LMNB2

lamin B2, the group of Lamins|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:2427638-2456959

Previous symbols: [ "LMN2" ]

Links

ENSG00000176619NCBI:84823OMIM:150341HGNC:6638Uniprot:Q03252AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Liopdystrophy, partial, acquired; Microcephaly 27, primary, autosomal dominant; Epilepsy, progressive myoclonic, 9AD/ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal; Neurologic16826530; 22768673; 25954030; 33033404

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LMNB2 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
154
clinvar
5
clinvar
159
missense
3
clinvar
271
clinvar
50
clinvar
13
clinvar
337
nonsense
3
clinvar
3
start loss
0
frameshift
1
clinvar
2
clinvar
3
splice donor/acceptor (+/-2bp)
2
clinvar
2
Total 4 0 278 204 18
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LMNB2protein_codingprotein_codingENST00000325327 1229359
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000041400000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6593593960.9070.00002993991
Missense in Polyphen113153.710.735161492
Synonymous-0.4741871791.050.00001441252
Loss of Function4.95028.50.000.00000142330

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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