GNPNAT1
glucosamine-phosphate N-acetyltransferase 1, the group of GCN5 related N-acetyltransferases
Basic information
Region (hg38): 14:52775193-52791668
Links
Phenotypes
GenCC
Source:
- osteochondrodysplasia (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Rhizomelic dysplasia, Ain-Naz type | 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 | Musculoskeletal | 32591345 |
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 GNPNAT1 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 | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 0 |
Variants in GNPNAT1
This is a list of pathogenic ClinVar variants found in the GNPNAT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-52778322-A-G | not specified | Uncertain significance (May 27, 2022) | ||
| 14-52778328-G-A | not specified | Uncertain significance (Jan 29, 2024) | ||
| 14-52778346-C-T | not specified | Uncertain significance (May 09, 2023) | ||
| 14-52778360-C-A | not specified | Uncertain significance (Aug 19, 2024) | ||
| 14-52778405-G-A | not specified | Uncertain significance (Jan 30, 2024) | ||
| 14-52778448-T-C | not specified | Uncertain significance (Dec 19, 2022) | ||
| 14-52778453-A-G | Uncertain significance (Sep 29, 2022) | |||
| 14-52778458-C-T | Uncertain significance (Sep 29, 2022) | |||
| 14-52780704-A-G | Rhizomelic dysplasia, Ain-Naz type | Uncertain significance (-) | ||
| 14-52781810-G-A | not specified | Uncertain significance (Sep 23, 2023) | ||
| 14-52781830-G-A | not specified | Uncertain significance (Mar 19, 2024) | ||
| 14-52781897-T-C | not specified | Uncertain significance (Dec 04, 2023) | ||
| 14-52781903-C-T | Rhizomelic dysplasia, Ain-Naz type | Pathogenic (Oct 29, 2021) | ||
| 14-52783449-C-G | not specified | Uncertain significance (Apr 09, 2024) | ||
| 14-52783467-C-T | not specified | Uncertain significance (Oct 06, 2021) | ||
| 14-52784514-G-A | not specified | Uncertain significance (Jul 12, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GNPNAT1 | protein_coding | protein_coding | ENST00000216410 | 5 | 16475 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0124 | 0.865 | 125709 | 0 | 18 | 125727 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.33 | 55 | 90.6 | 0.607 | 0.00000407 | 1199 |
| Missense in Polyphen | 7 | 20.676 | 0.33855 | 269 | ||
| Synonymous | -0.329 | 34 | 31.6 | 1.07 | 0.00000144 | 351 |
| Loss of Function | 1.27 | 4 | 7.83 | 0.511 | 3.25e-7 | 118 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000302 | 0.0000302 |
| Ashkenazi Jewish | 0.000200 | 0.000198 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.000108 | 0.000106 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- UDP-<i>N</i>-acetyl-D-galactosamine biosynthesis II;Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Sialuria or French Type Sialuria;Sialuria or French Type Sialuria;2-Hydroxyglutric Aciduria (D And L Form);Amino Sugar Metabolism;G(M2)-Gangliosidosis: Variant B, Tay-sachs disease;Tay-Sachs Disease;Homocarnosinosis;Hyperinsulinism-Hyperammonemia Syndrome;Succinic semialdehyde dehydrogenase deficiency;4-Hydroxybutyric Aciduria/Succinic Semialdehyde Dehydrogenase Deficiency;Salla Disease/Infantile Sialic Acid Storage Disease;Glutamate Metabolism;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Aminosugars metabolism;Post-translational protein modification;Metabolism of proteins;UDP-<i>N</i>-acetyl-D-glucosamine biosynthesis II;Aminosugars metabolism;Synthesis of UDP-N-acetyl-glucosamine;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation
(Consensus)
Recessive Scores
- pRec
- 0.124
Intolerance Scores
- loftool
- 0.491
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- 0.179
- hipred
- Y
- hipred_score
- 0.517
- ghis
- 0.600
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.964
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gnpnat1
- Phenotype
- embryo phenotype; growth/size/body region 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); cellular phenotype;
Gene ontology
- Biological process
- liver development;glucosamine metabolic process;N-acetylglucosamine biosynthetic process;UDP-N-acetylglucosamine biosynthetic process;cellular response to leukemia inhibitory factor
- Cellular component
- Golgi membrane;late endosome;endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cytosol;endosome membrane
- Molecular function
- glucosamine 6-phosphate N-acetyltransferase activity;identical protein binding;monosaccharide binding