LPXN
Basic information
Region (hg38): 11:58526871-58578220
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (46 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPXN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004811.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 44 | 46 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 44 | 3 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LPXN | protein_coding | protein_coding | ENST00000528954 | 9 | 51350 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000191 | 0.890 | 125728 | 0 | 20 | 125748 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.396 | 198 | 214 | 0.924 | 0.0000114 | 2580 |
| Missense in Polyphen | 63 | 83.515 | 0.75436 | 1042 | ||
| Synonymous | 0.124 | 79 | 80.4 | 0.982 | 0.00000423 | 722 |
| Loss of Function | 1.58 | 12 | 19.6 | 0.613 | 9.14e-7 | 246 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000401 | 0.000398 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000889 | 0.0000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000659 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional coactivator for androgen receptor (AR) and serum response factor (SRF). Contributes to the regulation of cell adhesion, spreading and cell migration and acts as a negative regulator in integrin-mediated cell adhesion events. Suppresses the integrin-induced tyrosine phosphorylation of paxillin (PXN). May play a critical role as an adapter protein in the formation of the adhesion zone in osteoclasts. Negatively regulates B-cell antigen receptor (BCR) signaling. {ECO:0000269|PubMed:17640867, ECO:0000269|PubMed:18451096, ECO:0000269|PubMed:18497331, ECO:0000269|PubMed:20543562}.;
- Pathway
- TCR;AndrogenReceptor
(Consensus)
Recessive Scores
- pRec
- 0.134
Intolerance Scores
- loftool
- 0.225
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.45
Haploinsufficiency Scores
- pHI
- 0.397
- hipred
- N
- hipred_score
- 0.229
- ghis
- 0.572
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0895
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lpxn
- Phenotype
Gene ontology
- Biological process
- cell adhesion;negative regulation of cell adhesion;signal transduction;regulation of cell adhesion mediated by integrin;negative regulation of B cell receptor signaling pathway;protein-containing complex assembly;regulation of nucleic acid-templated transcription
- Cellular component
- podosome;nucleus;cytoplasm;cytosol;plasma membrane;focal adhesion;membrane;nuclear speck;cell projection;perinuclear region of cytoplasm
- Molecular function
- transcription coregulator activity;protein binding;metal ion binding