AMY2B
Basic information
Region (hg38): 1:103553815-103579534
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 AMY2B 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 | 61 | 65 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 61 | 5 | 1 |
Variants in AMY2B
This is a list of pathogenic ClinVar variants found in the AMY2B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-103571609-T-C | not specified | Uncertain significance (Nov 22, 2023) | ||
1-103571616-T-G | not specified | Uncertain significance (Nov 22, 2023) | ||
1-103571630-A-G | not specified | Uncertain significance (Feb 28, 2024) | ||
1-103571630-A-T | not specified | Uncertain significance (Apr 25, 2022) | ||
1-103571661-A-G | not specified | Uncertain significance (Feb 24, 2025) | ||
1-103571676-G-A | not specified | Uncertain significance (Dec 16, 2022) | ||
1-103571688-T-C | not specified | Uncertain significance (Dec 11, 2024) | ||
1-103571693-C-A | not specified | Uncertain significance (Feb 03, 2022) | ||
1-103571693-C-T | Benign (Dec 20, 2017) | |||
1-103571721-C-T | not specified | Uncertain significance (Nov 15, 2024) | ||
1-103571729-T-C | not specified | Uncertain significance (Sep 26, 2024) | ||
1-103571736-G-C | not specified | Uncertain significance (Feb 16, 2023) | ||
1-103571747-C-A | not specified | Uncertain significance (Sep 17, 2021) | ||
1-103571747-C-T | not specified | Uncertain significance (Jul 19, 2023) | ||
1-103571754-G-A | not specified | Uncertain significance (Jun 22, 2021) | ||
1-103572113-T-C | not specified | Uncertain significance (Jan 27, 2025) | ||
1-103572134-G-A | not specified | Uncertain significance (Feb 10, 2022) | ||
1-103572137-A-G | not specified | Likely benign (Dec 07, 2023) | ||
1-103572207-G-C | not specified | Uncertain significance (Apr 22, 2022) | ||
1-103572216-A-G | not specified | Uncertain significance (Jul 14, 2023) | ||
1-103573100-C-G | not specified | Likely benign (Sep 29, 2023) | ||
1-103573201-A-T | not specified | Uncertain significance (Feb 11, 2025) | ||
1-103573226-G-C | not specified | Uncertain significance (Sep 07, 2022) | ||
1-103573720-C-T | not specified | Uncertain significance (May 13, 2024) | ||
1-103573735-C-G | not specified | Uncertain significance (Aug 27, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
AMY2B | protein_coding | protein_coding | ENST00000361355 | 10 | 25720 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
5.88e-30 | 0.00000150 | 125565 | 0 | 167 | 125732 | 0.000664 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -2.52 | 388 | 271 | 1.43 | 0.0000144 | 3394 |
Missense in Polyphen | 135 | 107.19 | 1.2594 | 1392 | ||
Synonymous | -1.55 | 104 | 85.7 | 1.21 | 0.00000425 | 919 |
Loss of Function | -1.64 | 39 | 29.4 | 1.33 | 0.00000181 | 293 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00157 | 0.00157 |
Ashkenazi Jewish | 0.000496 | 0.000496 |
East Asian | 0.000761 | 0.000761 |
Finnish | 0.0000467 | 0.0000462 |
European (Non-Finnish) | 0.000424 | 0.000422 |
Middle Eastern | 0.000761 | 0.000761 |
South Asian | 0.00167 | 0.00167 |
Other | 0.000818 | 0.000815 |
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
- 0.387
Intolerance Scores
- loftool
- 0.232
- rvis_EVS
- 0.11
- rvis_percentile_EVS
- 62
Haploinsufficiency Scores
- pHI
- 0.121
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.399
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.273
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
- Cellular component
- extracellular exosome
- Molecular function
- alpha-amylase activity;metal ion binding;alpha-amylase activity (releasing maltohexaose)