WNT9B

protein-coding

Wnt family member 9B, the group of Wnt family

Gene summary

The WNT gene family consists of structurally related genes that encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. Study of its expression in the teratocarcinoma cell line NT2 suggests that it may be implicated in the early process of neuronal differentiation of NT2 cells induced by retinoic acid. This gene is clustered with WNT3, another family member, in the chromosome 17q21 region. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

Previous symbols:

WNT15

MANE transcript

NM_003396.3

Inheritance

ClinVar variants

P:2U:62B:27

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr17:46,833,201-46,886,730

External References & Databases

Ensembl (ENSG00000158955)

Transcript & Mutation Effects

hg38 • Region Span ~53.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

renal agenesisMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0018470

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WNT9B variants in ClinVar

8 Conditions Cataloged

not providedTotal: 48

Inborn genetic diseasesTotal: 47

WNT9B-related disorderTotal: 10

Chronic kidney diseaseTotal: 2

Cystic renal dysplasiaTotal: 1

not specifiedTotal: 1

Renal dysplasiaTotal: 1

Renal hypoplasiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003396.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				12 clinvar	5 clinvar	17
missense		1 clinvar	61 clinvar	4 clinvar	6 clinvar	72
nonsense						0
start loss						0
frameshift		1 clinvar	1 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	0	2	62	16	11	91

Highest pathogenic variant AF is 0.000014894928

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003396.3	RefSeq	NP_003387.1	4	MANE Select
ENST00000290015.7	Ensembl	ENSP00000290015.2	4	MANE Select
NM_001320458.2	RefSeq	NP_001307387.1	5	Standard
ENST00000393461.2	Ensembl	ENSP00000377105.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

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

Molecular Function

frizzled binding
co-receptor binding
receptor ligand activity

Cellular Component

extracellular region
extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000290015
Coding exons: 4
Length: 53530
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125724
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.803	182	215	0.846	0.0000142	2256
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000090	0.0000088	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.183

Intolerance Scores

LoFtool: 0.459
RVIS EVS: 0.53
RVIS percentile EVS: 80.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.677

Gene Damage Prediction

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