NAPG
Basic information
Region (hg38): 18:10525905-10552764
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAPG gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in NAPG
This is a list of pathogenic ClinVar variants found in the NAPG region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-10532788-A-G | not specified | Uncertain significance (Dec 19, 2022) | ||
| 18-10533538-T-G | not specified | Uncertain significance (Jun 11, 2021) | ||
| 18-10539786-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
| 18-10539835-C-A | not specified | Uncertain significance (Jun 29, 2023) | ||
| 18-10539852-G-A | not specified | Uncertain significance (Jun 30, 2022) | ||
| 18-10540046-G-C | not specified | Uncertain significance (Feb 13, 2024) | ||
| 18-10540345-G-A | not specified | Uncertain significance (Sep 14, 2022) | ||
| 18-10540390-G-A | not specified | Uncertain significance (Jun 03, 2022) | ||
| 18-10546337-C-T | not specified | Uncertain significance (Aug 15, 2023) | ||
| 18-10546340-C-T | not specified | Uncertain significance (Apr 18, 2024) | ||
| 18-10546357-GAAA-G | Uncertain significance (Mar 01, 2023) | |||
| 18-10548308-G-A | not specified | Uncertain significance (Nov 17, 2023) | ||
| 18-10549022-G-A | not specified | Uncertain significance (Apr 08, 2024) | ||
| 18-10549065-A-G | not specified | Uncertain significance (Feb 13, 2024) | ||
| 18-10550210-G-A | not specified | Uncertain significance (Jul 22, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NAPG | protein_coding | protein_coding | ENST00000322897 | 12 | 26857 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0812 | 0.918 | 124626 | 0 | 12 | 124638 | 0.0000481 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.569 | 135 | 155 | 0.871 | 0.00000773 | 2002 |
| Missense in Polyphen | 31 | 43.652 | 0.71016 | 533 | ||
| Synonymous | 0.355 | 52 | 55.4 | 0.939 | 0.00000279 | 563 |
| Loss of Function | 3.10 | 6 | 21.5 | 0.279 | 0.00000127 | 259 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000558 | 0.0000556 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000551 | 0.0000531 |
| Middle Eastern | 0.0000558 | 0.0000556 |
| South Asian | 0.000139 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for vesicular transport between the endoplasmic reticulum and the Golgi apparatus.;
- Pathway
- miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;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
- 0.127
Intolerance Scores
- loftool
- 0.620
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.58
Haploinsufficiency Scores
- pHI
- 0.149
- hipred
- N
- hipred_score
- 0.426
- ghis
- 0.648
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.747
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Napg
- Phenotype
Gene ontology
- Biological process
- intracellular protein transport;intra-Golgi vesicle-mediated transport;protein stabilization;membrane fusion;protein-containing complex assembly
- Cellular component
- mitochondrion;lysosomal membrane;vacuolar membrane;SNARE complex;myelin sheath;synapse;extracellular exosome
- Molecular function
- soluble NSF attachment protein activity;protein binding;syntaxin binding