NEB
Basic information
Region (hg38): 2:151485336-151734487
Previous symbols: [ "NEM2" ]
Links
Phenotypes
GenCC
Source:
- nemaline myopathy 2 (Definitive), mode of inheritance: AR
- nemaline myopathy 2 (Definitive), mode of inheritance: AR
- lethal multiple pterygium syndrome (Supportive), mode of inheritance: AR
- severe congenital nemaline myopathy (Supportive), mode of inheritance: AR
- intermediate nemaline myopathy (Supportive), mode of inheritance: AD
- typical nemaline myopathy (Supportive), mode of inheritance: AD
- childhood-onset nemaline myopathy (Supportive), mode of inheritance: AD
- nemaline myopathy 2 (Limited), mode of inheritance: AD
- nemaline myopathy 2 (Strong), mode of inheritance: AR
- nemaline myopathy 2 (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Nemaline myopathy 2, autosomal recessive; Arthrogryposis multiplex congenita 6 | 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 | 10051637; 10619714; 12207937; 15221447; 16917880; 19232495; 19805734; 21798101; 22367672; 23010307; 25205138; 26578207; 27933661; 28336317; 29274205; 33376055 |
ClinVar
This is a list of variants' phenotypes submitted to
- Nemaline_myopathy_2 (10710 variants)
- not_provided (1898 variants)
- Inborn_genetic_diseases (970 variants)
- Arthrogryposis_multiplex_congenita_6 (717 variants)
- not_specified (540 variants)
- Nemaline_myopathy (323 variants)
- NEB-related_disorder (218 variants)
- See_cases (7 variants)
- Nemaline_Myopathy,_Recessive (5 variants)
- Congenital_structural_myopathy (4 variants)
- Congenital_myopathy (4 variants)
- Limb-girdle_muscular_dystrophy (4 variants)
- Nebulin-related_early-onset_distal_myopathy (3 variants)
- Peripheral_neuropathy (2 variants)
- Progressive_proximal_muscle_weakness (2 variants)
- Distal_myopathy (2 variants)
- Limb_pain (2 variants)
- Muscle_weakness (2 variants)
- Congenital_muscular_dystrophy (2 variants)
- Actin_accumulation_myopathy (2 variants)
- Muscular_dystrophy (2 variants)
- Abnormality_of_the_neck (1 variants)
- Dysphagia (1 variants)
- Abnormality_of_the_musculature (1 variants)
- Non-immune_hydrops_fetalis (1 variants)
- Low-set_ears (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEB gene is commonly pathogenic or not. These statistics are base on transcript: NM_001164508.2. 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 | 112 | 3272 | 73 | 3468 | ||
missense | 49 | 2827 | 1236 | 39 | 4155 | |
nonsense | 209 | 291 | 507 | |||
start loss | 0 | |||||
frameshift | 345 | 494 | 843 | |||
splice donor/acceptor (+/-2bp) | 46 | 383 | 23 | 453 | ||
Total | 608 | 1224 | 2973 | 4509 | 112 |
Highest pathogenic variant AF is 0.0011467724
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
NEB | protein_coding | protein_coding | ENST00000397345 | 180 | 249152 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.56e-41 | 1.00 | 124483 | 0 | 365 | 124848 | 0.00146 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.0409 | 3782 | 3.77e+3 | 1.00 | 0.000208 | 56792 |
Missense in Polyphen | 1817 | 1893.8 | 0.95943 | 28149 | ||
Synonymous | -0.364 | 1373 | 1.36e+3 | 1.01 | 0.0000788 | 14549 |
Loss of Function | 11.6 | 145 | 393 | 0.369 | 0.0000205 | 5971 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00297 | 0.00286 |
Ashkenazi Jewish | 0.000902 | 0.000795 |
East Asian | 0.00137 | 0.00134 |
Finnish | 0.000978 | 0.000974 |
European (Non-Finnish) | 0.00175 | 0.00167 |
Middle Eastern | 0.00137 | 0.00134 |
South Asian | 0.00142 | 0.00137 |
Other | 0.00170 | 0.00165 |
dbNSFP
Source:
- Function
- FUNCTION: This giant muscle protein may be involved in maintaining the structural integrity of sarcomeres and the membrane system associated with the myofibrils. Binds and stabilize F-actin.;
- Pathway
- Striated Muscle Contraction;Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling;Striated Muscle Contraction;Muscle contraction
(Consensus)
Recessive Scores
- pRec
- 0.379
Intolerance Scores
- loftool
- 0.995
- rvis_EVS
- 0.88
- rvis_percentile_EVS
- 88.9
Haploinsufficiency Scores
- pHI
- 0.149
- hipred
- N
- hipred_score
- 0.270
- ghis
- 0.492
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.744
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Neb
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; vision/eye phenotype; muscle phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- neb
- Affected structure
- skeletal muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- aggregated
Gene ontology
- Biological process
- muscle organ development;somatic muscle development;muscle filament sliding;regulation of actin filament length;muscle fiber development;cardiac muscle thin filament assembly
- Cellular component
- cytosol;actin cytoskeleton;Z disc;extracellular exosome
- Molecular function
- protein binding;structural constituent of muscle;actin filament binding