AMY1B

Summary

AMY1B (amylase alpha 1B, HGNC:475) is a protein-coding gene on chromosome 1p21.1, encoding Alpha-amylase 1B (P0DTE7). Calcium-binding enzyme that initiates starch digestion in the oral cavity.

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.

Source: NCBI Gene 277 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 9 total
• MANE Select transcript: NM_001008218

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:475
Approved symbol	AMY1B
Name	amylase alpha 1B
Location	1p21.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000174876
Ensembl biotype	protein_coding
OMIM	104701
Entrez	277

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000330330, ENST00000370080, ENST00000425410, ENST00000464691, ENST00000903269, ENST00000903270, ENST00000903271, ENST00000903272, ENST00000942052, ENST00000942053, ENST00000942054

RefSeq mRNA: 6 — MANE Select: NM_001008218 NM_001008218, NM_001386925, NM_001422120, NM_001422123, NM_001422127, NM_001422129

CCDS: CCDS30783

Canonical transcript exons

ENST00000330330 — 11 exons

Exon	Start	End
ENSE00001681850	103689194	103689312
ENSE00001720483	103691488	103691610
ENSE00001738141	103691294	103691393
ENSE00001760424	103696042	103696210
ENSE00001765498	103695472	103695685
ENSE00001926974	103687415	103687638
ENSE00003466783	103692427	103692560
ENSE00003575864	103693979	103694176
ENSE00003597392	103693300	103693530
ENSE00003670179	103688958	103689083
ENSE00003785906	103694980	103695126

Expression profiles

Bgee: expression breadth broad, 75 present calls, max score 80.02.

Top tissues by expression

108 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	80.02	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.98	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.37	gold quality
tonsil	UBERON:0002372	75.54	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	75.49	gold quality
fallopian tube	UBERON:0003889	66.95	gold quality
body of pancreas	UBERON:0001150	58.84	gold quality
saliva-secreting gland	UBERON:0001044	58.74	gold quality
right lobe of thyroid gland	UBERON:0001119	55.58	gold quality
minor salivary gland	UBERON:0001830	54.71	gold quality
endometrium	UBERON:0001295	54.06	gold quality
lung	UBERON:0002048	52.33	gold quality
pancreas	UBERON:0001264	50.84	gold quality
upper lobe of left lung	UBERON:0008952	50.58	gold quality
thyroid gland	UBERON:0002046	50.48	gold quality
left lobe of thyroid gland	UBERON:0001120	49.86	gold quality
stromal cell of endometrium	CL:0002255	49.00	gold quality
endocervix	UBERON:0000458	47.76	gold quality
placenta	UBERON:0001987	45.29	gold quality
skeletal muscle tissue	UBERON:0001134	44.37	gold quality
sural nerve	UBERON:0015488	43.88	gold quality
ventricular zone	UBERON:0003053	43.29	gold quality
ganglionic eminence	UBERON:0004023	42.29	gold quality
uterine cervix	UBERON:0000002	40.77	gold quality
muscle tissue	UBERON:0002385	40.44	gold quality
cortical plate	UBERON:0005343	39.76	gold quality
urinary bladder	UBERON:0001255	39.02	gold quality
bone marrow cell	CL:0002092	38.65	gold quality
monocyte	CL:0000576	38.23	gold quality
bone marrow	UBERON:0002371	38.12	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	24.54

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 6)

• These findings confirm that sAA is sensitive to the effects of potentially stressful stimuli (state variance) and at the same time demonstrate its relative robustness and stability across time and conditions (trait variance). (PMID:21827821)
• results show a strong association between acute physical stressor-induced elevations in sAA levels and patients with MDD. (PMID:22063648)
• Diurnal and stress-response salivary alpha amylase patterns were related to child adiposity: decreased morning alpha amylase was associated with increased BMI. (PMID:25588701)
• AMY1 copy number was significantly correlated with the variation observed in salivary amylase production and enzyme activity but did not explain the majority of observed variation between individuals. AMY1-odd and AMY1-even haplotypes showed a different relationship between copy number and expression levels, but the difference was not statistically significant. (PMID:28219410)
• At baseline, a modest association between AMY1 gene copy number and BMI (P = 0.04) was observed but AMY1 gene copy was not associated with baseline glycemic variables. (PMID:30982860)
• AMY1 Gene Copy Number Correlates With Glucose Absorption and Visceral Fat Volume, but Not with Insulin Resistance. (PMID:32697825)

Cross-species orthologs

12 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	Amy-d	FBGN0000078
drosophila_melanogaster	Amy-p	FBGN0000079
drosophila_melanogaster	Mal-A2	FBGN0002569
drosophila_melanogaster	Mal-A3	FBGN0002571
drosophila_melanogaster	Amyrel	FBGN0020506
drosophila_melanogaster	Mal-B1	FBGN0032381
drosophila_melanogaster	Mal-B2	FBGN0032382
drosophila_melanogaster	Mal-A4	FBGN0033294
drosophila_melanogaster	Mal-A7	FBGN0033296
drosophila_melanogaster	Mal-A8	FBGN0033297
drosophila_melanogaster	Mal-A6	FBGN0050360
caenorhabditis_elegans		WBGENE00008220

Paralogs (7): GBE1 (ENSG00000114480), SLC3A1 (ENSG00000138079), SLC3A2 (ENSG00000168003), AMY1C (ENSG00000187733), AMY1A (ENSG00000237763), AMY2B (ENSG00000240038), AMY2A (ENSG00000243480)

Protein

Protein identifiers

Alpha-amylase 1B — P0DTE7 (reviewed: P0DTE7)

All UniProt accessions (2): P0DTE7, Q5T084

UniProt curated annotations — full annotation on UniProt →

Function. Calcium-binding enzyme that initiates starch digestion in the oral cavity. Catalyzes the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds, yielding a mixture of maltose, isomaltose, small amounts of glucose as well as small linear and branched oligosaccharides called dextrins.

Subunit / interactions. Monomer.

Subcellular location. Secreted.

Cofactor. Binds 1 Ca(2+) ion per subunit. Binds 1 Cl(-) ion per subunit.

Similarity. Belongs to the glycosyl hydrolase 13 family.

RefSeq proteins (6): NP_001008219, NP_001373854, NP_001409049, NP_001409052, NP_001409056, NP_001409058 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006046	Alpha_amylase	Family
IPR006047	GH13_cat_dom	Domain
IPR006048	A-amylase/branching_C	Domain
IPR013780	Glyco_hydro_b	Homologous_superfamily
IPR017853	GH_hydrolase_sf	Homologous_superfamily
IPR031319	A-amylase_C	Domain

Pfam: PF00128, PF02806

UniProt features (23 total): binding site 7, disulfide bond 5, modified residue 4, glycosylation site 2, active site 2, signal peptide 1, chain 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DTE7-F1	96.57	0.96

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 315 (transition state stabilizer); 212 (nucleophile); 248 (proton donor)

Ligand- & substrate-binding residues (7): 352; 115; 173; 182; 210; 216; 313

Post-translational modifications (4): 16, 365, 427, 474

Disulfide bonds (5): 43–101, 85–130, 156–175, 393–399, 465–477

Glycosylation sites (2): 427, 476

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-189085	Digestion of dietary carbohydrate
R-HSA-8935690	Digestion
R-HSA-8963743	Digestion and absorption

MSigDB gene sets: 26 (showing top): GOBP_OLIGOSACCHARIDE_METABOLIC_PROCESS, REACTOME_DIGESTION_OF_DIETARY_CARBOHYDRATE, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, KEGG_STARCH_AND_SUCROSE_METABOLISM, chr1p21, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_GLYCOSYL_BONDS, GOMF_HYDROLASE_ACTIVITY_HYDROLYZING_O_GLYCOSYL_COMPOUNDS, LU_EZH2_TARGETS_DN, GOMF_AMYLASE_ACTIVITY, GOMF_CHLORIDE_ION_BINDING, REACTOME_DIGESTION, REACTOME_DIGESTION_AND_ABSORPTION, ANDERSON_BLOOD_CN54GP140_ADJUVANTED_WITH_GLA_AF_AGE_18_45YO_3DY_UP, KANNAN_BLOOD_2012_2013_TIV_AGE_65PLS_REVACCINATED_IN_6_9_MO_VS_REVACCINATED_IN_12_13_MOS_DN, HOFT_CD4_POSITIVE_ALPHA_BETA_MEMORY_T_CELL_BCG_VACCINE_AGE_18_45YO_ID_7DY_TOP_100_DEG_EX_VIVO_DN

GO Biological Process (2): carbohydrate metabolic process (GO:0005975), oligosaccharide metabolic process (GO:0009311)

GO Molecular Function (8): alpha-amylase activity (GO:0004556), calcium ion binding (GO:0005509), chloride ion binding (GO:0031404), catalytic activity (GO:0003824), hydrolase activity (GO:0016787), hydrolase activity, acting on glycosyl bonds (GO:0016798), cation binding (GO:0043169), metal ion binding (GO:0046872)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), extracellular exosome (GO:0070062), extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Digestion	1
Digestion and absorption	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
primary metabolic process	1
carbohydrate metabolic process	1
amylase activity	1
metal ion binding	1
anion binding	1
molecular_function	1
catalytic activity	1
hydrolase activity	1
ion binding	1
cation binding	1
extracellular vesicle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: H2N0D4, O18344, O18345, O18408, O18420, O18552, O76260, O76261, O76262, O76263, O76264, O76265, O76284, O76459, O77011, O77012, O77013, O77014, O77015, O77016, O77018, O77019, O77020, O77021, O77022, O97396, P00687, P00688, P00689, P00690, P04063, P04746, P04750, P08144, P09107, P0DTE7, P0DTE8, P0DUB6, P19961, P54215

Diamond homologs: A0A096XJN4, B0KZK1, H2N0D4, O18344, O18345, O18408, O18420, O18552, O76260, O76261, O76262, O76263, O76264, O76265, O76284, O76459, O77011, O77012, O77013, O77014, O77015, O77016, O77018, O77019, O77020, O77021, O77022, O97396, P00687, P00688, P00689, P00690, P04746, P08144, P08486, P09107, P09794, P0DTE7, P0DTE8, P0DUB6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

9 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	7
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1441 predictions. Top by Δscore:

Variant	Effect	Δscore
1:103688952:A:AC	donor_gain	1.0000
1:103688953:C:CC	donor_gain	1.0000
1:103688953:CTTA:C	donor_gain	1.0000
1:103688954:TTA:T	donor_loss	1.0000
1:103688956:A:AC	donor_gain	1.0000
1:103688956:A:AT	donor_loss	1.0000
1:103688956:AC:A	donor_gain	1.0000
1:103688957:C:CG	donor_gain	1.0000
1:103688957:CC:C	donor_gain	1.0000
1:103688957:CCA:C	donor_gain	1.0000
1:103688957:CCAG:C	donor_gain	1.0000
1:103688957:CCAGT:C	donor_gain	1.0000
1:103689079:TGTTC:T	acceptor_gain	1.0000
1:103689080:GTTC:G	acceptor_gain	1.0000
1:103689081:TTC:T	acceptor_gain	1.0000
1:103689082:TC:T	acceptor_gain	1.0000
1:103689083:CC:C	acceptor_gain	1.0000
1:103689083:CCTAA:C	acceptor_loss	1.0000
1:103689084:C:CC	acceptor_gain	1.0000
1:103689085:T:G	acceptor_loss	1.0000
1:103689091:C:CT	acceptor_gain	1.0000
1:103689309:CATC:C	acceptor_gain	1.0000
1:103689312:CCT:C	acceptor_gain	1.0000
1:103689318:T:C	acceptor_gain	1.0000
1:103689318:T:TC	acceptor_gain	1.0000
1:103689321:C:CT	acceptor_gain	1.0000
1:103689322:A:T	acceptor_gain	1.0000
1:103691292:A:AC	donor_gain	1.0000
1:103691293:C:CG	donor_gain	1.0000
1:103691293:CTTTT:C	donor_gain	1.0000

AlphaMissense

3419 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1027055250 (1:103690858 C>T), RS1055294018 (1:103697424 C>CTT), RS1156236606 (1:103696938 C>G,T), RS1156704764 (1:103691165 C>G), RS1159777418 (1:103691259 G>C), RS1160954497 (1:103697341 AC>A), RS1163117751 (1:103697009 A>T), RS1165218625 (1:103691385 T>C), RS1166617241 (1:103697100 G>A), RS1168584195 (1:103690911 G>A), RS1170860619 (1:103690867 T>A,G), RS1171132897 (1:103697409 C>G), RS1173332158 (1:103691355 G>T), RS1174248651 (1:103691621 A>C), RS1174738722 (1:103691748 A>G)

Disease associations

OMIM: gene MIM:104701 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PubChem BioAssay actives

30 with measured affinity, of 327 total; 6 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
(2S)-N-[(2S)-1-amino-3-(1H-imidazol-5-yl)-1-oxopropan-2-yl]-5-(diaminomethylideneamino)-2-[[(2S)-2-[[(2S)-2-[[(2R)-2-[(3S,10S,13S,16S)-10-(hydroxymethyl)-3,13-bis[(4-hydroxyphenyl)methyl]-2,5,9,12,15-pentaoxo-7-thia-1,4,8,11,14-pentazabicyclo[14.3.0]nonadecan-8-yl]-3-sulfanylpropanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]-3-methylbutanoyl]amino]pentanamide	1802659: Inhibition Assay (piHA-Dm) from Article 10.1016/j.chembiol.2017.02.001: “Rapid Discovery of Potent and Selective Glycosidase-Inhibiting De Novo Peptides.”	ic50	0.0340	uM
(7R,8S,9S,10R)-7-[[(2S,3R,4R,5S,6R)-5-[(2R,3R,4S,5S,6R)-3,4-dihydroxy-6-methyl-5-[[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino]oxan-2-yl]oxy-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxymethyl]-8,9,10-trihydroxy-2-sulfanylidene-6-oxa-1,3-diazaspiro[4.5]decan-4-one	1248395: Non-competitive inhibition of human salivary alpha-amylase using GalG2CNP as substrate assessed as CNP liberation by Lineweaver-Burk plot analysis	ki	0.1900	uM
(3R,4R,5S,6R)-5-[(2R,3R,4R,5S,6R)-5-[(2R,3R,4S,5S,6R)-3,4-dihydroxy-6-methyl-5-[[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino]oxan-2-yl]oxy-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-(hydroxymethyl)oxane-2,3,4-triol	1248385: Inhibition of human salivary alpha-amylase using GalG2CNP as substrate by UV-Vis spectrophotometric analysis	ic50	0.5000	uM
5-[5-[[4-[5-[3,4-dihydroxy-6-methyl-5-[[4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino]oxan-2-yl]oxy-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-5,6-dihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino]-3,4-dihydroxy-6-methyloxan-2-yl]oxy-6-(hydroxymethyl)oxane-2,3,4-triol	1248392: Inhibition of human salivary alpha-amylase using GalG2CNP as substrate	ki	0.7000	uM
[(2R,3R,4S,5R,6S)-3,4,5,6-tetrakis[(3,4,5-trihydroxybenzoyl)oxy]oxan-2-yl]methyl 3,4,5-trihydroxybenzoate	1248394: Inhibition of human salivary alpha-amylase using GalG2CNP as substrate assessed as CNP liberation by spectrophotometric analysis	ic50	2.3500	uM
5,6,7-trihydroxy-2-(4-hydroxyphenyl)chromen-4-one	1798320: In Vitro alpha-Amylase Activity Assay from Article 10.1021/jm800115x: “Flavonoids for controlling starch digestion: structural requirements for inhibiting human alpha-amylase.”	ic50	9.6400	uM

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Ethanol	affects cotreatment, decreases expression, increases abundance	1
Arsenicals	decreases expression	1
Gasoline	affects cotreatment, decreases expression, increases abundance	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, decreases expression, increases abundance	1
Tunicamycin	decreases expression	1
Thapsigargin	decreases expression	1
1-Butanol	affects cotreatment, decreases expression, increases abundance	1
Particulate Matter	affects cotreatment, decreases expression, increases abundance	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.