WNT7B

protein-coding

Wnt family member 7B, the group of Wnt family

Gene summary

This gene is a member of the WNT gene family, which 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. Among members of the human WNT family, this gene product is most similar to WNT7A protein. [provided by RefSeq, Oct 2008]

MANE transcript

NM_058238.3

Inheritance

ClinVar variants

P:6U:42B:6

Top phenotype

multiple congenital anomalies/dysmorphic syndrome

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr22:45,920,366-45,977,162

External References & Databases

Ensembl (ENSG00000188064)

Transcript & Mutation Effects

hg38 • Region Span ~56.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

multiple congenital anomalies/dysmorphic syndromeLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019042

Submitter: Ambry Genetics

Tourette syndromeNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

multiple congenital anomalies/dysmorphic syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0019042

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WNT7B variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 6

Microphthalmia, syndromic 9Total: 5

Anophthalmia-microphthalmia syndromeTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_058238.3. 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			1 clinvar	4 clinvar	2 clinvar	7
missense	1 clinvar	1 clinvar	40 clinvar			42
nonsense	3 clinvar					3
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	4	2	42	4	2	54

Highest pathogenic variant AF is 0.00000821317

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_058238.3	RefSeq	NP_478679.1	4	MANE Select
ENST00000339464.9	Ensembl	ENSP00000341032.4	4	MANE Select
NM_001410806.1	RefSeq	NP_001397735.1	4	Standard
ENST00000409496.7	Ensembl	ENSP00000386546.3	4	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

in utero embryonic development
metanephros morphogenesis
activation of JUN kinase activity
regulation of signaling receptor activity
Wnt signaling pathway

Molecular Function

frizzled binding
receptor ligand activity

Cellular Component

extracellular region
extracellular space
endoplasmic reticulum lumen
Golgi lumen
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000339464
Coding exons: 4
Length: 56768
Individuals with no LoFs: 125701
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125712
p: 0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.99	171	262	0.653	0.0000198	2265
Missense (PolyPhen)		56	112.56	0.49751		989
Synonymous	-2.02	139	112	1.24	0.00000932	672
Loss of Function	2.12	8	17.6	0.455	0.00000101	162

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors. Functions in the canonical Wnt/beta- catenin signaling pathway in vascular smooth muscle cells. Required for normal fusion of the chorion and the allantois during placenta development. {ECO:0000250|UniProtKB:P28047}.;

Recessive Scores

pRec: 0.216

Intolerance Scores

LoFtool: 0.601
RVIS EVS: -1.09
RVIS percentile EVS: 7.05

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.503

Gene Damage Prediction

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