AMY2A

amylase alpha 2A, the group of Amylases alpha

Basic information

Region (hg38): 1:103617427-103625780

Previous symbols: [ "AMY2" ]

Links

ENSG00000243480NCBI:279OMIM:104650HGNC:477Uniprot:P04746AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AMY2A gene.

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
clinvar
2
missense
21
clinvar
1
clinvar
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)3117186
1-103617492-T-C not specified Uncertain significance (Aug 12, 2021)2273418
1-103617510-G-A not specified Uncertain significance (Jun 10, 2024)3293560
1-103617513-C-T not specified Uncertain significance (May 26, 2023)2526715
1-103617556-T-C not specified Uncertain significance (Feb 13, 2024)3117174
1-103617585-C-G not specified Uncertain significance (Oct 29, 2021)2342111
1-103618081-C-A Benign (Dec 31, 2019)775571
1-103618930-C-A not specified Uncertain significance (Jan 26, 2022)2355793
1-103618954-A-G not specified Uncertain significance (Jan 08, 2024)3117193
1-103618955-C-T Likely benign (Aug 22, 2018)774798
1-103619038-G-C not specified Uncertain significance (Apr 09, 2024)3293539
1-103619567-G-A not specified Uncertain significance (Apr 08, 2022)3117198
1-103619578-C-A not specified Uncertain significance (Mar 24, 2023)2566598
1-103619585-A-G not specified Uncertain significance (Nov 17, 2022)2326958
1-103619608-G-A not specified Uncertain significance (May 31, 2023)2516073
1-103619668-A-G not specified Uncertain significance (Sep 26, 2023)3117209
1-103619773-A-T not specified Uncertain significance (Apr 25, 2022)2400118
1-103620605-C-T not specified Uncertain significance (Apr 08, 2024)3293550
1-103620638-G-A not specified Uncertain significance (Oct 26, 2022)2260882
1-103620665-G-A not specified Uncertain significance (Aug 02, 2021)2365554
1-103620668-A-G not specified Uncertain significance (Feb 05, 2024)3117220
1-103623866-G-T not specified Uncertain significance (Jun 16, 2024)3293571
1-103623874-T-C Likely benign (Dec 31, 2019)767682
1-103624107-T-A not specified Uncertain significance (Apr 11, 2023)2570097
1-103624113-G-T not specified Uncertain significance (Mar 06, 2023)2494746

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
AMY2Aprotein_codingprotein_codingENST00000414303 108404
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
8.54e-120.02111251870581252450.000232
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.021751411.240.000007053301
Missense in Polyphen5854.1641.07081363
Synonymous-1.976043.51.380.00000203899
Loss of Function-0.4251614.31.128.38e-7285

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009050.0000905
Ashkenazi Jewish0.000.00
East Asian0.00005470.0000544
Finnish0.00009290.0000927
European (Non-Finnish)0.0004270.000425
Middle Eastern0.00005470.0000544
South Asian0.0001320.000131
Other0.0001650.000164

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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)