FZD3
frizzled class receptor 3, the group of G protein-coupled receptors, Class F frizzled
Basic information
Region (hg38): 8:28494204-28574267
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FZD3 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 | 3 | |||||
| missense | 18 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 18 | 0 | 3 |
Variants in FZD3
This is a list of pathogenic ClinVar variants found in the FZD3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-28503022-G-T | not specified | Uncertain significance (Oct 02, 2023) | ||
| 8-28503069-A-G | not specified | Uncertain significance (Sep 13, 2023) | ||
| 8-28503131-C-T | not specified | Uncertain significance (Oct 06, 2021) | ||
| 8-28503149-A-C | not specified | Uncertain significance (May 31, 2024) | ||
| 8-28503150-T-C | not specified | Uncertain significance (Jun 03, 2022) | ||
| 8-28520681-G-A | not specified | Uncertain significance (Oct 21, 2021) | ||
| 8-28527166-C-T | not specified | Uncertain significance (Apr 15, 2024) | ||
| 8-28527307-C-T | not specified | Uncertain significance (Mar 29, 2023) | ||
| 8-28527455-G-A | not specified | Uncertain significance (Nov 15, 2021) | ||
| 8-28527462-T-G | Benign (Dec 31, 2019) | |||
| 8-28527554-A-G | not specified | Uncertain significance (Aug 13, 2021) | ||
| 8-28527641-AT-A | Colorectal cancer | Pathogenic (-) | ||
| 8-28527757-G-A | not specified | Uncertain significance (Jun 30, 2022) | ||
| 8-28527790-A-G | not specified | Uncertain significance (Dec 18, 2023) | ||
| 8-28527804-G-A | Benign (Jan 09, 2019) | |||
| 8-28527871-T-G | not specified | Uncertain significance (Jun 10, 2024) | ||
| 8-28528100-G-A | not specified | Uncertain significance (Apr 07, 2023) | ||
| 8-28551619-G-A | not specified | Uncertain significance (Dec 12, 2023) | ||
| 8-28555755-G-A | not specified | Uncertain significance (Sep 14, 2023) | ||
| 8-28555778-T-G | not specified | Uncertain significance (Feb 16, 2023) | ||
| 8-28555799-G-GA | Corpus callosum, agenesis of;Hydrocephalus;Arthrogryposis multiplex congenita;Multicystic kidney dysplasia • Congenital cerebellar hypoplasia | Likely pathogenic (Feb 18, 2019) | ||
| 8-28555809-C-T | not specified | Uncertain significance (Oct 16, 2023) | ||
| 8-28555858-C-T | Benign (Aug 30, 2018) | |||
| 8-28555859-C-T | not specified | Uncertain significance (Sep 13, 2023) | ||
| 8-28555908-C-G | not specified | Uncertain significance (May 12, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FZD3 | protein_coding | protein_coding | ENST00000240093 | 6 | 80047 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000436 | 0.999 | 125722 | 0 | 24 | 125746 | 0.0000954 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.64 | 240 | 386 | 0.622 | 0.0000209 | 4404 |
| Missense in Polyphen | 59 | 147.38 | 0.40033 | 1763 | ||
| Synonymous | 0.292 | 122 | 126 | 0.967 | 0.00000641 | 1287 |
| Loss of Function | 3.14 | 11 | 29.4 | 0.375 | 0.00000181 | 316 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000166 | 0.000163 |
| Finnish | 0.0000476 | 0.0000462 |
| European (Non-Finnish) | 0.000116 | 0.000114 |
| Middle Eastern | 0.000166 | 0.000163 |
| South Asian | 0.000201 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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. Activation by Wnt5A stimulates PKC activity via a G-protein-dependent mechanism. Involved in transduction and intercellular transmission of polarity information during tissue morphogenesis and/or in differentiated tissues. Plays a role in controlling early axon growth and guidance processes necessary for the formation of a subset of central and peripheral major fiber tracts. Required for the development of major fiber tracts in the central nervous system, including: the anterior commissure, the corpus callosum, the thalamocortical, corticothalamic and nigrostriatal tracts, the corticospinal tract, the fasciculus retroflexus, the mammillothalamic tract, the medial lemniscus, and ascending fiber tracts from the spinal cord to the brain. In the peripheral nervous system, controls axon growth in distinct populations of cranial and spinal motor neurons, including the facial branchimotor nerve, the hypoglossal nerve, the phrenic nerve, and motor nerves innervating dorsal limbs. Involved in the migration of cranial neural crest cells. May also be implicated in the transmission of sensory information from the trunk and limbs to the brain. Controls commissural sensory axons guidance after midline crossing along the anterior-posterior axis in the developing spinal cord in a Wnt-dependent signaling pathway. Together with FZD6, 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. Promotes neurogenesis by maintaining sympathetic neuroblasts within the cell cycle in a beta-catenin-dependent manner (By similarity). {ECO:0000250|UniProtKB:Q61086}.;
- 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);Axon guidance - 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);MicroRNAs 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);WNT-Core;Neural Crest Differentiation;Association Between Physico-Chemical Features and Toxicity Associated Pathways;ESC Pluripotency Pathways;Wnt Signaling Pathway and Pluripotency;Wnt Signaling in Kidney Disease;EMT transition in Colorectal Cancer;Wnt Signaling Pathway;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;Asymmetric localization of PCP proteins;PCP/CE pathway;Ca2+ pathway;Beta-catenin independent WNT signaling;GPCR signaling-G alpha i;Wnt;Wnt Canonical;Wnt Mammals
(Consensus)
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- loftool
- 0.373
- rvis_EVS
- -0.89
- rvis_percentile_EVS
- 10.3
Haploinsufficiency Scores
- pHI
- 0.483
- hipred
- Y
- hipred_score
- 0.563
- ghis
- 0.614
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.945
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fzd3
- Phenotype
- homeostasis/metabolism phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; reproductive system phenotype; normal 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); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; vision/eye phenotype;
Zebrafish Information Network
- Gene name
- fzd3a
- Affected structure
- CoPA
- Phenotype tag
- abnormal
- Phenotype quality
- decreased process quality
Gene ontology
- Biological process
- establishment of planar polarity;neuron migration;neural tube closure;hair follicle development;positive regulation of neuroblast proliferation;G protein-coupled receptor signaling pathway;Wnt signaling pathway, calcium modulating pathway;neuron differentiation;cell proliferation in midbrain;non-canonical Wnt signaling pathway;post-anal tail morphogenesis;dopaminergic neuron axon guidance;serotonergic neuron axon guidance;inner ear morphogenesis;response to drug;negative regulation of mitotic cell cycle, embryonic;response to electrical stimulus;canonical Wnt signaling pathway;Wnt signaling pathway, planar cell polarity pathway;sympathetic ganglion development;commissural neuron axon guidance;negative regulation of execution phase of apoptosis;midbrain morphogenesis;planar cell polarity pathway involved in axon guidance
- Cellular component
- cytoplasm;plasma membrane;cell surface;integral component of membrane;apical plasma membrane;lateral plasma membrane;axon;dendrite;filopodium tip;neuronal cell body;presynaptic active zone
- Molecular function
- G protein-coupled receptor activity;protein binding;Wnt-protein binding;PDZ domain binding;Wnt-activated receptor activity