NEBL

protein-coding

nebulette, 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]

Previous symbols:
  • C10orf113

MANE transcript

NM_006393.3

Inheritance

AD

ClinVar variants

P:1U:773B:326

Top phenotype

Primary dilated cardiomyopathy

gnomAD constraint

pLI —, LoF o/e 0.92

Max pathogenic AF

—

Genomic locus

chr10:20,779,973-21,293,011

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~513.0 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

familial dilated cardiomyopathyLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0016333

Submitter: G2P

dilated cardiomyopathyMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0005021

Submitter: PanelApp Australia

hypertrophic cardiomyopathyMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0005045

Submitter: PanelApp Australia

dilated cardiomyopathyLIMITED

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

14 Conditions Cataloged
Primary dilated cardiomyopathyTotal: 957
not specifiedTotal: 719
not providedTotal: 171
NEBL-related disorderTotal: 64
Cardiovascular phenotypeTotal: 11
Hypertrophic cardiomyopathyTotal: 3
Sudden unexplained deathTotal: 2
Wolff-Parkinson-White patternTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
10
clinvar
267
clinvar
2
clinvar
279
missense
679
clinvar
52
clinvar
1
clinvar
732
nonsense
19
clinvar
2
clinvar
21
start loss
1
clinvar
1
frameshift
1
clinvar
34
clinvar
35
splice donor/acceptor (+/-2bp)
30
clinvar
1
clinvar
1
clinvar
32
Total0177332241100

Highest pathogenic variant AF is 0.00000621912

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006393.3RefSeqNP_006384.128MANE Select
ENST00000377122.9EnsemblENSP00000366326.428MANE Select
NM_001173484.2RefSeqNP_001166955.17Standard
NM_001377322.1RefSeqNP_001364251.18Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.9406065441.110.00002826803
Missense (PolyPhen)169176.010.960192197
Synonymous-1.282111891.120.00001141690
Loss of Function0.6275863.40.9150.00000355773

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00150.0015notable
Latino/Admixed American0.00220.0021notable
Ashkenazi Jewish0.00110.0011notable
East Asian0.000870.00082rare
Finnish0.00360.0036notable
European (Non-Finnish)0.00400.0040notable
South Asian0.00120.0012notable
Other0.00280.0028notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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