NAPB
NSF attachment protein beta
Basic information
Region (hg38): 20:23374519-23421519
Links
Phenotypes
GenCC
Source:
- developmental and epileptic encephalopathy 107 (Strong), mode of inheritance: AR
- developmental and epileptic encephalopathy 107 (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Developmental and epileptic encephalopathy 107 | 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 | Neurologic | 26235277; 28097321; 33189936 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (29 variants)
- Developmental_and_epileptic_encephalopathy-107 (5 variants)
- not_provided (3 variants)
- NAPB-related_disorder (2 variants)
- Prostate_cancer (1 variants)
- Developmental_and_epileptic_encephalopathy,_1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAPB gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022080.3. 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 | 1 | |||||
| missense | 30 | 31 | ||||
| nonsense | 3 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 3 | 1 | 32 | 1 | 1 |
Highest pathogenic variant AF is 6.841836e-7
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NAPB | protein_coding | protein_coding | ENST00000377026 | 11 | 46967 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.112 | 0.887 | 125720 | 0 | 7 | 125727 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.60 | 95 | 150 | 0.632 | 0.00000681 | 1975 |
| Missense in Polyphen | 34 | 56.605 | 0.60065 | 744 | ||
| Synonymous | 0.598 | 45 | 50.4 | 0.893 | 0.00000237 | 502 |
| Loss of Function | 2.85 | 5 | 18.1 | 0.277 | 7.63e-7 | 241 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000292 | 0.0000292 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000451 | 0.0000440 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for vesicular transport between the endoplasmic reticulum and the Golgi apparatus. {ECO:0000250}.;
- Pathway
- Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Intra-Golgi traffic;COPI-mediated anterograde transport;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.292
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.12
Haploinsufficiency Scores
- pHI
- 0.314
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.636
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.581
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Napb
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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);
Zebrafish Information Network
- Gene name
- napbb
- Affected structure
- horizontal cell
- Phenotype tag
- abnormal
- Phenotype quality
- absent
Gene ontology
- Biological process
- intracellular protein transport;regulation of synaptic vesicle priming;synaptic transmission, glutamatergic;SNARE complex disassembly
- Cellular component
- vacuolar membrane;SNARE complex;synaptobrevin 2-SNAP-25-syntaxin-1a complex;extracellular exosome
- Molecular function
- soluble NSF attachment protein activity;protein binding;syntaxin binding