NBEAL1
protein-codingneurobeachin like 1, the group of Armadillo like helical domain containing|BEACH domain containing |WD repeat domain containing
Gene summary
Predicted to be active in cytosol and membrane. [provided by Alliance of Genome Resources, Jun 2026]
- ALS2CR17
- ALS2CR16
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~211.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NBEAL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001378026.1. 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 | 2 | 8 | 3 | 13 | ||
| missense | 344 | 13 | 3 | 360 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 1 | 4 | |||
| Total | 0 | 0 | 349 | 22 | 6 | 377 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001364955.1 | 55 | MANE Select | |
| Ensembl | ENSP00000508055.1 | 55 | MANE Select | |
| RefSeq | NP_001107604.1 | 54 | Standard | |
| Ensembl | ENSP00000388466.2 | 18 | Standard |
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000449802
- Coding exons
- 54
- Length
- 211500
- Individuals with no LoFs
- 124466
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 326
- Defined
- 124792
- p
- 0.00131
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.88 | 1068 | 1.26e+3 | 0.851 | 0.0000621 | 17636 |
| Missense (PolyPhen) | 321 | 443.09 | 0.72445 | 6222 | ||
| Synonymous | 1.82 | 392 | 441 | 0.890 | 0.0000222 | 4948 |
| Loss of Function | 5.07 | 77 | 142 | 0.541 | 0.00000815 | 1845 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00072 | 0.00071 | rare |
| Latino/Admixed American | 0.00063 | 0.00061 | rare |
| Ashkenazi Jewish | 0.00051 | 0.00050 | rare |
| East Asian | 0.0025 | 0.0025 | notable |
| Finnish | 0.0049 | 0.0049 | notable |
| European (Non-Finnish) | 0.00070 | 0.00069 | rare |
| South Asian | 0.0018 | 0.0017 | notable |
| Other | 0.0013 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0930
Intolerance Scores
- LoFtool
- 0.967
- RVIS EVS
- 1.19
- RVIS percentile EVS
- 92.85
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.144
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |