AMDHD2
protein-codingamidohydrolase domain containing 2
Gene summary
Enables N-acetylglucosamine-6-phosphate deacetylase activity. Involved in negative regulation of UDP-N-acetylglucosamine biosynthetic process. Located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.1 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 AMDHD2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001330449.2. 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 | 1 | ||||
| missense | 54 | 54 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 54 | 1 | 0 | 55 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001317378.1 | 11 | MANE Select | |
| Ensembl | ENSP00000293971.6 | 11 | MANE Select | |
| RefSeq | NP_001139287.1 | 11 | Standard | |
| RefSeq | NP_001397872.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Amino sugar and nucleotide sugar metabolism - Homo sapiens (human)
- Sialuria or French Type Sialuria
- Sialuria or French Type Sialuria
- Amino Sugar Metabolism
- G(M2)-Gangliosidosis: Variant B, Tay-sachs disease
Biological Process
- carbohydrate metabolic process
- N-acetylglucosamine catabolic process
- UDP-N-acetylglucosamine biosynthetic process
- N-acetylneuraminate catabolic process
Molecular Function
- protein binding
- N-acetylglucosamine-6-phosphate deacetylase activity
- metal ion binding
- N-acetylgalactosamine-6-phosphate deacetylase activity
Cellular Component
- nucleus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000413459
- Coding exons
- 11
- Length
- 11066
- Individuals with no LoFs
- 125675
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 25
- Defined
- 125700
- p
- 0.0000994
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.520 | 341 | 369 | 0.924 | 0.0000233 | 3732 |
| Missense (PolyPhen) | 79 | 121.27 | 0.65143 | 1220 | ||
| Synonymous | -3.74 | 226 | 165 | 1.37 | 0.0000115 | 1313 |
| Loss of Function | 2.12 | 7 | 16.2 | 0.431 | 6.93e-7 | 196 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000084 | 0.000079 | rare |
| South Asian | 0.00036 | 0.00036 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Hydrolyzes the N-glycolyl group from N- glycolylglucosamine 6-phosphate (GlcNGc-6-P) in the N- glycolylneuraminic acid (Neu5Gc) degradation pathway. Although human is not able to catalyze formation of Neu5Gc due to the inactive CMAHP enzyme, Neu5Gc is present in food and must be degraded. {ECO:0000269|PubMed:22692205}.;
Recessive Scores
- pRec
- 0.154
Intolerance Scores
- LoFtool
- 0.198
- RVIS EVS
- -0.2
- RVIS percentile EVS
- 39.21
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.987
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |