FZD6

protein-coding

frizzled class receptor 6, the group of G protein-coupled receptors, Class F frizzled

Gene summary

This gene represents a member of the 'frizzled' gene family, which encode 7-transmembrane domain proteins that are receptors for Wnt signaling proteins. The protein encoded by this family member contains a signal peptide, a cysteine-rich domain in the N-terminal extracellular region, and seven transmembrane domains, but unlike other family members, this protein does not contain a C-terminal PDZ domain-binding motif. This protein functions as a negative regulator of the canonical Wnt/beta-catenin signaling cascade, thereby inhibiting the processes that trigger oncogenic transformation, cell proliferation, and inhibition of apoptosis. Alternative splicing results in multiple transcript variants, some of which do not encode a protein with a predicted signal peptide.[provided by RefSeq, Aug 2011]

MANE transcript

NM_003506.4

Inheritance

AR

ClinVar variants

P:9U:90B:9

Top phenotype

Nail disorder, nonsyndromic noncongenital 10

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr8:103,298,433-103,332,866

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~34.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hydrops fetalisSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0015193

Submitter: PanelApp Australia

nonsyndromic congenital nail disorder 1DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008060

Submitter: G2P

autosomal recessive nail dysplasiaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0029051

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Nail disorder, nonsyndromic noncongenital 10AR

Manifestation: Dermatologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 21665003Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FZD6 variants in ClinVar

8 Conditions Cataloged
Inborn genetic diseasesTotal: 84
Nonsyndromic congenital nail disorder 1Total: 11
FZD6-related disorderTotal: 7
not providedTotal: 4
Nail diseaseTotal: 2
Non-immune hydrops fetalisTotal: 1
NephroblastomaTotal: 1
Skin disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003506.4. 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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
4
clinvar
1
clinvar
8
missense
2
clinvar
1
clinvar
85
clinvar
4
clinvar
92
nonsense
3
clinvar
1
clinvar
4
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
3
Total639081108

Highest pathogenic variant AF is 0.00002299805

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003506.4RefSeqNP_003497.26MANE Select
ENST00000358755.5EnsemblENSP00000351605.46MANE Select
NM_001164615.2RefSeqNP_001158087.16Standard
NM_001164616.2RefSeqNP_001158088.16Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
fzd6Danio rerio

Structure: ethmoid cartilage

Quality: decreased size

abnormal

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

  • neural tube closure
  • hair follicle development
  • G protein-coupled receptor signaling pathway
  • Wnt signaling pathway, calcium modulating pathway
  • platelet activation

Molecular Function

  • amyloid-beta binding
  • G protein-coupled receptor activity
  • protein binding
  • Wnt-protein binding
  • ubiquitin protein ligase binding

Cellular Component

  • plasma membrane
  • integral component of plasma membrane
  • cell surface
  • apical plasma membrane
  • apicolateral plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000358755
Coding exons
6
Length
34434
Individuals with no LoFs
125697
Homozygous LoFs
0
Heterozygous LoFs
51
Defined
125748
p
0.000203
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.402973730.7960.00001914632
Missense (PolyPhen)109163.590.66632115
Synonymous0.6101251340.9330.000007371376
Loss of Function1.222229.10.7560.00000170340

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.000140.00014rare
Ashkenazi Jewish00.0absent
East Asian0.000160.00016rare
Finnish0.000140.00014rare
European (Non-Finnish)0.000240.00024rare
South Asian0.000330.00029rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Receptor for Wnt proteins. Most of frizzled receptors are coupled to the beta-catenin canonical signaling pathway, which leads to the activation of disheveled proteins, inhibition of GSK- 3 kinase, nuclear accumulation of beta-catenin and activation of Wnt target genes. A second signaling pathway involving PKC and calcium fluxes has been seen for some family members, but it is not yet clear if it represents a distinct pathway or if it can be integrated in the canonical pathway, as PKC seems to be required for Wnt-mediated inactivation of GSK-3 kinase. Both pathways seem to involve interactions with G-proteins. May be involved in transduction and intercellular transmission of polarity information during tissue morphogenesis and/or in differentiated tissues. Together with FZD3, is involved in the neural tube closure and plays a role in the regulation of the establishment of planar cell polarity (PCP), particularly in the orientation of asymmetric bundles of stereocilia on the apical faces of a subset of auditory and vestibular sensory cells located in the inner ear (By similarity). {ECO:0000250|UniProtKB:Q61089}.;
Disease
DISEASE: Nail disorder, non-syndromic congenital, 10 (NDNC10) [MIM:614157]: A nail disorder characterized by a variable degree of onychauxis (thick nails), hyponychia, and onycholysis of all nails, with claw-shaped fingernails in some individuals. No other anomalies of ectodermal tissues, including hair, teeth, sweat glands, or skin, are noted, and individuals with dysplastic nails have normal hearing and normal psychomotor development. {ECO:0000269|PubMed:21665003}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Rare non-synonymous variants in FZD6 may contribute to neural tube defects, congenital malformations of the central nervous system and adjacent structures related to defective neural tube closure during the first trimester of pregnancy.;

Recessive Scores

pRec
0.191

Intolerance Scores

LoFtool
0.287
RVIS EVS
1
RVIS percentile EVS
90.72

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.289

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh
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