LMNB2
gene geneOn this page
Summary
LMNB2 (lamin B2, HGNC:6638) is a protein-coding gene on chromosome 19p13.3, encoding Lamin-B2 (Q03252). Lamins are intermediate filament proteins that assemble into a filamentous meshwork, and which constitute the major components of the nuclear lamina, a fibrous layer on the nucleoplasmic side of the inner nuclear membrane.
This gene encodes a B type nuclear lamin. The nuclear lamina consists of a two-dimensional matrix of proteins located next to the inner nuclear membrane. The lamin family of proteins make up the matrix and are highly conserved in evolution. During mitosis, the lamina matrix is reversibly disassembled as the lamin proteins are phosphorylated. Lamin proteins are thought to be involved in nuclear stability, chromatin structure and gene expression. Vertebrate lamins consist of two types, A and B. Mutations in this gene are associated with acquired partial lipodystrophy.
Source: NCBI Gene 84823 — RefSeq curated summary.
At a glance
- Gene–disease (curated): progressive myoclonic epilepsy type 9 (Strong, GenCC) — +4 more curated relationships
- Clinical variants (ClinVar): 705 total — 4 pathogenic (top 5% of genes corpus-wide)
- GTEx eGene: eQTL in 8 tissues, sQTL in 3 (q < 0.05)
- Phenotypes (HPO): 66
- Constraint (gnomAD): pLI 1.00 (loss-of-function intolerant), LOEUF 0.40 (moderately constrained)
- MANE Select transcript:
NM_032737 - Interaction hub: 2,338 STRING partners (top 5% of genes corpus-wide)
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:6638 |
| Approved symbol | LMNB2 |
| Name | lamin B2 |
| Location | 19p13.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000176619 |
| Ensembl biotype | protein_coding |
| OMIM | 150341 |
| Entrez | 84823 |
Gene structure
Transcript identifiers
Ensembl transcripts: 20 — 11 protein_coding, 4 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay, 1 retained_intron
MANE Select: ENST00000325327
Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 1, TSL 3: 2, TSL 5: 2
ENST00000325327, ENST00000475819, ENST00000490554, ENST00000527409, ENST00000532465, ENST00000534495, ENST00000867388, ENST00000867389, ENST00000917221, ENST00000917222, ENST00000917223, ENST00000917224, ENST00000917225, ENST00000917226, ENST00001007961, ENST00001034820, ENST00001034821, ENST00001073484, ENST00001073485, ENST00001142321
RefSeq mRNA: 1 — MANE Select: NM_032737
NM_032737
CCDS: CCDS12090
Canonical transcript exons
ENST00000325327 — 12 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000655672 | 2438163 | 2438288 |
| ENSE00001052208 | 2444404 | 2444540 |
| ENSE00001150160 | 2438375 | 2438531 |
| ENSE00001150172 | 2456670 | 2456959 |
| ENSE00001247707 | 2428166 | 2430952 |
| ENSE00003466453 | 2431548 | 2431658 |
| ENSE00003489516 | 2434295 | 2434515 |
| ENSE00003497284 | 2432416 | 2432523 |
| ENSE00003539631 | 2434788 | 2434913 |
| ENSE00003563021 | 2435001 | 2435171 |
| ENSE00003588969 | 2433826 | 2434105 |
| ENSE00003594665 | 2431783 | 2431902 |
Expression profiles
Bgee: expression breadth ubiquitous, 194 present calls, max score 97.24.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 37.0023 / max 234.9255, expressed in 1815 samples.
Highest expression (Bgee): ventricular zone, testis, ganglionic eminence, endometrium epithelium, embryo.
Genetic regulation across tissues (GTEx eQTL / sQTL)
LMNB2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 8 tissues and its splicing (sQTL) in 3 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.
11 significant tissue × QTL associations:
| Tissue | QTL | q-value | Slope | Lead variant |
|---|---|---|---|---|
| Testis | sqtl | 3.0e-07 | +0.47 | 19:2437078:A:G |
| Muscle Skeletal | eqtl | 9.9e-05 | -0.18 | 19:2419362:C:A |
| Colon Sigmoid | eqtl | 2.1e-03 | +0.52 | 19:1892953:C:G |
| Thyroid | eqtl | 1.2e-02 | +0.30 | 19:2975764:G:A |
| Esophagus Muscularis | eqtl | 1.7e-02 | +0.32 | 19:3220865:A:AC |
| Adipose Subcutaneous | eqtl | 1.9e-02 | -0.24 | 19:3143566:C:T |
| Brain Hypothalamus | sqtl | 2.8e-02 | +0.47 | 19:1667051:G:C |
| Nerve Tibial | eqtl | 3.4e-02 | +0.32 | 19:3220865:A:AC |
| Cells EBV-transformed lymphocytes | sqtl | 4.0e-02 | -1.53 | 19:2427943:G:T |
| Testis | eqtl | 4.4e-02 | -0.10 | 19:2419251:T:C |
| Skin Sun Exposed Lower leg | eqtl | 4.5e-02 | +0.21 | 19:1567044:C:T |
FANTOM5 promoters
4 alternative TSS:
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 178172 | 35.3543 | 1814 |
| 178171 | 1.4369 | 857 |
| 178169 | 0.1916 | 72 |
| 178170 | 0.0195 | 3 |
Top tissues by expression
showing 100 of 285 tissues by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| ventricular zone | UBERON:0003053 | 97.24 | gold quality |
| left testis | UBERON:0004533 | 95.73 | gold quality |
| right testis | UBERON:0004534 | 95.62 | gold quality |
| ganglionic eminence | UBERON:0004023 | 94.82 | gold quality |
| endometrium epithelium | UBERON:0004811 | 94.78 | gold quality |
| embryo | UBERON:0000922 | 94.43 | gold quality |
| secondary oocyte | CL:0000655 | 93.89 | gold quality |
| stromal cell of endometrium | CL:0002255 | 93.22 | gold quality |
| testis | UBERON:0000473 | 92.33 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 90.95 | gold quality |
| esophagus mucosa | UBERON:0002469 | 90.17 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 90.13 | gold quality |
| hindlimb stylopod muscle | UBERON:0004252 | 89.53 | gold quality |
| gastrocnemius | UBERON:0001388 | 89.34 | gold quality |
| apex of heart | UBERON:0002098 | 88.84 | gold quality |
| muscle of leg | UBERON:0001383 | 88.70 | gold quality |
| gingival epithelium | UBERON:0001949 | 88.10 | silver quality |
| oocyte | CL:0000023 | 87.81 | gold quality |
| cortical plate | UBERON:0005343 | 87.76 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 87.41 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 86.82 | gold quality |
| esophagus squamous epithelium | UBERON:0006920 | 86.79 | gold quality |
| cerebellar cortex | UBERON:0002129 | 86.76 | gold quality |
| epithelium of esophagus | UBERON:0001976 | 86.34 | gold quality |
| left adrenal gland | UBERON:0001234 | 86.25 | gold quality |
| right adrenal gland | UBERON:0001233 | 86.09 | gold quality |
| left adrenal gland cortex | UBERON:0035825 | 85.98 | gold quality |
| right atrium auricular region | UBERON:0006631 | 85.78 | gold quality |
| adenohypophysis | UBERON:0002196 | 85.71 | gold quality |
| esophagus | UBERON:0001043 | 85.68 | gold quality |
| cerebellum | UBERON:0002037 | 85.55 | gold quality |
| gingiva | UBERON:0001828 | 85.52 | silver quality |
| right adrenal gland cortex | UBERON:0035827 | 85.44 | gold quality |
| heart left ventricle | UBERON:0002084 | 85.23 | gold quality |
| transverse colon | UBERON:0001157 | 85.08 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 84.94 | gold quality |
| vermiform appendix | UBERON:0001154 | 84.60 | gold quality |
| cardiac ventricle | UBERON:0002082 | 84.60 | gold quality |
| granulocyte | CL:0000094 | 84.45 | gold quality |
| adrenal cortex | UBERON:0001235 | 84.29 | gold quality |
| body of stomach | UBERON:0001161 | 84.08 | gold quality |
| adrenal gland | UBERON:0002369 | 84.02 | gold quality |
| cardiac atrium | UBERON:0002081 | 83.94 | gold quality |
| metanephros cortex | UBERON:0010533 | 83.87 | gold quality |
| rectum | UBERON:0001052 | 83.80 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 83.74 | gold quality |
| pituitary gland | UBERON:0000007 | 83.54 | gold quality |
| squamous epithelium | UBERON:0006914 | 83.50 | gold quality |
| paraflocculus | UBERON:0005351 | 83.33 | gold quality |
| sural nerve | UBERON:0015488 | 83.17 | gold quality |
| monocyte | CL:0000576 | 83.14 | gold quality |
| heart | UBERON:0000948 | 83.12 | gold quality |
| ectocervix | UBERON:0012249 | 83.06 | gold quality |
| mononuclear cell | CL:0000842 | 83.04 | gold quality |
| right ovary | UBERON:0002118 | 83.04 | gold quality |
| leukocyte | CL:0000738 | 82.98 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 82.95 | gold quality |
| stomach | UBERON:0000945 | 82.82 | gold quality |
| muscle organ | UBERON:0001630 | 82.76 | gold quality |
| left uterine tube | UBERON:0001303 | 82.75 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 82.74 | gold quality |
| left ovary | UBERON:0002119 | 82.71 | gold quality |
| upper lobe of left lung | UBERON:0008952 | 82.63 | gold quality |
| adrenal tissue | UBERON:0018303 | 82.48 | gold quality |
| placenta | UBERON:0001987 | 82.38 | gold quality |
| right frontal lobe | UBERON:0002810 | 82.36 | gold quality |
| ileal mucosa | UBERON:0000331 | 82.32 | silver quality |
| colon | UBERON:0001155 | 82.12 | gold quality |
| spleen | UBERON:0002106 | 82.11 | gold quality |
| small intestine | UBERON:0002108 | 81.94 | gold quality |
| large intestine | UBERON:0000059 | 81.85 | gold quality |
| body of uterus | UBERON:0009853 | 81.85 | gold quality |
| intestine | UBERON:0000160 | 81.84 | gold quality |
| minor salivary gland | UBERON:0001830 | 81.72 | gold quality |
| cartilage tissue | UBERON:0002418 | 81.70 | silver quality |
| upper lobe of lung | UBERON:0008948 | 81.64 | gold quality |
| caecum | UBERON:0001153 | 81.62 | gold quality |
| prefrontal cortex | UBERON:0000451 | 81.59 | gold quality |
| skin of abdomen | UBERON:0001416 | 81.53 | gold quality |
| mouth mucosa | UBERON:0003729 | 81.53 | gold quality |
| thyroid gland | UBERON:0002046 | 81.29 | gold quality |
| skin of leg | UBERON:0001511 | 81.22 | gold quality |
| cingulate cortex | UBERON:0003027 | 81.18 | gold quality |
| lymph node | UBERON:0000029 | 81.13 | gold quality |
| lower esophagus | UBERON:0013473 | 81.07 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 81.02 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 80.98 | gold quality |
| omental fat pad | UBERON:0010414 | 80.96 | gold quality |
| right lobe of liver | UBERON:0001114 | 80.95 | gold quality |
| peritoneum | UBERON:0002358 | 80.92 | gold quality |
| left coronary artery | UBERON:0001626 | 80.90 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 80.84 | gold quality |
| ovary | UBERON:0000992 | 80.81 | gold quality |
| vagina | UBERON:0000996 | 80.68 | gold quality |
| islet of Langerhans | UBERON:0000006 | 80.67 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 80.45 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 80.38 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 80.31 | gold quality |
| amygdala | UBERON:0001876 | 80.25 | gold quality |
| smooth muscle tissue | UBERON:0001135 | 80.12 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 6.31 |
HPA expression
RNA tissue specificity: Low tissue specificity
showing 60 of 80 HPA tissues / cells by nTPM:
| Tissue / cell | Axis | nTPM | Protein (IHC) |
|---|---|---|---|
| Thymus | tissue | 21.5 | |
| Bone marrow | tissue | 16.3 | medium |
| Appendix | tissue | 14.5 | low |
| Cerebellum | tissue | 14.2 | high |
| Placenta | tissue | 13.8 | low |
| Locus coeruleus | tissue | 13.1 | |
| Skeletal muscle | tissue | 12.9 | medium |
| Hippocampus | tissue | 12.2 | high |
| Lymph node | tissue | 12.0 | medium |
| Pituitary gland | tissue | 11.9 | |
| Vagina | tissue | 11.9 | low |
| Small intestine | tissue | 11.5 | low |
| Corpus callosum | tissue | 11.1 | |
| Nucleus accumbens | tissue | 11.0 | |
| Postcentral gyrus | tissue | 10.6 | |
| Duodenum | tissue | 10.3 | low |
| Colon | tissue | 9.9 | low |
| Tonsil | tissue | 9.9 | medium |
| Skin 1 | tissue | 9.6 | medium |
| Choroid plexus | tissue | 9.2 | |
| Stomach 1 | tissue | 8.9 | medium |
| Esophagus | tissue | 8.9 | medium |
| Midbrain | tissue | 8.4 | |
| Superior colliculi | tissue | 8.3 | |
| Medulla oblongata | tissue | 8.1 | |
| Thalamus | tissue | 8.0 | |
| Hypothalamus | tissue | 7.9 | |
| Spinal cord | tissue | 7.9 | |
| Ovary | tissue | 7.8 | medium |
| Substantia nigra | tissue | 7.8 | |
| Spleen | tissue | 7.7 | medium |
| Pons | tissue | 7.5 | |
| Periaqueductal gray | tissue | 7.3 | |
| Septum | tissue | 7.2 | |
| Urinary bladder | tissue | 7.0 | medium |
| Ventral forebrain | tissue | 7.0 | |
| Frontal cortex | tissue | 6.9 | |
| Cerebral cortex | tissue | 6.8 | high |
| Adipose tissue | tissue | 6.8 | medium |
| Olfactory bulb | tissue | 6.8 | |
| Somatosensory cortex | tissue | 6.8 | |
| Hippocampal formation | tissue | 6.7 | |
| Putamen | tissue | 6.6 | |
| Caudate putamen | tissue | 6.4 | |
| Occipital cortex | tissue | 6.4 | |
| Motor cortex | tissue | 6.3 | |
| Amygdala | tissue | 6.3 | |
| Basal ganglia | tissue | 6.1 | high |
| Entorhinal cortex | tissue | 6.0 | |
| Fallopian tube | tissue | 6.0 | high |
| Retrosplenial cortex | tissue | 5.9 | |
| Prefrontal cortex | tissue | 5.8 | |
| Rectum | tissue | 5.8 | medium |
| Retrosplenial and cingulate cortex | tissue | 5.7 | |
| Insular cortex | tissue | 5.7 | |
| Temporal cortex | tissue | 5.6 | |
| Salivary gland | tissue | 5.5 | medium |
| Smooth muscle | tissue | 5.2 | low |
| Endometrium 1 | tissue | 5.0 | medium |
| Lung | tissue | 5.0 | high |
Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Flocculonodular lobe (19.4), Cerebellar cortex (18.5), Vermis (18.5), Ventromedial nucleus (17.6), Arcuate nucleus (16.9).
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
Targeting LMNB2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).
showing 30 of 72 miRNAs:
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-656-3P | 100.00 | 72.15 | 2788 |
| HSA-MIR-6867-5P | 100.00 | 82.21 | 3464 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-520D-5P | 99.98 | 73.34 | 4883 |
| HSA-MIR-524-5P | 99.98 | 73.43 | 4882 |
| HSA-MIR-3148 | 99.97 | 75.06 | 6478 |
| HSA-MIR-551B-5P | 99.96 | 71.28 | 3493 |
| HSA-MIR-6778-3P | 99.96 | 67.29 | 2693 |
| HSA-LET-7C-3P | 99.95 | 73.42 | 2862 |
| HSA-MIR-6508-5P | 99.92 | 70.67 | 2465 |
| HSA-MIR-5680 | 99.91 | 69.83 | 3421 |
| HSA-MIR-4492 | 99.87 | 68.25 | 3611 |
| HSA-MIR-8067 | 99.86 | 69.59 | 2260 |
| HSA-MIR-4698 | 99.84 | 71.41 | 4303 |
| HSA-MIR-1321 | 99.84 | 65.30 | 1811 |
| HSA-MIR-4756-5P | 99.84 | 64.98 | 1809 |
| HSA-MIR-4739 | 99.84 | 65.25 | 1832 |
| HSA-MIR-4495 | 99.82 | 72.08 | 3080 |
| HSA-MIR-6756-5P | 99.82 | 67.97 | 2466 |
| HSA-MIR-3133 | 99.81 | 70.92 | 3506 |
| HSA-MIR-4320 | 99.75 | 65.80 | 793 |
| HSA-MIR-1255A | 99.74 | 68.09 | 744 |
| HSA-MIR-1255B-5P | 99.74 | 68.16 | 741 |
| HSA-MIR-149-3P | 99.72 | 68.22 | 3963 |
| HSA-MIR-33A-3P | 99.70 | 70.27 | 3362 |
| HSA-MIR-6766-5P | 99.68 | 67.70 | 2325 |
| HSA-MIR-5004-5P | 99.68 | 66.63 | 1294 |
| HSA-MIR-29B-2-5P | 99.67 | 68.98 | 1726 |
| HSA-MIR-6887-3P | 99.66 | 67.83 | 1778 |
Functional genomics
gnomAD constraint: pLI 1, LOEUF 0.399, missense Z 0.641 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD
Regional missense constraint (gnomAD)
ENST00000325327 splits into 3 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD
| Region (GRCh38) | Missense obs / exp | o/e | Constrained |
|---|---|---|---|
| 19:2,430,914–2,438,401 | 609 / 630.9 | 0.97 | no |
| 19:2,438,402–2,456,873 | 145 / 228.9 | 0.63 | no |
| 19:2,456,874–2,456,933 | 35 / 23.9 | 1.47 | no |
Literature-anchored findings (GeneRIF, showing 23)
- analysis of protein-DNA interactions at the human lamin B2 replication origin (PMID:12902329)
- The proteins bound in vivo at the LMNB2 replication origin were investigated along the cell cycle. (PMID:12912926)
- This analysis reveals the modular structure of the lamin B2 origin and supports the idea that sequence elements close to the replication start site play an important role in origin activation. (PMID:15024083)
- the distinctive ensemble of heterotypic lamin interactions in a particular cell type affects the stability of the lamin polymer (PMID:15284226)
- the lamin B2 origin adopts a structure partly composed of intramolecular TAT triads (PMID:15611042)
- lamin B was essential for the formation of the mitotic matrix that tethers a number of spindle assembly factors; propose that lamin B is a structural component of the spindle matrix that promotes microtubule assembly and organization in mitosis (PMID:16543417)
- Three new rare heterozygous mutations are the first reported for LMNB2 and are the first reported among patients with acquired partial lipodystrophy. (PMID:16826530)
- human lamin B(2) is indeed synthesized as a longer version than previously reported, because it contains these additional 20 amino acids (PMID:17070523)
- The human DNA replication origin, located in the lamin B2 gene, interacts with the DNA topoisomerases I and II in a cell cycle-modulated manner. (PMID:17290216)
- Using shotgun mass spectrometry, we found this protein differentially expressed in the dorsolateral prefrontal cortex from patients with schizophrenia. (PMID:19165527)
- These findings indicate that a lamin dimer principally has the freedom for a “combinatorial” head-to-tail association with all types of lamins, a property that might be of significant importance for the assembly of the nuclear lamina. (PMID:20004208)
- Studies indicate that the lamin-binding proteins implicated in laminopathies include lamin B2 and nuclear envelope proteins. (PMID:21400569)
- Mutation in LMNB2 gene is associated with partial lipodystrophy. (PMID:22768673)
- Treating normal human fibroblasts with farnesyltransferase inhibitors causes the accumulation of unprocessed lamin B2 and lamin A and a decrease in mature lamin B1 (PMID:23475125)
- Nuclear envelope remodelling during human spermiogenesis involves somatic B-type lamins and a spermatid-specific B3 lamin isoform. (PMID:25477337)
- Mutation of the nuclear lamin gene LMNB2 in progressive myoclonus epilepsy with early ataxia. (PMID:25954030)
- our studies strongly implicate an overarching role for Lamin B2 in the maintenance of nuclear architecture since loss of Lamin B2 relieves the spatial positional constraints required for maintaining conserved localization of aneuploid chromosome territories in the interphase nucleus. (PMID:26921073)
- Lamin B2 promotes the malignant phenotype of non-small cell lung cancer cells by upregulating dimethylation of histone 3 lysine 9. (PMID:32416090)
- Heterozygous lamin B1 and lamin B2 variants cause primary microcephaly and define a novel laminopathy. (PMID:33033404)
- LMNB2 is a prognostic biomarker and correlated with immune infiltrates in hepatocellular carcinoma. (PMID:33211382)
- LMNB2 promotes the progression of colorectal cancer by silencing p21 expression. (PMID:33782407)
- Lamin B2 contributes to the proliferation of bladder cancer cells via activating the expression of cell division cycleassociated protein 3. (PMID:35775376)
- The role of lamin B2 in human diseases. (PMID:37044185)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | lmnb2 | ENSDARG00000101624 |
| mus_musculus | Lmnb2 | ENSMUSG00000062075 |
| rattus_norvegicus | Lmnb2 | ENSRNOG00000025742 |
Paralogs (68): KRT33A (ENSG00000006059), VIM (ENSG00000026025), KRT31 (ENSG00000094796), NEFM (ENSG00000104722), KRT23 (ENSG00000108244), KRT37 (ENSG00000108417), KRT32 (ENSG00000108759), KRT18 (ENSG00000111057), LMNB1 (ENSG00000113368), KRT36 (ENSG00000126337), KRT17 (ENSG00000128422), GFAP (ENSG00000131095), KRT34 (ENSG00000131737), KRT33B (ENSG00000131738), NES (ENSG00000132688), PRPH (ENSG00000135406), KRT85 (ENSG00000135443), KRT7 (ENSG00000135480), KRT71 (ENSG00000139648), INA (ENSG00000148798), LMNTD1 (ENSG00000152936), LMNA (ENSG00000160789), KRT84 (ENSG00000161849), KRT82 (ENSG00000161850), KRT80 (ENSG00000167767), KRT1 (ENSG00000167768), KRT24 (ENSG00000167916), KRT8 (ENSG00000170421), KRT78 (ENSG00000170423), KRT86 (ENSG00000170442), KRT75 (ENSG00000170454), KRT6C (ENSG00000170465), KRT4 (ENSG00000170477), KRT74 (ENSG00000170484), KRT72 (ENSG00000170486), KRT83 (ENSG00000170523), BFSP2 (ENSG00000170819), KRT19 (ENSG00000171345), KRT15 (ENSG00000171346), KRT38 (ENSG00000171360), KRT13 (ENSG00000171401), KRT9 (ENSG00000171403), KRT20 (ENSG00000171431), KRT27 (ENSG00000171446), KRT2 (ENSG00000172867), KRT28 (ENSG00000173908), DES (ENSG00000175084), SYNM (ENSG00000182253), KRT76 (ENSG00000185069), KRT6B (ENSG00000185479), KRT79 (ENSG00000185640), KRT73 (ENSG00000186049), KRT5 (ENSG00000186081), KRT26 (ENSG00000186393), KRT10 (ENSG00000186395), KRT3 (ENSG00000186442), KRT16 (ENSG00000186832), KRT14 (ENSG00000186847), KRT12 (ENSG00000187242), KRT77 (ENSG00000189182)
+8 more (showing top 60).
Mouse-model phenotypes
Observed phenotypes of the mouse ortholog (MGI:96796) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 16 distinct phenotype terms.
| Mouse phenotype (MP) | Records |
|---|---|
| abnormal neuronal precursor proliferation | 2 |
| abnormal neuronal migration | 2 |
| neonatal lethality, complete penetrance | 2 |
| decreased brain size | 1 |
| abnormal forebrain morphology | 1 |
| abnormal cerebral cortex morphology | 1 |
| abnormal cerebral cortex lamination | 1 |
| abnormal hippocampus layer morphology | 1 |
| abnormal cerebellum morphology | 1 |
| absent cerebellar foliation | 1 |
| thin external granule cell layer | 1 |
| respiratory failure | 1 |
| increased circulating creatinine level | 1 |
| abnormal cortical plate morphology | 1 |
| absent Purkinje cell layer | 1 |
| disorganized cerebral cortex lamination | 1 |
Additional cross-species homologs
Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.
| Organism | UniProt | Identity | Method |
|---|---|---|---|
| Sus scrofa | Q3ZD69 | 96.1% | Diamond |
| Macaca fascicularis | Q4R899 | 89.8% | Diamond |
| Caenorhabditis briggsae | Q5WN60 | 81.1% | Diamond |
| Gallus gallus | P14731 | 79.5% | Diamond |
| Lymnaea stagnalis | Q6QUW1 | 73.9% | Diamond |
| Xenopus laevis | P21910 | 71.1% | Diamond |
| Hypsibius exemplaris | A0A125S9M6 | 65.8% | Diamond |
| Caenorhabditis elegans | Q21443 | 40.5% | Diamond |
Genomic neighbors (locus context)
Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).
| Symbol | Type | Entrez |
|---|---|---|
| MIR7108 | ncRNA | 102466806 |
| TIMM13 | protein-coding | 26517 |
| TMPRSS9 | protein-coding | 360200 |
| GADD45B | protein-coding | 4616 |
| LINC01775 | ncRNA | 101928602 |
| SPPL2B | protein-coding | 56928 |
| LSM7 | protein-coding | 51690 |
Protein
Protein identifiers
Lamin-B2 — Q03252 (reviewed: Q03252)
All UniProt accessions (1): Q03252
UniProt curated annotations — full annotation on UniProt →
Function. Lamins are intermediate filament proteins that assemble into a filamentous meshwork, and which constitute the major components of the nuclear lamina, a fibrous layer on the nucleoplasmic side of the inner nuclear membrane. Lamins provide a framework for the nuclear envelope, bridging the nuclear envelope and chromatin, thereby playing an important role in nuclear assembly, chromatin organization, nuclear membrane and telomere dynamics. The structural integrity of the lamina is strictly controlled by the cell cycle, as seen by the disintegration and formation of the nuclear envelope in prophase and telophase, respectively.
Subunit / interactions. Dimer. Lamin dimers then assemble into dimeric head-to-tail polymers. Ultimately, two head-to-tail polymers assemble laterally into a protofilament with a uniformly shaped rod of 3.5 nm in diameter. Interacts with TMEM43.
Subcellular location. Nucleus lamina.
Post-translational modifications. B-type lamins undergo a series of modifications, such as farnesylation and phosphorylation. Increased phosphorylation of the lamins occurs before envelope disintegration and probably plays a role in regulating lamin associations. Phosphorylation plays a key role in lamin organization, subcellular localization and nuclear envelope disintegration. Phosphorylation by CDK1 at Ser-37 and Ser-407 at the onset of mitosis drives lamin disassembly and nuclear envelope breakdown.
Disease relevance. 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. Intellectual disability in some cases. APLD is a sporadic disorder of unknown etiology. The disease is caused by variants affecting the gene represented in this entry. Epilepsy, progressive myoclonic 9 (EPM9) [MIM:616540] A form of progressive myoclonic epilepsy, a clinically and genetically heterogeneous group of disorders defined by the combination of action and reflex myoclonus, other types of epileptic seizures, and progressive neurodegeneration and neurocognitive impairment. EPM9 is an autosomal recessive form characterized by myoclonus, tonic-clonic seizures, ataxia, and delayed psychomotor development. The disease may be caused by variants affecting the gene represented in this entry. Microcephaly 27, primary, autosomal dominant (MCPH27) [MIM:619180] A form of microcephaly, a disease defined as a head circumference more than 3 standard deviations below the age, sex and ethnically matched mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. MCPH27 is an autosomal dominant form apparent in early childhood and associated with global developmental delay, delayed walking, inability to walk, impaired intellectual development, and poor or absent speech. Brain imaging may show enlarged ventricles or gyral abnormalities in some patients. The disease is caused by variants affecting the gene represented in this entry.
Similarity. Belongs to the intermediate filament family.
RefSeq proteins (1): NP_116126* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001322 | Lamin_tail_dom | Domain |
| IPR018039 | IF_conserved | Conserved_site |
| IPR036415 | Lamin_tail_dom_sf | Homologous_superfamily |
| IPR039008 | IF_rod_dom | Domain |
Pfam: PF00038, PF00932
UniProt features (60 total): modified residue 13, region of interest 10, strand 10, sequence variant 7, cross-link 5, compositionally biased region 4, domain 2, sequence conflict 2, chain 1, propeptide 1, short sequence motif 1, lipid moiety-binding region 1, glycosylation site 1, helix 1, turn 1
Structure
Experimental structures (PDB)
2 structures by resolution:
| PDB | Title | Method | Resolution (Å) |
|---|---|---|---|
| 5BNW | The active site of O-GlcNAc transferase imposes constraints on substrate sequence | X-RAY DIFFRACTION | 2.4 |
| 2LLL | Solution NMR structure of C-terminal globular domain of human Lamin-B2, Northeast … | SOLUTION NMR |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q03252-F1 | 79.82 | 0.62 |
Human Protein Atlas
Protein class: Predicted intracellular proteins, Plasma proteins, Disease related genes, Human disease related genes, Congenital disorders of metabolism, Other congenital disorders of metabolism, Congenital malformations, Congenital malformations of the nervous system, Epilepsy
Protein evidence: Evidence at protein level
Subcellular location (HPA, imaging): nuclear membrane
Antibody reliability (HPA): IH enhanced · IF supported
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Post-translational modifications (19)
| Type | Positions |
|---|---|
| Phosphothreonine | 23, 34 |
| Phosphoserine | 37, 316, 407, 420, 422, 424, 426, 497 |
| N6-acetyllysine | 81 |
| Omega-n-methylarginine | 433 |
| Cysteine methyl ester | 617 |
| S-farnesyl cysteine | 617 |
| Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo2) | 77, 81, 195, 255, 489 |
Glycosylation sites (1)
| Type | Positions |
|---|---|
| O-linked (glcnac) threonine | 413 |
Function
Pathways and Gene Ontology
Reactome pathways
0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).
MSigDB gene sets: 376 (showing top):
MORF_DNMT1, MODULE_52, HORIUCHI_WTAP_TARGETS_DN, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, MORF_ESPL1, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GEORGES_CELL_CYCLE_MIR192_TARGETS, MORF_RRM1, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, MODULE_16, PATIL_LIVER_CANCER, PUJANA_CHEK2_PCC_NETWORK, MODULE_118, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC
GO Biological Process (6): nuclear envelope organization (GO:0006998), nuclear migration (GO:0007097), heterochromatin formation (GO:0031507), nuclear pore localization (GO:0051664), protein localization to nuclear envelope (GO:0090435), cytoskeleton organization (GO:0007010)
GO Molecular Function (3): structural constituent of cytoskeleton (GO:0005200), identical protein binding (GO:0042802), protein binding (GO:0005515)
GO Cellular Component (4): nuclear lamina (GO:0005652), intermediate filament (GO:0005882), nuclear membrane (GO:0031965), nuclear envelope (GO:0005635)
GO top-level categories
28 GO namespaces:
| Category | Terms |
|---|---|
| nucleus organization | 2 |
| nuclear envelope | 2 |
| nucleus | 2 |
| endomembrane system organization | 1 |
| membrane organization | 1 |
| intracellular transport | 1 |
| nucleus localization | 1 |
| establishment of organelle localization | 1 |
| cellular component assembly | 1 |
| heterochromatin boundary formation | 1 |
| negative regulation of gene expression, epigenetic | 1 |
| heterochromatin organization | 1 |
| protein-containing complex localization | 1 |
| localization within membrane | 1 |
| protein localization to nucleus | 1 |
| organelle organization | 1 |
| structural molecule activity | 1 |
| cytoskeleton | 1 |
| cytoskeleton organization | 1 |
| protein binding | 1 |
| binding | 1 |
| nuclear periphery | 1 |
| cellular anatomical structure | 1 |
| intermediate filament cytoskeleton | 1 |
| polymeric cytoskeletal fiber | 1 |
| organelle membrane | 1 |
| endomembrane system | 1 |
| organelle envelope | 1 |
Experimentally-supported GO annotations
GO terms backed by direct experimental evidence (ECO experimental codes) — 2 of 13 annotations. The rest are phylogenetic / computational / electronic (IEA).
2 experimentally-supported GO terms:
| GO term | NS | Evidence |
|---|---|---|
| nuclear membrane | CC | direct assay |
| identical protein binding | MF | physical interaction |
Protein interactions and networks
STRING
showing 15 of 2,338 interactions by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| LMNB2 | LBR | Q14739 | 893 |
| LMNB2 | TIMM13 | P62206 | 853 |
| LMNB2 | SENP2 | Q9HC62 | 759 |
| LMNB2 | ACTB | P02570 | 725 |
| LMNB2 | EMD | P50402 | 717 |
| LMNB2 | GAPDH | P00354 | 684 |
| LMNB2 | SENP3 | Q9H4L4 | 655 |
| LMNB2 | RGPD1 | P0C839 | 650 |
| LMNB2 | TM7SF2 | O76062 | 631 |
| LMNB2 | RANGAP1 | P46060 | 622 |
| LMNB2 | PXDN | Q92626 | 610 |
| LMNB2 | PXDNL | A1KZ92 | 610 |
| LMNB2 | HMOX1 | P09601 | 607 |
| LMNB2 | NFKBIA | P25963 | 591 |
| LMNB2 | LEMD3 | Q9Y2U8 | 587 |
IntAct
Human interaction partners of LMNB2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).
showing 30 of 33 partners by confidence:
| Partner | Interaction type | MIscore | Records |
|---|---|---|---|
| LMNB1 | physical association | 0.850 | 4 |
| LMNA | physical association | 0.850 | 3 |
| AMOT | physical association | 0.560 | 3 |
| AMOTL2 | physical association | 0.560 | 3 |
| CA8 | physical association | 0.560 | 3 |
| CCDC120 | physical association | 0.560 | 3 |
| CCDC88B | physical association | 0.560 | 3 |
| CDC37 | physical association | 0.560 | 3 |
| EFHC2 | physical association | 0.560 | 3 |
| FH | physical association | 0.560 | 3 |
| GOLGA2 | physical association | 0.560 | 3 |
| LZTS1 | physical association | 0.560 | 3 |
| MFAP1 | physical association | 0.560 | 3 |
| MID2 | physical association | 0.560 | 3 |
| OVOL1 | physical association | 0.560 | 3 |
| PIBF1 | physical association | 0.560 | 3 |
| POU6F2 | physical association | 0.560 | 3 |
| PPP1R13B | physical association | 0.560 | 3 |
| TFIP11 | physical association | 0.560 | 3 |
| THAP1 | physical association | 0.560 | 3 |
| TP53BP2 | physical association | 0.560 | 3 |
| TRIM27 | physical association | 0.560 | 3 |
| TSGA10IP | physical association | 0.560 | 3 |
| USP2 | physical association | 0.560 | 3 |
| WASHC3 | physical association | 0.560 | 3 |
| ZC2HC1C | physical association | 0.560 | 3 |
| ZFHX3 | physical association | 0.560 | 3 |
| GPR101 | physical association | 0.400 | 1 |
| SFI1 | physical association | 0.400 | 1 |
| ZBTB3 | physical association | 0.400 | 1 |
BioGRID (321 interactions; top human partners by supporting records): LMNB1 (Affinity Capture-Western; 15 records), LMNA (Affinity Capture-MS; 14 records), FNTB (Affinity Capture-MS; 3 records), TMPO (Proximity Label-MS; 3 records), ANLN (Affinity Capture-MS; 2 records), ARHGEF1 (Affinity Capture-MS; 2 records), BRD4 (Affinity Capture-MS; 2 records), CDC42 (Affinity Capture-MS; 2 records), CLEC4D (Affinity Capture-MS; 2 records), CLEC4E (Affinity Capture-MS; 2 records), HYPK (Affinity Capture-MS; 2 records), IFITM3 (Affinity Capture-MS; 2 records), MYC (Affinity Capture-MS; 2 records), PARK2 (Affinity Capture-MS; 2 records), PRNP (Affinity Capture-MS; 2 records)
Disease & clinical
Genetic variants
Variant evidence for LMNB2: 705 ClinVar records (4 pathogenic / likely pathogenic). Per-variant detail is on Sugi Variant.
ClinVar
705 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 4 |
| Likely pathogenic | 0 |
| Uncertain significance | 318 |
| Likely benign | 282 |
| Benign | 50 |
Top pathogenic / likely-pathogenic (4)
Showing all 4 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.
| Variant ID | HGVS | Classification | Review | Submitters |
|---|---|---|---|---|
| 997434 | NM_032737.4(LMNB2):c.1192G>A (p.Glu398Lys) | Pathogenic | criteria provided, multiple submitters, no conflicts | 4 |
| 3366973 | NM_032737.4(LMNB2):c.578_579del (p.Val193fs) | Pathogenic | criteria provided, single submitter | 1 |
| 208980 | NM_032737.4(LMNB2):c.469C>T (p.His157Tyr) | Pathogenic | no assertion criteria provided | 1 |
| 997435 | NM_032737.4(LMNB2):c.160A>C (p.Asn54His) | Pathogenic | no assertion criteria provided | 1 |
Per-variant reference — Sugi Variant
Explore LMNB2’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.
SpliceAI
Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 35 predictions of 742):
| Position(s) | Effect | Δscore | Sites |
|---|---|---|---|
| 19:2431546–2431547 | donor_loss | 1.0000 | 4 |
| 19:2431659–2431660 | acceptor_loss | 1.0000 | 5 |
| 19:2432414–2432415 | donor_loss | 1.0000 | 5 |
| 19:2432524–2432525 | acceptor_loss | 1.0000 | 3 |
| 19:2433817 | donor_gain | 1.0000 | |
| 19:2434106–2434107 | acceptor_loss | 1.0000 | 4 |
| 19:2434293–2434294 | donor_loss | 1.0000 | 5 |
| 19:2434298 | donor_gain | 1.0000 | |
| 19:2434516–2434517 | acceptor_loss | 1.0000 | 6 |
| 19:2434520 | acceptor_gain | 1.0000 |
AlphaMissense
1,018 missense substitutions predicted likely pathogenic (of 4,026 scored), across 345 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:
| Residue | Likely-pathogenic substitutions | Mean am_pathogenicity | Max am_pathogenicity |
|---|---|---|---|
| N54 | 8 | 0.984 | 0.998 |
| N490 | 8 | 0.957 | 0.993 |
| D385 | 8 | 0.947 | 0.973 |
| D108 | 8 | 0.942 | 0.977 |
| N210 | 8 | 0.929 | 0.982 |
| F517 | 8 | 0.917 | 0.997 |
| F221 | 8 | 0.911 | 0.981 |
| N71 | 8 | 0.903 | 0.960 |
| D379 | 8 | 0.818 | 0.906 |
| D207 | 8 | 0.787 | 0.881 |
| E387 | 7 | 0.990 | 0.996 |
| W554 | 7 | 0.981 | 0.997 |
| R401 | 7 | 0.956 | 0.990 |
| E398 | 7 | 0.948 | 0.985 |
| E46 | 7 | 0.946 | 0.987 |
| I61 | 7 | 0.931 | 0.997 |
| D55 | 7 | 0.926 | 0.946 |
| E399 | 7 | 0.923 | 0.973 |
| W501 | 7 | 0.906 | 0.990 |
| W548 | 7 | 0.892 | 0.986 |
HPA cancer prognostics
RNA cancer specificity: Low cancer specificity
Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.
4 prognostic cancer types:
| Cancer | Prognostic | p-value |
|---|---|---|
| Lung Adenocarcinoma (TCGA) | unfavorable | 5.89e-06 |
| Liver Hepatocellular Carcinoma (TCGA) | unfavorable | 0.000174 |
| Prostate Adenocarcinoma (TCGA) | unfavorable | 0.000208 |
| Liver Hepatocellular Carcinoma (validation) | unfavorable | 0.000394 |
Disease associations
OMIM: gene MIM:150341 | disease phenotypes: MIM:616540, MIM:619180
GenCC curated gene-disease
5 curated gene-disease records:
| Disease | Classification | Inheritance | Records |
|---|---|---|---|
| progressive myoclonic epilepsy type 9 | Strong | Autosomal recessive | 4 |
| microcephaly 27, primary, autosomal dominant | Strong | Autosomal dominant | 4 |
| microcephaly | Moderate | Autosomal dominant | |
| central nervous system malformation | Limited | Autosomal recessive | |
| lipodystrophy, partial, acquired, susceptibility to | Limited | Autosomal dominant | 3 |
Genomics England panels (PanelApp)
Clinical diagnostic gene panels including this gene (7 panels, 3 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.
7 panels:
| Panel | Rating |
|---|---|
| DDG2P | green |
| Fetal anomalies | green |
| Severe microcephaly | green |
| Hypotonic infant | amber |
| Intellectual disability | amber |
| Leukodystrophy, childhood onset | amber |
| Paediatric disorders | amber |
Mondo (5): progressive myoclonic epilepsy type 9 (MONDO:0014685), microcephaly 27, primary, autosomal dominant (MONDO:0030929), central nervous system malformation (MONDO:0020022), lipodystrophy, partial, acquired, susceptibility to (MONDO:0100476), microcephaly (MONDO:0001149)
Orphanet (1): Progressive myoclonic epilepsy type 9 (Orphanet:457265)
HPO phenotypes
showing 60 of 66 phenotypes (HPO-id order):
| HPO | Term |
|---|---|
| HP:0000006 | Autosomal dominant inheritance |
| HP:0000007 | Autosomal recessive inheritance |
| HP:0000028 | Cryptorchidism |
| HP:0000054 | Micropenis |
| HP:0000093 | Proteinuria |
| HP:0000100 | Nephrotic syndrome |
| HP:0000147 | Polycystic ovaries |
| HP:0000171 | Microglossia |
| HP:0000243 | Trigonocephaly |
| HP:0000365 | Hearing impairment |
| HP:0000750 | Delayed speech and language development |
| HP:0000790 | Hematuria |
| HP:0000793 | Membranoproliferative glomerulonephritis |
| HP:0000819 | Diabetes mellitus |
| HP:0000855 | Insulin resistance |
| HP:0001007 | Hirsutism |
| HP:0001182 | Tapered finger |
| HP:0001249 | Intellectual disability |
| HP:0001250 | Seizure |
| HP:0001263 | Global developmental delay |
| HP:0001274 | Agenesis of corpus callosum |
| HP:0001336 | Myoclonus |
| HP:0001382 | Joint hypermobility |
| HP:0001397 | Hepatic steatosis |
| HP:0001840 | Metatarsus adductus |
| HP:0002066 | Gait ataxia |
| HP:0002069 | Bilateral tonic-clonic seizure |
| HP:0002119 | Ventriculomegaly |
| HP:0002123 | Generalized myoclonic seizure |
| HP:0002133 | Status epilepticus |
| HP:0002230 | Generalized hirsutism |
| HP:0002307 | Drooling |
| HP:0002359 | Frequent falls |
| HP:0002650 | Scoliosis |
| HP:0002719 | Recurrent infections |
| HP:0002721 | Immunodeficiency |
| HP:0002829 | Arthralgia |
| HP:0002907 | Microscopic hematuria |
| HP:0002960 | Autoimmunity |
| HP:0003119 | Abnormal circulating lipid concentration |
| HP:0003198 | Myopathy |
| HP:0003577 | Congenital onset |
| HP:0003621 | Juvenile onset |
| HP:0003676 | Progressive |
| HP:0003700 | Generalized amyotrophy |
| HP:0003745 | Sporadic |
| HP:0004209 | Clinodactyly of the 5th finger |
| HP:0005328 | Progeroid facial appearance |
| HP:0005421 | Decreased circulating complement C3 concentration |
| HP:0009002 | Loss of truncal subcutaneous adipose tissue |
| HP:0009019 | Progressive loss of facial adipose tissue |
| HP:0009056 | Loss of subcutaneous adipose tissue from upper limbs |
| HP:0009381 | Short finger |
| HP:0009778 | Short thumb |
| HP:0009879 | Simplified gyral pattern |
| HP:0011451 | Primary microcephaly |
| HP:0011463 | Childhood onset |
| HP:0012450 | Chronic constipation |
| HP:0012510 | Extra-axial cerebrospinal fluid accumulation |
| HP:0030043 | Hip subluxation |
MeSH disease descriptors
2 disease descriptors:
| Descriptor | Name | Tree numbers |
|---|---|---|
| D008831 | Microcephaly | C05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500 |
| D009421 | Nervous System Malformations | C10.500; C16.131.666 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: yes
ChEMBL targets (1): CHEMBL5465302 (SINGLE PROTEIN)
PharmGKB: 1 entry (CPIC guideline: no)
Binding affinities (BindingDB)
1 measured of 1 human assays (2 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.
| Ligand | Measure | Value |
|---|---|---|
| CHEMBL5653589 | KD | 1440 nM |
ChEMBL bioactivities
2 potent at pChembl≥5 of 3 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).
| pChembl | Type | Value | Unit | Molecule |
|---|---|---|---|---|
| 5.79 | Kd | 1629 | nM | CHEMBL5653589 |
| 5.79 | ED50 | 1629 | nM | CHEMBL5653589 |
PubChem BioAssay actives
1 with measured affinity, of 5 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.
| Compound | Assay | Type | Value | Unit |
|---|---|---|---|---|
| 4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide | 2148657: Binding affinity to human LMNB2 incubated for 45 mins by Kinobead based pull down assay | kd | 1.6292 | uM |
CTD chemical–gene interactions
73 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | decreases expression, increases expression | 5 |
| bisphenol A | affects expression, decreases expression, increases expression, affects cotreatment | 4 |
| Benzo(a)pyrene | affects methylation, increases expression, increases mutagenesis | 3 |
| cobaltous chloride | decreases expression | 2 |
| Copper | affects binding, decreases expression | 2 |
| Tamoxifen | affects expression, affects cotreatment, decreases expression | 2 |
| Valproic Acid | affects expression, increases methylation | 2 |
| Cyclosporine | decreases expression, decreases methylation | 2 |
| Raloxifene Hydrochloride | affects expression, affects cotreatment, decreases expression | 2 |
| afuresertib | decreases expression | 1 |
| FR900359 | affects phosphorylation | 1 |
| bisphenol F | increases expression | 1 |
| 2,4,6-tribromophenol | decreases expression | 1 |
| methylmercuric chloride | increases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| methylselenic acid | decreases expression | 1 |
| pyrogallol 1,3-dimethyl ether | affects cotreatment, affects localization, increases expression | 1 |
| decabromobiphenyl ether | increases expression | 1 |
| methylparaben | increases expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | decreases expression | 1 |
| tetrabromobisphenol A | decreases expression | 1 |
| zinc chromate | increases abundance, decreases expression | 1 |
| 2,3-bis(3’-hydroxybenzyl)butyrolactone | affects cotreatment, increases expression | 1 |
| coumarin | decreases phosphorylation | 1 |
| cupric oxide | decreases expression | 1 |
| flavone | decreases expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| chromium hexavalent ion | decreases expression, increases abundance | 1 |
| perfluorooctane sulfonic acid | decreases expression | 1 |
| perfluoro-n-nonanoic acid | decreases expression | 1 |
ChEMBL screening assays
2 unique, capped per target: 2 binding
Representative assays (with source publication via chembl_document):
| Assay ID | Type | Description | Source paper |
|---|---|---|---|
| CHEMBL5338472 | Binding | Binding affinity to Lmnb2 (unknown origin) assessed as fold change in protein upregulation at 200 uM preincubated for 2 hrs followed by pronase addition and measured after 30 mins by coomassie blue staining based SDS-PAGE gel analysis | Structurally Diverse Alkaloids with Anti-Renal-Fibrosis Activity from the Centipede Scolopendra subspinipes mutilans. — *J Nat Prod* |
Cellosaurus cell lines
2 cell lines: 2 cancer cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_SV69 | HAP1 LMNB2 (-) 1 | Cancer cell line | Male |
| CVCL_XQ20 | HAP1 LMNB2 (-) 2 | Cancer cell line | Male |
Clinical trials (associated diseases)
Via MONDO — disease-level, not drug-specific.
showing 60 of 211 trials:
| NCT | Phase | Status | Title |
|---|---|---|---|
| NCT04586348 | Phase 4 | UNKNOWN | Prenatal Iodine Supplementation and Early Childhood Neurodevelopment |
| NCT04873115 | Phase 4 | UNKNOWN | Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties, |
| NCT02559102 | Phase 3 | COMPLETED | Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants |
| NCT02757079 | Phase 3 | COMPLETED | Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders |
| NCT06915480 | Phase 3 | RECRUITING | Reducing Missed Appointments |
| NCT07377032 | Phase 3 | RECRUITING | TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders |
| NCT02909959 | Phase 2 | COMPLETED | Sulforaphane for the Treatment of Young Men With Autism Spectrum Disorder |
| NCT06081348 | Phase 2 | RECRUITING | Sertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders |
| NCT06352372 | Phase 2 | COMPLETED | Safety and Efficacy of tPBM for Epileptiform Activity in Autism |
| NCT00503191 | Phase 1 | COMPLETED | NeuroModulation Technique Treatment of Autism |
| NCT04475848 | Phase 1 | COMPLETED | A Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants |
| NCT06300398 | Phase 1 | COMPLETED | IAMA-6 Oral Dose Study in Healthy Adults |
| NCT06566066 | Not specified | RECRUITING | Register for Patients With Thyroid Hormone Resistance. |
| NCT01783041 | Phase 2/3 | COMPLETED | Effect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants |
| NCT05767385 | Phase 2/3 | COMPLETED | Fetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior |
| NCT05675098 | Early Phase 1 | NOT_YET_RECRUITING | Central Nervous System Stimulants and Physical Function in Children With Cerebral Palsy |
| NCT00783783 | Not specified | COMPLETED | CYP2D6 Pharmacogenetics in Risperidone-Treated Children |
| NCT01778504 | Not specified | RECRUITING | Studying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders |
| NCT01850784 | Not specified | UNKNOWN | High Energy Formula Feeding in Infants With Congenital Heart Disease |
| NCT01922791 | Not specified | COMPLETED | Nutrition and Pregnancy Intervention Study |
| NCT01942525 | Not specified | UNKNOWN | Influence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants |
| NCT02003170 | Not specified | COMPLETED | Etiology and Early Diagnosis of Neurodevelopmental Disorders |
| NCT02118649 | Not specified | COMPLETED | Enhancing Behavior and Brain Response to Visual Targets Using a Computer Game |
| NCT02557191 | Not specified | TERMINATED | Biomarkers, Neurodevelopment and Preterm Infants |
| NCT02690675 | Not specified | COMPLETED | Iron Supplement Effect on Child Development |
| NCT02694003 | Not specified | COMPLETED | Better Nights, Better Days for Children With Neurodevelopment Disorders |
| NCT02792894 | Not specified | COMPLETED | Family Networks (FaNs) for Children With Developmental Disorders and Delays |
| NCT02871674 | Not specified | UNKNOWN | Good Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial |
| NCT02887157 | Not specified | COMPLETED | Analyzing Retinal Microanatomy in ROP |
| NCT02898298 | Not specified | COMPLETED | Positive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder |
| NCT02912780 | Not specified | UNKNOWN | Introduction of Microsystems in a Level 3 Neonatal Intensive Care Unit |
| NCT03023293 | Not specified | COMPLETED | n-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum |
| NCT03023644 | Not specified | COMPLETED | Improving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study |
| NCT03032991 | Not specified | UNKNOWN | Early Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers |
| NCT03088189 | Not specified | TERMINATED | Effect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring |
| NCT03096028 | Not specified | COMPLETED | Developmental Origins of Mental Health Disorders |
| NCT03148782 | Not specified | COMPLETED | Brain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase |
| NCT03172104 | Not specified | COMPLETED | Neurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age |
| NCT03222375 | Not specified | RECRUITING | SQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism |
| NCT03229928 | Not specified | COMPLETED | Clinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge |
| NCT03232489 | Not specified | UNKNOWN | Study for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice |
| NCT03381027 | Not specified | COMPLETED | BABY SMART (Study of Massage Therapy, Sleep And neurodevelopMenT) |
| NCT03388294 | Not specified | COMPLETED | Evaluation of a Novel Intervention for Infants At Risk for Neurodevelopmental Disorders |
| NCT03410810 | Not specified | UNKNOWN | Childhood Outcomes of Preterm Brain Abnormalities |
| NCT03492060 | Not specified | RECRUITING | Longitudinal Study of Neurogenetic Disorders |
| NCT03577756 | Not specified | COMPLETED | Neurodevelopmental Assessment of Infants With Cystic Fibrosis |
| NCT03654248 | Not specified | COMPLETED | Let’s Get Organized in Adult Psychiatric/habilitation Care |
| NCT03659279 | Not specified | COMPLETED | Let’s Get Organized Feasibility Study |
| NCT03722615 | Not specified | COMPLETED | Epidemiology of Congenital Cytomegalovirus in a High HIV Prevalence Setting, South Africa |
| NCT03770832 | Not specified | ACTIVE_NOT_RECRUITING | Wearable Sensors and Video Recordings to Monitor Motor Development |
| NCT03830879 | Not specified | RECRUITING | Shenzhen Birth Cohort Study |
| NCT03835689 | Not specified | COMPLETED | Strongest FamiliesTM Neurodevelopmental |
| NCT03882788 | Not specified | COMPLETED | The Effect of Anesthesia on Neurodevelopmental Outcome (NDO) |
| NCT03922087 | Not specified | COMPLETED | No-worry Baby Project |
| NCT03977259 | Not specified | ACTIVE_NOT_RECRUITING | Targeting Human Milk Fortification to Improve Preterm Infant Growth and Brain Development |
| NCT04043572 | Not specified | UNKNOWN | The Biomarkers of Neurological Disease in Utero Study |
| NCT04096430 | Not specified | RECRUITING | Evaluation of Effectiveness of Child-oriented Goal-setting in Paediatric Rehabilitation (the ENGAGE Approach) |
| NCT04108273 | Not specified | COMPLETED | Brain Plasticity Underlying Acquisition of New Organizational Skills in Children |
| NCT04201509 | Not specified | COMPLETED | Validity of Neurocognitive Assessment Methods in Childhood ADHD |
| NCT04233775 | Not specified | UNKNOWN | Altered Cerebral Growth and Development in Infants With Congenital Heart Disease |
Predicted chemistry — Sugi Predict
The predicted patent-compound landscape for LMNB2 across ~30M SureChEMBL compounds — explore on Sugi Predict.
Related Atlas pages
- Associated diseases: progressive myoclonic epilepsy type 9, central nervous system malformation, microcephaly 27, primary, autosomal dominant, lipodystrophy, partial, acquired, susceptibility to, microcephaly
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): acquired partial lipodystrophy, central nervous system malformation, lipodystrophy, partial, acquired, susceptibility to, microcephaly 27, primary, autosomal dominant, progressive myoclonic epilepsy type 9