GNPNAT1
protein-codingglucosamine-phosphate N-acetyltransferase 1, the group of GCN5 related N-acetyltransferases
Gene summary
Enables identical protein binding activity. Predicted to be involved in UDP-N-acetylglucosamine biosynthetic process. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0005516
Submitter: Franklin by Genoox
linical investigations were carried out for four affected individuals in the recruited family. Patients presented with short stature due to extreme shortening of the proximal segments of the limbs, he also suffered from hip dysplasia and severe platyspondyly. WGS data analyses identified a homozygous missense variant c.226G>A; p.(Glu76Lys) in GNPNAT1, segregating with the disease. https://doi.org/10.1136/jmedgenet-2020-106929
Inheritance Pattern: AR
Disease ID:MONDO:0859203
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Musculoskeletal
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GNPNAT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_198066.4. 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 | 1 | 2 | 3 | |||
| missense | 1 | 21 | 22 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 1 | 0 | 23 | 2 | 0 | 26 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_932332.1 | 5 | MANE Select | |
| Ensembl | ENSP00000216410.3 | 5 | MANE Select | |
| Ensembl | ENSP00000452310.1 | 4 | Standard | |
| Ensembl | ENSP00000452032.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- liver development
- glucosamine metabolic process
- N-acetylglucosamine biosynthetic process
- UDP-N-acetylglucosamine biosynthetic process
- cellular response to leukemia inhibitory factor
Molecular Function
- glucosamine 6-phosphate N-acetyltransferase activity
- identical protein binding
- monosaccharide binding
Cellular Component
- Golgi membrane
- late endosome
- endoplasmic reticulum
- endoplasmic reticulum-Golgi intermediate compartment
- Golgi apparatus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000216410
- Coding exons
- 5
- Length
- 16475
- Individuals with no LoFs
- 125709
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 18
- Defined
- 125727
- p
- 0.0000716
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.33 | 55 | 90.6 | 0.607 | 0.00000407 | 1199 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000030 | 0.000029 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00011 | 0.00011 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.124
Intolerance Scores
- LoFtool
- 0.491
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 49.39
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.964
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |