LMO7
protein-codingLIM domain 7, the group of LIM domain containing|PDZ domain containing
Gene summary
This gene encodes a protein containing a calponin homology (CH) domain, a PDZ domain, and a LIM domain, and may be involved in protein-protein interactions. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene, however, the full-length nature of some variants is not known. [provided by RefSeq, Jan 2009]
- FBXO20
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~239.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LMO7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001306080.2. 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 | 5 | 8 | 2 | 15 | ||
| missense | 230 | 21 | 2 | 253 | ||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 13 | 13 | ||||
| Total | 0 | 0 | 251 | 29 | 4 | 284 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001293009.1 | 31 | MANE Select | |
| Ensembl | ENSP00000366757.4 | 31 | MANE Select | |
| RefSeq | NP_001317512.1 | 24 | Standard | |
| RefSeq | NP_001353561.1 | 23 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| lmo7b | Danio rerio | Structure: post-vent region Quality: curved ventral abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Adherens junction - Homo sapiens (human)
- Post-translational protein modification
- Metabolism of proteins
- Immune System
- Adaptive Immune System
Biological Process
- protein polyubiquitination
- protein ubiquitination
- regulation of signaling
- regulation of cell adhesion
- post-translational protein modification
Molecular Function
- DNA-binding transcription factor activity
- ubiquitin-protein transferase activity
- metal ion binding
Cellular Component
- ubiquitin ligase complex
- nucleus
- nuclear envelope
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000465261
- Coding exons
- 23
- Length
- 239435
- Individuals with no LoFs
- 125649
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 99
- Defined
- 125748
- p
- 0.000394
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.168 | 752 | 739 | 1.02 | 0.0000401 | 9030 |
| Missense (PolyPhen) | 219 | 232.96 | 0.94007 | 2789 | ||
| Synonymous | -0.324 | 269 | 262 | 1.03 | 0.0000138 | 2638 |
| Loss of Function | 5.76 | 22 | 76.3 | 0.288 | 0.00000409 | 895 |
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 | 0.0 | absent |
| East Asian | 0.00055 | 0.00054 | rare |
| Finnish | 0.00042 | 0.00042 | rare |
| European (Non-Finnish) | 0.00045 | 0.00044 | rare |
| South Asian | 0.00029 | 0.00029 | rare |
| Other | 0.00050 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.119
Intolerance Scores
- LoFtool
- 0.945
- RVIS EVS
- 0.47
- RVIS percentile EVS
- 78.8
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.639
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | High | High |