AMY2A
Basic information
Region (hg38): 1:103617427-103625780
Previous symbols: [ "AMY2" ]
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 AMY2A 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 | 2 | |||||
missense | 21 | 22 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 21 | 2 | 1 |
Variants in AMY2A
This is a list of pathogenic ClinVar variants found in the AMY2A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-103617454-T-G | not specified | Uncertain significance (Nov 18, 2022) | ||
1-103617492-T-C | not specified | Uncertain significance (Aug 12, 2021) | ||
1-103617510-G-A | not specified | Uncertain significance (Jun 10, 2024) | ||
1-103617513-C-T | not specified | Uncertain significance (May 26, 2023) | ||
1-103617556-T-C | not specified | Uncertain significance (Feb 13, 2024) | ||
1-103617585-C-G | not specified | Uncertain significance (Oct 29, 2021) | ||
1-103618081-C-A | Benign (Dec 31, 2019) | |||
1-103618930-C-A | not specified | Uncertain significance (Jan 26, 2022) | ||
1-103618954-A-G | not specified | Uncertain significance (Jan 08, 2024) | ||
1-103618955-C-T | Likely benign (Aug 22, 2018) | |||
1-103619038-G-C | not specified | Uncertain significance (Apr 09, 2024) | ||
1-103619567-G-A | not specified | Uncertain significance (Apr 08, 2022) | ||
1-103619578-C-A | not specified | Uncertain significance (Mar 24, 2023) | ||
1-103619585-A-G | not specified | Uncertain significance (Nov 17, 2022) | ||
1-103619608-G-A | not specified | Uncertain significance (May 31, 2023) | ||
1-103619668-A-G | not specified | Uncertain significance (Sep 26, 2023) | ||
1-103619773-A-T | not specified | Uncertain significance (Apr 25, 2022) | ||
1-103620605-C-T | not specified | Uncertain significance (Apr 08, 2024) | ||
1-103620638-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
1-103620665-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
1-103620668-A-G | not specified | Uncertain significance (Feb 05, 2024) | ||
1-103623866-G-T | not specified | Uncertain significance (Jun 16, 2024) | ||
1-103623874-T-C | Likely benign (Dec 31, 2019) | |||
1-103624107-T-A | not specified | Uncertain significance (Apr 11, 2023) | ||
1-103624113-G-T | not specified | Uncertain significance (Mar 06, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
AMY2A | protein_coding | protein_coding | ENST00000414303 | 10 | 8404 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
8.54e-12 | 0.0211 | 125187 | 0 | 58 | 125245 | 0.000232 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -1.02 | 175 | 141 | 1.24 | 0.00000705 | 3301 |
Missense in Polyphen | 58 | 54.164 | 1.0708 | 1363 | ||
Synonymous | -1.97 | 60 | 43.5 | 1.38 | 0.00000203 | 899 |
Loss of Function | -0.425 | 16 | 14.3 | 1.12 | 8.38e-7 | 285 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000905 | 0.0000905 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000547 | 0.0000544 |
Finnish | 0.0000929 | 0.0000927 |
European (Non-Finnish) | 0.000427 | 0.000425 |
Middle Eastern | 0.0000547 | 0.0000544 |
South Asian | 0.000132 | 0.000131 |
Other | 0.000165 | 0.000164 |
dbNSFP
Source:
- Pathway
- Starch and sucrose metabolism - Homo sapiens (human);Carbohydrate digestion and absorption - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Digestion of dietary carbohydrate;Endohydrolysis of 1,4-alpha-D-glucosidic linkages in polysaccharides by alpha-amylase;Digestion;Digestion and absorption
(Consensus)
Recessive Scores
- pRec
- 0.489
Haploinsufficiency Scores
- pHI
- 0.132
- hipred
- N
- hipred_score
- 0.238
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.842
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Amy2a5
- Phenotype
Gene ontology
- Biological process
- carbohydrate metabolic process;carbohydrate catabolic process;polysaccharide digestion
- Cellular component
- extracellular region;extracellular space;extracellular exosome
- Molecular function
- alpha-amylase activity;calcium ion binding;chloride ion binding;alpha-amylase activity (releasing maltohexaose)