙ OMIM:601396 ∙ HGNC:12789 ∙ Uniprot:Q93098 ∙ 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 WNT8B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WNT8B 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						0
missense			6 clinvar		1 clinvar	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	6	0	1

Variants in WNT8B

This is a list of pathogenic ClinVar variants found in the WNT8B region.

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

Position	Phenotype	Significance	ClinVar
10-100481004-G-A	not specified	Uncertain significance (Jul 26, 2022)	2352167
10-100481108-C-T	not specified	Uncertain significance (Apr 22, 2022)	2284682
10-100481915-G-T	not specified	Uncertain significance (Sep 14, 2022)	2312127
10-100482273-G-A		Benign (Jul 13, 2018)	782771
10-100482564-A-C	not specified	Uncertain significance (Feb 06, 2024)	3190758
10-100482650-C-T	not specified	Uncertain significance (May 15, 2024)	3333234
10-100482676-G-T	not specified	Uncertain significance (Nov 22, 2022)	2329043
10-100482688-A-G	not specified	Uncertain significance (Feb 12, 2024)	3190759
10-100482762-C-A		Benign (Jul 13, 2018)	782772

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WNT8B	protein_coding	protein_coding	ENST00000343737	6	20704

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0110	0.981	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.92	128	206	0.623	0.00000976	2254
Missense in Polyphen		40	78.992	0.50638		902
Synonymous	0.169	82	84.0	0.977	0.00000393	711
Loss of Function	2.32	6	16.0	0.375	6.89e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000340	0.000326
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000165	0.000163
Other	0.000354	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors. May play an important role in the development and differentiation of certain forebrain structures, notably the hippocampus. {ECO:0000269|PubMed:9536085}.;
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);EMT transition in Colorectal Cancer;Signaling by GPCR;Signaling by WNT;Signal Transduction;wnt lrp6 signalling;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Disassembly of the destruction complex and recruitment of AXIN to the membrane;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;TCF dependent signaling in response to WNT;Wnt Mammals (Consensus)

Recessive Scores

pRec: 0.203

Intolerance Scores

loftool: 0.386
rvis_EVS: -0.05
rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

pHI: 0.507
hipred: Y
hipred_score: 0.875
ghis: 0.424

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.239

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Wnt8b
Phenotype

Zebrafish Information Network

Gene name: wnt8b
Affected structure: anterior commissure
Phenotype tag: abnormal
Phenotype quality: has fewer parts of type

Gene ontology

Biological process: signal transduction;gastrulation;nervous system development;regulation of signaling receptor activity;Wnt signaling pathway;neuron differentiation;response to estradiol;response to retinoic acid;cell fate commitment;determination of dorsal identity;canonical Wnt signaling pathway;cellular response to retinoic acid;beta-catenin destruction complex disassembly
Cellular component: extracellular region;extracellular space
Molecular function: frizzled binding;receptor ligand activity