LMBR1
protein-codinglimb development membrane protein 1
Gene summary
This gene encodes a member of the LMBR1-like membrane protein family. Another member of this protein family has been shown to be a lipocalin transmembrane receptor. A highly conserved, cis-acting regulatory module for the sonic hedgehog gene is located within an intron of this gene. Consequently, disruption of this genic region can alter sonic hedgehog expression and affect limb patterning, but it is not known if this gene functions directly in limb development. Mutations and chromosomal deletions and rearrangements in this genic region are associated with acheiropody and preaxial polydactyly, which likely result from altered sonic hedgehog expression. [provided by RefSeq, Jul 2008]
- C7orf2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~224.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0017454
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0007615
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0008515
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0007615
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0008270
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0008700
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0008700
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0008515
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0008700
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0008270
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; 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: Some conditions may be due to variants in ZRS, a SHH-regulatory element within an LMBR1 intron
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LMBR1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022458.4. 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 | 4 | 21 | 4 | 29 | ||
| missense | 78 | 8 | 86 | |||
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | 2 | |||
| splice donor/acceptor (+/-2bp) | 1 | 9 | 10 | |||
| Total | 1 | 1 | 95 | 29 | 4 | 130 |
Highest pathogenic variant AF is 0.000020083158
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071903.2 | 17 | MANE Select | |
| Ensembl | ENSP00000326604.7 | 17 | MANE Select | |
| RefSeq | NP_001337882.1 | 18 | Standard | |
| RefSeq | NP_001337883.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- embryonic digit morphogenesis
Cellular Component
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000353442
- Coding exons
- 17
- Length
- 224279
- Individuals with no LoFs
- 125641
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 106
- Defined
- 125747
- p
- 0.000422
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.849 | 206 | 243 | 0.847 | 0.0000122 | 3128 |
| Missense (PolyPhen) | 85 | 108.02 | 0.7869 | 1425 | ||
| Synonymous | 0.197 | 89 | 91.4 | 0.974 | 0.00000505 | 942 |
| Loss of Function | 2.33 | 18 | 32.3 | 0.557 | 0.00000194 | 382 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00012 | rare |
| Latino/Admixed American | 0.00037 | 0.00032 | rare |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.00023 | 0.00022 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00065 | 0.00063 | rare |
| South Asian | 0.00029 | 0.00026 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Putative membrane receptor.;
- Disease
- DISEASE: Acheiropody (ACHP) [MIM:200500]: Very rare condition characterized by bilateral congenital amputations of the hands and feet. The specific malformative phenotype consists of a complete amputation of the distal epiphysis of the humerus, amputation of the tibial diaphysis and aplasia of the radius, ulna, fibula and of all the bones of the hands and feet. {ECO:0000269|PubMed:11090342}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Syndactyly 4 (SDTY4) [MIM:186200]: A form of syndactyly, a congenital anomaly of the hand or foot marked by persistence of the webbing between adjacent digits that are more or less completely attached. SDTY4 is characterized by complete bilateral syndactyly (involving all digits 1 to 5). A frequent association with polydactyly (with six metacarpals and six digits) has been reported. Feet are affected occasionally. {ECO:0000269|PubMed:18417549, ECO:0000269|PubMed:24456159}. Note=The disease is caused by mutations affecting the gene represented in this entry. Disease-causing mutations consists of duplications (89-589 kb) involving the ZPA regulatory sequence (ZRS), a SHH long-range cis-regulatory element, located in LMBR1 intron 5. The mutations do not alter normal LMBR1 expression and function, but affect SHH limb expression. {ECO:0000269|PubMed:24456159}.; DISEASE: Hypoplasia or aplasia of tibia with polydactyly (THYP) [MIM:188740]: An autosomal dominant disease characterized by hypoplastic or absent tibia, and polydactyly. {ECO:0000269|PubMed:19847792, ECO:0000269|PubMed:24777739, ECO:0000269|PubMed:24965254}. Note=The disease is caused by mutations affecting the gene represented in this entry. Disease- causing mutations are located in intron 5 of LMBR1. The mutations do not alter normal LMBR1 expression and function, but disrupt a long-range, cis-regulatory element of SHH expression contained in LMBR1 intron 5. {ECO:0000269|PubMed:19847792, ECO:0000269|PubMed:24777739, ECO:0000269|PubMed:24965254}.; DISEASE: Laurin-Sandrow syndrome (LSS) [MIM:135750]: A rare autosomal dominant disorder characterized by polysyndactyly of hands and/or feet, mirror image duplication of the feet, nasal defects, and loss of identity between fibula and tibia. Some patients do not have nasal abnormalities (segmental Laurin-Sandrow syndrome). {ECO:0000269|PubMed:24456159}. Note=The disease is caused by mutations affecting the gene represented in this entry. Disease-causing mutations consists of duplications (16-75 kb) involving the ZPA regulatory sequence (ZRS), a SHH long-range cis- regulatory element, located in LMBR1 intron 5. The mutations do not alter normal LMBR1 expression and function, but affect SHH limb expression. {ECO:0000269|PubMed:24456159}.;
Recessive Scores
- pRec
- 0.128
Intolerance Scores
- LoFtool
- 0.798
- RVIS EVS
- -0.54
- RVIS percentile EVS
- 20.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.471
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |