AMY1A
protein-codingamylase alpha 1A, the group of Amylases alpha
Gene summary
Amylases are secreted proteins that hydrolyze 1,4-alpha-glucoside bonds in oligosaccharides and polysaccharides, and thus catalyze the first step in digestion of dietary starch and glycogen. The human genome has a cluster of several amylase genes that are expressed at high levels in either salivary gland or pancreas. This gene encodes an amylase isoenzyme produced by the salivary gland. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]
- AMY1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.8 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 AMY1A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004038.4. 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 | 1 | ||||
| missense | 10 | 1 | 11 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 10 | 2 | 0 | 12 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004029.2 | 10 | MANE Select | |
| Ensembl | ENSP00000359100.4 | 10 | MANE Select | |
| RefSeq | NP_001008222.1 | 10 | Standard | |
| Ensembl | ENSP00000408386.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Starch and sucrose metabolism - Homo sapiens (human)
- Carbohydrate digestion and absorption - Homo sapiens (human)
- Salivary secretion - Homo sapiens (human)
- Glycogen synthetase deficiency
- Glycogenosis, Type III. Cori disease, Debrancher glycogenosis
Biological Process
- carbohydrate metabolic process
Molecular Function
- alpha-amylase activity
- protein binding
- metal ion binding
- alpha-amylase activity (releasing maltohexaose)
Cellular Component
- extracellular space
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000370083
- Coding exons
- 10
- Length
- 9262
- Individuals with no LoFs
- 110315
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 30
- Defined
- 110346
- p
- 0.000140
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0522 | 32 | 31.2 | 1.03 | 0.00000151 | 3401 |
| Missense (PolyPhen) | 20 | 16.41 | 1.2188 | 1546 | ||
| Synonymous | 0.151 | 8 | 8.56 | 0.934 | 3.66e-7 | 923 |
| Loss of Function | -0.124 | 5 | 4.71 | 1.06 | 3.59e-7 | 289 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00026 | 0.00025 | rare |
| Ashkenazi Jewish | 0.00039 | 0.00036 | rare |
| East Asian | 0.00012 | 0.00012 | rare |
| Finnish | 0.00011 | 0.00010 | rare |
| European (Non-Finnish) | 0.00011 | 0.000099 | rare |
| South Asian | 0.00025 | 0.00024 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.481
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.755
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |