ROR2
protein-codingreceptor tyrosine kinase like orphan receptor 2, the group of Receptor tyrosine kinases|I-set domain containing
Gene summary
The protein encoded by this gene is a receptor protein tyrosine kinase and type I transmembrane protein that belongs to the ROR subfamily of cell surface receptors. The protein may be involved in the early formation of the chondrocytes and may be required for cartilage and growth plate development. Mutations in this gene can cause brachydactyly type B, a skeletal disorder characterized by hypoplasia/aplasia of distal phalanges and nails. In addition, mutations in this gene can cause the autosomal recessive form of Robinow syndrome, which is characterized by skeletal dysplasia with generalized limb bone shortening, segmental defects of the spine, brachydactyly, and a dysmorphic facial appearance. [provided by RefSeq, Jul 2008]
- NTRKR2
- BDB
- BDB1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~387.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0007220
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0009999
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0009999
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007220
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0009999
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009999
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009999
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0007220
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0007220
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Genitourinary; Musculoskeletal; Renal
Intervention: Cardiovascular
Rationale: The condition can involve congenital cardiac anomalies, and awareness may allow early management
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ROR2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004560.4. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 11 | 200 | 3 | 214 | ||
| missense | 18 | 433 | 50 | 9 | 510 | |
| nonsense | 18 | 8 | 4 | 30 | ||
| start loss | 1 | 1 | ||||
| frameshift | 15 | 12 | 3 | 30 | ||
| splice donor/acceptor (+/-2bp) | 2 | 1 | 1 | 4 | ||
| Total | 36 | 39 | 452 | 250 | 12 | 789 |
Highest pathogenic variant AF is 0.00013393654
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004551.2 | 9 | MANE Select | |
| Ensembl | ENSP00000364860.3 | 9 | MANE Select | |
| RefSeq | NP_001305133.1 | 8 | Standard | |
| Ensembl | ENSP00000364867.1 | 10 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| ror2 | Danio rerio | Structure: head Quality: malformed abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- WNT-Ncore
- TGF-Ncore
- Cardiac Progenitor Differentiation
- Ectoderm Differentiation
- Wnt Signaling Pathway
Biological Process
- cartilage condensation
- somitogenesis
- signal transduction
- transmembrane receptor protein tyrosine kinase signaling pathway
- Wnt signaling pathway, calcium modulating pathway
Molecular Function
- transmembrane receptor protein tyrosine kinase activity
- frizzled binding
- protein binding
- ATP binding
- Wnt-protein binding
Cellular Component
- microtubule
- plasma membrane
- integral component of plasma membrane
- cell surface
- axon
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000375708
- Coding exons
- 9
- Length
- 387072
- Individuals with no LoFs
- 125684
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 64
- Defined
- 125748
- p
- 0.000255
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.143 | 584 | 594 | 0.983 | 0.0000427 | 6118 |
| Missense (PolyPhen) | 150 | 189.35 | 0.7922 | 2087 | ||
| Synonymous | -3.00 | 330 | 268 | 1.23 | 0.0000214 | 1937 |
| Loss of Function | 3.73 | 14 | 39.2 | 0.357 | 0.00000247 | 385 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00051 | 0.00049 | rare |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00049 | 0.00046 | rare |
| European (Non-Finnish) | 0.00021 | 0.00020 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Tyrosine-protein kinase receptor which may be involved in the early formation of the chondrocytes. It seems to be required for cartilage and growth plate development (By similarity). Phosphorylates YWHAB, leading to induction of osteogenesis and bone formation (PubMed:17717073). In contrast, has also been shown to have very little tyrosine kinase activity in vitro. May act as a receptor for wnt ligand WNT5A which may result in the inhibition of WNT3A-mediated signaling (PubMed:25029443). {ECO:0000250|UniProtKB:Q9Z138, ECO:0000269|PubMed:17717073, ECO:0000269|PubMed:25029443}.;
- Disease
- DISEASE: Brachydactyly B1 (BDB1) [MIM:113000]: A form of brachydactyly. Brachydactyly defines a group of inherited malformations characterized by shortening of the digits due to abnormal development of the phalanges and/or the metacarpals. In brachydactyly type B1 the middle phalanges are short but in addition the terminal phalanges are rudimentary or absent. Both fingers and toes are affected. The thumbs and big toes are usually deformed. Symphalangism is also a feature. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Robinow syndrome autosomal recessive (RRS) [MIM:268310]: A recessive form of Robinow syndrome, a disease characterized by short-limb dwarfism, costovertebral segmentation defects and abnormalities of the head, face and external genitalia. The clinical signs are generally far more severe in recessive cases, particularly skeletal abnormalities. All patients with the recessive form suffer from vertebral segmentation abnormalities, resulting in scoliosis and chest deformities. Rib fusions are considered to be characteristic of the autosomal recessive form. Patients can also present brachydactyly, with extensive aplasia/hypoplasia of the phalanges and metacarpals/metatarsals, and brachy-syn-polydactyly of the hands and oligodactyly of the feet. {ECO:0000269|PubMed:10932186, ECO:0000269|PubMed:10932187}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- LoFtool
- 0.0625
- RVIS EVS
- -1.07
- RVIS percentile EVS
- 7.35
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.947
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |