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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for LMNA |
 Gene summary |
| Gene information | Gene symbol | LMNA | Gene ID | 4000 |
| Gene name | lamin A/C | |
| Synonyms | CDCD1|CDDC|CMD1A|CMT2B1|EMD2|FPL|FPLD|FPLD2|HGPS|IDC|LDP1|LFP|LGMD1B|LMN1|LMNC|LMNL1|MADA|PRO1 | |
| Cytomap | 1q22 | |
| Type of gene | protein-coding | |
| Description | lamin70 kDa laminepididymis secretory sperm binding proteinlamin A/C-like 1mandibuloacral dysplasia type Aprelamin-A/Crenal carcinoma antigen NY-REN-32 | |
| Modification date | 20200329 | |
| UniProtAcc | ||
| Context | - 30781626(Hippocampal LMNA Gene Expression is Increased in Late-Stage Alzheimer's Disease) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| LMNA | GO:0090343 | positive regulation of cell aging | 20458013 |
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Gene structures and expression levels for LMNA |
| Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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ENSG00000160789
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000368299.7 | LMNA-205:protein_coding:LMNA | 6.266593e+01 | 1.826995e+00 | 2.273427e-03 | 1.024657e-02 |
| TC | DOWN | ENST00000498722.2 | LMNA-217:retained_intron:LMNA | 5.522276e+01 | -8.009005e-01 | 3.285297e-04 | 4.125922e-03 |
| TC | UP | ENST00000368299.7 | LMNA-205:protein_coding:LMNA | 2.731308e+02 | 8.389253e-01 | 6.472541e-03 | 4.058325e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for LMNA |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_139077 | chr1 | 156083025:156083184:156090999:156091097:156093709:156093811 | 156090999:156091097 |
| exon_skip_193240 | chr1 | 156137113:156137232:156137654:156137743:156138488:156138757 | 156137654:156137743 |
| exon_skip_253186 | chr1 | 156115204:156115274:156130617:156130773:156134403:156134446 | 156130617:156130773 |
| exon_skip_55575 | chr1 | 156114964:156115274:156130617:156130773:156134403:156134446 | 156130617:156130773 |
| exon_skip_57207 | chr1 | 156137191:156137232:156137654:156137743:156138488:156138607 | 156137654:156137743 |
| exon_skip_77785 | chr1 | 156082948:156083184:156090999:156091097:156093709:156093778 | 156090999:156091097 |
| exon_skip_89169 | chr1 | 156082948:156083184:156090999:156091097:156093709:156093811 | 156090999:156091097 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for LMNA |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000368300 | 156130617 | 156130773 | Frame-shift |
| ENST00000368300 | 156137654 | 156137743 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000368300 | 156130617 | 156130773 | Frame-shift |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000368300 | 156130617 | 156130773 | Frame-shift |
| ENST00000368300 | 156137654 | 156137743 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LMNA |
p-ENSG00000160789_img4.png |
| Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000368300 | 3207 | 664 | 156137654 | 156137743 | 1822 | 1910 | 536 | 566 |
| Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000368300 | 3207 | 664 | 156137654 | 156137743 | 1822 | 1910 | 536 | 566 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| P02545 | 536 | 566 | 537 | 566 | Alternative sequence | ID=VSP_002468;Note=In isoform ADelta10. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8621584;Dbxref=PMID:8621584 |
| P02545 | 536 | 566 | 537 | 543 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1IFR |
| P02545 | 536 | 566 | 1 | 661 | Chain | ID=PRO_0000398835;Note=Prelamin-A/C |
| P02545 | 536 | 566 | 1 | 646 | Chain | ID=PRO_0000063810;Note=Lamin-A/C |
| P02545 | 536 | 566 | 428 | 545 | Domain | Note=LTD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01187 |
| P02545 | 536 | 566 | 546 | 546 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P48678 |
| P02545 | 536 | 566 | 548 | 548 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P48678 |
| P02545 | 536 | 566 | 541 | 541 | Natural variant | ID=VAR_039786;Note=In CMD1A%3B grossly abnormal nuclear shape with the nuclear envelope producing prominent lobules in about 10%25 of cultured skin fibroblasts from heterozygous patients. R->C;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO |
| P02545 | 536 | 566 | 541 | 541 | Natural variant | ID=VAR_039787;Note=In EDMD2. R->H;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14684700;Dbxref=dbSNP:rs61444459,PMID:14684700 |
| P02545 | 536 | 566 | 541 | 541 | Natural variant | ID=VAR_064975;Note=In EDMD2%3B mis-localized in the nucleus%3B does not alter nuclear size or shape. R->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20848652;Dbxref=dbSNP:rs61444459,PMID:20848652 |
| P02545 | 536 | 566 | 541 | 541 | Natural variant | ID=VAR_039788;Note=In EDMD2 and CMD1A%3B modest and non-specific nuclear membrane alterations%3B the phenotype is entirely reversed by coexpression of the S-541 mutation and wild-type lamin-C. R->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:000026 |
| P02545 | 536 | 566 | 542 | 542 | Natural variant | ID=VAR_034710;Note=In HGPS. K->N;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15286156;Dbxref=dbSNP:rs56673169,PMID:15286156 |
| P02545 | 536 | 566 | 384 | 664 | Region | Note=Tail |
| Lost protein functional features of individual exon skipping events in MSBB. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Lost protein functional features of individual exon skipping events in Mayo. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| P02545 | 536 | 566 | 537 | 566 | Alternative sequence | ID=VSP_002468;Note=In isoform ADelta10. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8621584;Dbxref=PMID:8621584 |
| P02545 | 536 | 566 | 537 | 543 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1IFR |
| P02545 | 536 | 566 | 1 | 661 | Chain | ID=PRO_0000398835;Note=Prelamin-A/C |
| P02545 | 536 | 566 | 1 | 646 | Chain | ID=PRO_0000063810;Note=Lamin-A/C |
| P02545 | 536 | 566 | 428 | 545 | Domain | Note=LTD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01187 |
| P02545 | 536 | 566 | 546 | 546 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P48678 |
| P02545 | 536 | 566 | 548 | 548 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P48678 |
| P02545 | 536 | 566 | 541 | 541 | Natural variant | ID=VAR_039786;Note=In CMD1A%3B grossly abnormal nuclear shape with the nuclear envelope producing prominent lobules in about 10%25 of cultured skin fibroblasts from heterozygous patients. R->C;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO |
| P02545 | 536 | 566 | 541 | 541 | Natural variant | ID=VAR_039787;Note=In EDMD2. R->H;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14684700;Dbxref=dbSNP:rs61444459,PMID:14684700 |
| P02545 | 536 | 566 | 541 | 541 | Natural variant | ID=VAR_064975;Note=In EDMD2%3B mis-localized in the nucleus%3B does not alter nuclear size or shape. R->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20848652;Dbxref=dbSNP:rs61444459,PMID:20848652 |
| P02545 | 536 | 566 | 541 | 541 | Natural variant | ID=VAR_039788;Note=In EDMD2 and CMD1A%3B modest and non-specific nuclear membrane alterations%3B the phenotype is entirely reversed by coexpression of the S-541 mutation and wild-type lamin-C. R->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:000026 |
| P02545 | 536 | 566 | 542 | 542 | Natural variant | ID=VAR_034710;Note=In HGPS. K->N;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15286156;Dbxref=dbSNP:rs56673169,PMID:15286156 |
| P02545 | 536 | 566 | 384 | 664 | Region | Note=Tail |
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3'-UTR located exon skipping events that lost miRNA binding sites in LMNA |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for LMNA |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for LMNA |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LMNA |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for LMNA |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for LMNA |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for LMNA |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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