WNT1

protein-coding

Wnt family member 1, the group of Wnt family

Gene summary

The WNT gene family consists of structurally related genes which 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. It is very conserved in evolution, and the protein encoded by this gene is known to be 98% identical to the mouse Wnt1 protein at the amino acid level. The studies in mouse indicate that the Wnt1 protein functions in the induction of the mesencephalon and cerebellum. This gene was originally considered as a candidate gene for Joubert syndrome, an autosomal recessive disorder with cerebellar hypoplasia as a leading feature. However, further studies suggested that the gene mutations might not have a significant role in Joubert syndrome. This gene is clustered with another family member, WNT10B, in the chromosome 12q13 region. [provided by RefSeq, Jul 2008]

Previous symbols:
  • INT1

MANE transcript

NM_005430.4

Inheritance

AR, AD

ClinVar variants

P:54U:172B:58

Top phenotype

Osteoprosis, autosomal dominant; Osteogenesis imperfecta, type XV

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr12:48,978,322-48,982,620

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~4.3 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

osteogenesis imperfecta type 15DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014086

Submitter: G2P

osteogenesis imperfecta type 15STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014086

Submitter: Labcorp Genetics (formerly Invitae)

osteogenesis imperfecta type 3SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0009804

Submitter: Orphanet

osteogenesis imperfecta type 4SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008148

Submitter: Orphanet

idiopathic juvenile osteoporosisSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0019409

Submitter: Labcorp Genetics (formerly Invitae)

idiopathic juvenile osteoporosisSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0019409

Submitter: PanelApp Australia

osteogenesis imperfecta type 15STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014086

Submitter: PanelApp Australia

idiopathic juvenile osteoporosisLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0019409

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Osteoprosis, autosomal dominant; Osteogenesis imperfecta, type XVAD/AR

Manifestation: Musculoskeletal

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

Comments: The use of bisphosphonates has been described to treat osteogenesis imperfecta, but it is unclear if an early (genetic) diagnosis would be advantageous

Refs: 23434763; 23499309; 23499310; 23656646Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WNT1 variants in ClinVar

11 Conditions Cataloged
not providedTotal: 248
Inborn genetic diseasesTotal: 47
Osteogenesis imperfecta type 15Total: 34
not specifiedTotal: 26
WNT1-related disorderTotal: 19
Osteogenesis imperfectaTotal: 17
OSTEOPOROSIS, EARLY-ONSET, SUSCEPTIBILITY TOTotal: 12
Osteogenesis imperfecta type IIITotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005430.4. 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
54
clinvar
1
clinvar
58
missense
1
clinvar
15
clinvar
165
clinvar
3
clinvar
184
nonsense
8
clinvar
5
clinvar
13
start loss
1
clinvar
1
frameshift
12
clinvar
10
clinvar
4
clinvar
26
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
2
Total2331172571284

Highest pathogenic variant AF is 0.000060271508

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005430.4RefSeqNP_005421.14MANE Select
ENST00000293549.4EnsemblENSP00000293549.34MANE Select

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
wnt1Danio rerio

Structure: glial cell

Quality: mislocalised

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

  • embryonic axis specification
  • branching involved in ureteric bud morphogenesis
  • positive regulation of protein phosphorylation
  • cell-cell signaling
  • myoblast fusion

Molecular Function

  • frizzled binding
  • cytokine activity
  • morphogen activity
  • protein domain specific binding
  • transcription regulatory region DNA binding

Cellular Component

  • extracellular region
  • extracellular space
  • cytoplasm
  • endoplasmic reticulum lumen
  • Golgi lumen

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000293549
Coding exons
4
Length
3062
Individuals with no LoFs
125699
Homozygous LoFs
0
Heterozygous LoFs
12
Defined
125711
p
0.0000477
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.061662090.7940.000009612336
Missense (PolyPhen)6488.1760.72582977
Synonymous2.276491.60.6990.00000433788
Loss of Function2.55312.90.2335.64e-7130

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish0.0000990.000099rare
East Asian0.000340.00033rare
Finnish0.0000740.000046rare
European (Non-Finnish)0.0000190.000018rare
South Asian0.0000330.000033rare
Other0.000180.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors (Probable). Acts in the canonical Wnt signaling pathway by promoting beta-catenin-dependent transcriptional activation (PubMed:23499309, PubMed:26902720, PubMed:28528193, PubMed:23656646). In some developmental processes, is also a ligand for the coreceptor RYK, thus triggering Wnt signaling (By similarity). Plays an essential role in the development of the embryonic brain and central nervous system (CNS) (By similarity). Has a role in osteoblast function, bone development and bone homeostasis (PubMed:23499309, PubMed:23656646). {ECO:0000250|UniProtKB:P04426, ECO:0000269|PubMed:23499309, ECO:0000269|PubMed:23656646, ECO:0000269|PubMed:26902720, ECO:0000269|PubMed:28528193, ECO:0000305}.;
Disease
DISEASE: Osteoporosis (OSTEOP) [MIM:166710]: A systemic skeletal disorder characterized by decreased bone mass and deterioration of bone microarchitecture without alteration in the composition of bone. The result is fragile bones and an increased risk of fractures, even after minimal trauma. Osteoporosis is a chronic condition of multifactorial etiology and is usually clinically silent until a fracture occurs. {ECO:0000269|PubMed:23499309, ECO:0000269|PubMed:23656646}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Osteogenesis imperfecta 15 (OI15) [MIM:615220]: An autosomal recessive form of osteogenesis imperfecta, a connective tissue disorder characterized by low bone mass, bone fragility and susceptibility to fractures after minimal trauma. Disease severity ranges from very mild forms without fractures to intrauterine fractures and perinatal lethality. Extraskeletal manifestations, which affect a variable number of patients, are dentinogenesis imperfecta, hearing loss, and blue sclerae. OI15 is characterized by early-onset recurrent fractures, bone deformity, significant reduction of bone density, short stature, and, in some patients, blue sclerae. Tooth development and hearing are normal. Learning and developmental delays and brain anomalies have been observed in some patients. {ECO:0000269|PubMed:23434763, ECO:0000269|PubMed:23499309, ECO:0000269|PubMed:23499310, ECO:0000269|PubMed:23656646}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Osteogenesis imperfecta 14 (OI14) [MIM:615066]: An autosomal recessive form of osteogenesis imperfecta, a connective tissue disorder characterized by low bone mass, bone fragility and susceptibility to fractures after minimal trauma. Disease severity ranges from very mild forms without fractures to intrauterine fractures and perinatal lethality. Extraskeletal manifestations, which affect a variable number of patients, are dentinogenesis imperfecta, hearing loss, and blue sclerae. OI14 is characterized by variable degrees of severity of multiple fractures and osteopenia, with normal teeth, sclerae, and hearing. Fractures first occur prenatally or by age 6 years. {ECO:0000269|PubMed:28528193}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.785

Intolerance Scores

LoFtool
0.337
RVIS EVS
0.1
RVIS percentile EVS
61.28

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.993

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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