NEBL
protein-codingnebulette, the group of LIM domain containing
Gene summary
This gene encodes a nebulin like protein that is abundantly expressed in cardiac muscle. The encoded protein binds actin and interacts with thin filaments and Z-line associated proteins in striated muscle. This protein may be involved in cardiac myofibril assembly. A shorter isoform of this protein termed LIM nebulette is expressed in non-muscle cells and may function as a component of focal adhesion complexes. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]
- C10orf113
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~513.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0016333
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0005021
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0005045
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0005021
Submitter: ClinGen
NEBL was originally evaluated for DCM by the ClinGen GCEP on 09/25/2020. Evidence of the association of this gene with DCM was re-evaluated using SOP v10 on 10/18/2024, resulting in a decrease in genetic evidence points at the time of recuration. As a result, the classification did not change. A summary of the information contributing to the classification of this gene at the time of re-evaluation is summarized herein. NEBL was evaluated for autosomal dominant dilated cardiomyopathy (DCM). Human genetic evidence supporting this gene-disease relationship includes case-level data. Arimura and colleagues (2000, PMID: 11140941) analyzed 83 DCM patients and 311 healthy controls, identifying 4 missense variants of unknown significance (VUSs) in 4 DCM cases. High minor allele frequencies (MAFs) and lack of segregation excluded these variants as evidence. Purevjav and colleagues (2010, PMID: 20951326) investigated a total of 260 DCM patients and 300 unrelated ethnic matched controls by direct DNA sequencing. Authors identified 4 missense VUSs. One of these variants (Q128R) was downgraded in level of evidence due to the lack of segregation. The other 3 variants were not scored because of their MAF. Perrot and colleagues (2016, PMID: 27186169) investigated a total of 389 patients with DCM, HCM, or LVNC, 320 Caucasian sex-matched controls and 192 Caucasian sex-matched blood donors and identified 3 missense VUSs in 4 families. One of these variants was also carried by healthy relatives and therefore was excluded, however this may be explained by reduced penetrance. The 2 other variants lacked segregation as well and therefore were also excluded. In addition, this gene-disease association is supported by animal models. Mastronotaro and colleagues (2015, PMID: 25987543) created a NEBL knockout mice that exhibited normal cardiac function up to 9 months of age but after 2 weeks of transaortic constriction (TAC), these mice showed Z-line widening since the age of 5 months and upregulation of cardiac stress genes (basal and after TAC) However, absence of clinical DCM features in KO-NEBL mice as well as Western Blot analysis which contradicted previous findings by showing a similar protein expression between knockout and wild-type mice, excluding it as evidence. Purevjav and colleagues (2010, PMID: 20951326) generated a transgenic mouse overexpressing WT or mutant NEBL under the control of the α-MyHC promoter (4 variants were tested). Mice overexpressing p.K60N or p.Q128R variants died within 1 year because of severe heart enlargement and heart failure. Mice overexpressing p.G202R or p.A592E were born and developed normally but after 6 months displayed reduced stress tolerance, cardiac enlargement due to left ventricle dilation, myocyte disarray, and interstitial cell infiltration. No further scorable variants or experimental evidences were identified during the re-curation process. In summary, there is limited evidence supporting the relationship between NEBL and DCM. More evidence is needed to support the relationship of NEBL and DCM. This classification was approved by the ClinGen Dilated Cardiomyopathy Working Group on 10/18/2024 (SOP Version 10).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NEBL variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006393.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 10 | 267 | 2 | 279 | ||
| missense | 679 | 52 | 1 | 732 | ||
| nonsense | 19 | 2 | 21 | |||
| start loss | 1 | 1 | ||||
| frameshift | 1 | 34 | 35 | |||
| splice donor/acceptor (+/-2bp) | 30 | 1 | 1 | 32 | ||
| Total | 0 | 1 | 773 | 322 | 4 | 1100 |
Highest pathogenic variant AF is 0.00000621912
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006384.1 | 28 | MANE Select | |
| Ensembl | ENSP00000366326.4 | 28 | MANE Select | |
| RefSeq | NP_001166955.1 | 7 | Standard | |
| RefSeq | NP_001364251.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- muscle fiber development
- cardiac muscle thin filament assembly
Molecular Function
- protein binding
- tropomyosin binding
- cytoskeletal protein binding
- structural constituent of muscle
- filamin binding
Cellular Component
- stress fiber
- Z disc
- I band
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000377122
- Coding exons
- 28
- Length
- 394215
- Individuals with no LoFs
- 125044
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 702
- Defined
- 125748
- p
- 0.00280
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.940 | 606 | 544 | 1.11 | 0.0000282 | 6803 |
| Missense (PolyPhen) | 169 | 176.01 | 0.96019 | 2197 | ||
| Synonymous | -1.28 | 211 | 189 | 1.12 | 0.0000114 | 1690 |
| Loss of Function | 0.627 | 58 | 63.4 | 0.915 | 0.00000355 | 773 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0015 | 0.0015 | notable |
| Latino/Admixed American | 0.0022 | 0.0021 | notable |
| Ashkenazi Jewish | 0.0011 | 0.0011 | notable |
| East Asian | 0.00087 | 0.00082 | rare |
| Finnish | 0.0036 | 0.0036 | notable |
| European (Non-Finnish) | 0.0040 | 0.0040 | notable |
| South Asian | 0.0012 | 0.0012 | notable |
| Other | 0.0028 | 0.0028 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Binds to actin and plays an important role in the assembly of the Z-disk. May functionally link sarcomeric actin to the desmin intermediate filaments in the heart muscle sarcomeres (PubMed:27733623). Isoform 2 might play a role in the assembly of focal adhesion (PubMed:15004028). {ECO:0000269|PubMed:15004028, ECO:0000269|PubMed:27733623}.;
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- LoFtool
- 0.970
- RVIS EVS
- 0.57
- RVIS percentile EVS
- 81.75
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.425
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |