WNT9B

Wnt family member 9B, the group of Wnt family

Basic information

Region (hg38): 17:46833201-46886730

Previous symbols: [ "WNT15" ]

Links

ENSG00000158955 ∙ NCBI:7484 ∙ OMIM:602864 ∙ HGNC:12779 ∙ Uniprot:O14905 ∙ 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 WNT9B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WNT9B 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				10	6	16
missense			25	6	5	36
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	25	16	11

Variants in WNT9B

This is a list of pathogenic ClinVar variants found in the WNT9B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-46851642-C-A			Uncertain significance (Nov 19, 2022)
17-46851643-G-GC		Renal dysplasia;Chronic kidney disease;Renal hypoplasia	Likely pathogenic (Jun 19, 2021)
17-46872524-G-A			Likely benign (Oct 29, 2023)
17-46872574-G-A			Benign (Nov 05, 2021)
17-46872574-G-C		WNT9B-related disorder	Likely benign (Oct 28, 2019)
17-46872579-A-G			Benign (Jan 22, 2024)
17-46872583-C-T			Benign/Likely benign (Oct 29, 2023)
17-46872601-G-A		WNT9B-related disorder	Likely benign (Mar 31, 2023)
17-46872607-C-T			Benign (Jan 23, 2024)
17-46872618-T-G			Uncertain significance (Oct 17, 2022)
17-46872623-C-T		Inborn genetic diseases	Uncertain significance (Apr 01, 2024)
17-46872627-G-A			Uncertain significance (Jul 10, 2023)
17-46872653-C-T		Inborn genetic diseases	Uncertain significance (Oct 25, 2023)
17-46872673-G-A			Likely benign (Oct 04, 2022)
17-46872720-G-A		WNT9B-related disorder	Benign (Aug 24, 2023)
17-46872729-G-A		WNT9B-related disorder	Likely benign (Mar 21, 2022)
17-46872756-T-C		WNT9B-related disorder	Benign (Jan 31, 2024)
17-46872759-G-T		Inborn genetic diseases	Uncertain significance (Jul 12, 2023)
17-46875094-G-C		WNT9B-related disorder	Likely benign (Sep 19, 2019)
17-46875141-C-T			Likely benign (Sep 11, 2023)
17-46875142-G-A			Benign (Dec 02, 2023)
17-46875155-C-A			Uncertain significance (Jul 16, 2021)
17-46875164-G-A			Uncertain significance (Aug 17, 2023)
17-46875165-G-T			Benign (Jan 29, 2024)
17-46875171-C-G			Uncertain significance (Feb 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WNT9B	protein_coding	protein_coding	ENST00000290015	4	53530

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.541	0.456	125718	0	6	125724	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.803	182	215	0.846	0.0000142	2256
Missense in Polyphen		76	102.92	0.73845		998
Synonymous	-0.114	98	96.6	1.01	0.00000616	766
Loss of Function	2.49	2	10.8	0.185	4.58e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000902	0.00000879
Middle Eastern	0.0000547	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors (PubMed:20093360). Functions in the canonical Wnt/beta-catenin signaling pathway. Plays a role in cranofacial development and is required for normal fusion of the palate during embryonic development (By similarity). {ECO:0000250|UniProtKB:O35468, ECO:0000305|PubMed:20093360}.
• 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);ESC Pluripotency Pathways;Wnt Signaling Pathway and Pluripotency;Wnt Signaling in Kidney Disease;EMT transition in Colorectal Cancer;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: 0.183

Intolerance Scores

• loftool: 0.459
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.96

Haploinsufficiency Scores

• pHI: 0.121
• hipred: Y
• hipred_score: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.677

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wnt9b
• 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); reproductive system phenotype; embryo phenotype; renal/urinary system phenotype; digestive/alimentary phenotype; growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: branching involved in ureteric bud morphogenesis;in utero embryonic development;regulation of protein phosphorylation;regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis;cell-cell signaling;multicellular organism development;cellular response to starvation;regulation of asymmetric cell division;regulation of signaling receptor activity;Wnt signaling pathway;neuron differentiation;male genitalia development;response to retinoic acid;regulation of tube size;positive regulation of catalytic activity;cell fate commitment;embryonic cranial skeleton morphogenesis;roof of mouth development;canonical Wnt signaling pathway;Wnt signaling pathway, planar cell polarity pathway;uterus morphogenesis;cornea development in camera-type eye;cellular response to retinoic acid;kidney rudiment formation;mesenchymal stem cell maintenance involved in nephron morphogenesis;collecting duct development;establishment of planar polarity involved in nephron morphogenesis;metanephric tubule formation;mesonephric duct formation;negative regulation of stem cell population maintenance;midbrain dopaminergic neuron differentiation;non-canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation
• Cellular component: extracellular region;extracellular space
• Molecular function: frizzled binding;co-receptor binding;receptor ligand activity