LMNB2
lamin B2, the group of Lamins|MicroRNA protein coding host genes
Basic information
Region (hg38): 19:2427638-2456959
Previous symbols: [ "LMN2" ]
Links
Phenotypes
GenCC
Source:
- microcephaly (Moderate), mode of inheritance: AD
- progressive myoclonic epilepsy type 9 (Limited), mode of inheritance: AR
- progressive myoclonic epilepsy type 9 (Supportive), mode of inheritance: AR
- lipodystrophy, partial, acquired, susceptibility to (Limited), mode of inheritance: AD
- progressive myoclonic epilepsy type 9 (Strong), mode of inheritance: AR
- microcephaly 27, primary, autosomal dominant (Strong), mode of inheritance: AD
- microcephaly 27, primary, autosomal dominant (Strong), mode of inheritance: AD
- lipodystrophy, partial, acquired, susceptibility to (Limited), mode of inheritance: AD
- progressive myoclonic epilepsy type 9 (Limited), mode of inheritance: AR
- microcephaly 27, primary, autosomal dominant (Limited), mode of inheritance: AD
- central nervous system malformation (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Liopdystrophy, partial, acquired; Microcephaly 27, primary, autosomal dominant; Epilepsy, progressive myoclonic, 9 | AD/AR | General | 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 | Craniofacial; Musculoskeletal; Neurologic | 16826530; 22768673; 25954030; 33033404 |
ClinVar
This is a list of variants' phenotypes submitted to
- Lipodystrophy,_partial,_acquired,_susceptibility_to (554 variants)
- Progressive_myoclonic_epilepsy_type_9 (553 variants)
- not_specified (108 variants)
- not_provided (59 variants)
- LMNB2-related_disorder (17 variants)
- Microcephaly_27,_primary,_autosomal_dominant (13 variants)
- Acquired_partial_lipodystrophy (3 variants)
- Neurodevelopmental_disorder (2 variants)
- Generalized_myoclonic_seizure (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMNB2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032737.4. 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 | 154 | 159 | ||||
| missense | 271 | 50 | 13 | 337 | ||
| nonsense | 3 | |||||
| start loss | 0 | |||||
| frameshift | 3 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 4 | 0 | 278 | 204 | 18 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LMNB2 | protein_coding | protein_coding | ENST00000325327 | 12 | 29359 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000414 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.659 | 359 | 396 | 0.907 | 0.0000299 | 3991 |
| Missense in Polyphen | 113 | 153.71 | 0.73516 | 1492 | ||
| Synonymous | -0.474 | 187 | 179 | 1.05 | 0.0000144 | 1252 |
| Loss of Function | 4.95 | 0 | 28.5 | 0.00 | 0.00000142 | 330 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Lamins are components of the nuclear lamina, a fibrous layer on the nucleoplasmic side of the inner nuclear membrane, which is thought to provide a framework for the nuclear envelope and may also interact with chromatin.;
- Disease
- DISEASE: Partial acquired lipodystrophy (APLD) [MIM:608709]: A rare childhood disease characterized by loss of subcutaneous fat from the face and trunk. Fat deposition on the pelvic girdle and lower limbs is normal or excessive. Most frequently, onset between 5 and 15 years of age. Most affected subjects are females and some show no other abnormality, but many develop glomerulonephritis, diabetes mellitus, hyperlipidemia, and complement deficiency. Mental retardation in some cases. APLD is a sporadic disorder of unknown etiology. {ECO:0000269|PubMed:16826530, ECO:0000269|PubMed:22768673}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epilepsy, progressive myoclonic 9 (EPM9) [MIM:616540]: An autosomal recessive form of progressive myoclonic epilepsy, a rare disease initially responsive to antiepileptic drugs which over time becomes refractory and can be associated with cognitive decline. EPM9 features include myoclonus, tonic-clonic seizures, ataxia, and psychomotor development. {ECO:0000269|PubMed:25954030}. Note=The disease may be caused by mutations affecting the gene represented in this entry.;
- Pathway
- Apoptosis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Gastric Cancer Network 2;Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation;tnfr1 signaling pathway;caspase cascade in apoptosis;hiv-1 nef: negative effector of fas and tnf;Caspase Cascade in Apoptosis
(Consensus)
Recessive Scores
- pRec
- 0.243
Intolerance Scores
- loftool
- rvis_EVS
- -1.13
- rvis_percentile_EVS
- 6.51
Haploinsufficiency Scores
- pHI
- 0.838
- hipred
- Y
- hipred_score
- 0.696
- ghis
- 0.701
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.804
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lmnb2
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); muscle phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; embryo phenotype;
Gene ontology
- Biological process
- biological_process
- Cellular component
- nuclear inner membrane;lamin filament;nuclear membrane
- Molecular function
- molecular_function;structural molecule activity;protein binding