AMY2B

Summary

AMY2B (amylase alpha 2B, HGNC:478) is a protein-coding gene on chromosome 1p21.1, encoding Alpha-amylase 2B (P19961).

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 pancreas.

Source: NCBI Gene 280 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 124 total
• MANE Select transcript: NM_001387437

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:478
Approved symbol	AMY2B
Name	amylase alpha 2B
Location	1p21.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000240038
Ensembl biotype	protein_coding
OMIM	104660
Entrez	280

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000361355, ENST00000435302, ENST00000453959, ENST00000462971, ENST00000477657, ENST00000481821, ENST00000491397, ENST00000684275

RefSeq mRNA: 3 — MANE Select: NM_001387437 NM_001386109, NM_001387437, NM_020978

CCDS: CCDS782

Canonical transcript exons

ENST00000684275 — 10 exons

Exon	Start	End
ENSE00001642465	103579311	103579534
ENSE00001712096	103577490	103577608
ENSE00001757213	103571589	103571770
ENSE00003491719	103577720	103577845
ENSE00003492811	103575441	103575540
ENSE00003566157	103574260	103574393
ENSE00003569561	103573708	103573938
ENSE00003586191	103572110	103572256
ENSE00003587145	103573063	103573260
ENSE00003612859	103575223	103575345

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.81.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3482 / max 343.4818, expressed in 54 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4300	0.1904	51
4301	0.1123	4
4299	0.0455	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of pancreas	UBERON:0001150	99.81	gold quality
right uterine tube	UBERON:0001302	98.46	gold quality
cerebellar hemisphere	UBERON:0002245	97.06	gold quality
cerebellar cortex	UBERON:0002129	97.02	gold quality
right hemisphere of cerebellum	UBERON:0014890	97.02	gold quality
cerebellum	UBERON:0002037	96.79	gold quality
mucosa of stomach	UBERON:0001199	96.29	gold quality
left lobe of thyroid gland	UBERON:0001120	96.04	gold quality
tibial nerve	UBERON:0001323	95.98	gold quality
thyroid gland	UBERON:0002046	95.93	gold quality
right lobe of thyroid gland	UBERON:0001119	95.83	gold quality
apex of heart	UBERON:0002098	95.76	gold quality
calcaneal tendon	UBERON:0003701	95.54	gold quality
nucleus accumbens	UBERON:0001882	95.40	gold quality
gastrocnemius	UBERON:0001388	95.15	gold quality
muscle of leg	UBERON:0001383	95.07	gold quality
pancreas	UBERON:0001264	95.01	gold quality
caudate nucleus	UBERON:0001873	94.77	gold quality
putamen	UBERON:0001874	94.59	gold quality
cortex of kidney	UBERON:0001225	94.53	gold quality
right frontal lobe	UBERON:0002810	94.53	gold quality
metanephros cortex	UBERON:0010533	94.30	gold quality
right atrium auricular region	UBERON:0006631	94.12	gold quality
pituitary gland	UBERON:0000007	94.11	gold quality
left ovary	UBERON:0002119	94.03	gold quality
right lung	UBERON:0002167	94.03	gold quality
subcutaneous adipose tissue	UBERON:0002190	94.03	gold quality
thoracic mammary gland	UBERON:0005200	94.03	gold quality
endocervix	UBERON:0000458	93.97	gold quality
left uterine tube	UBERON:0001303	93.91	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	39.86
E-GEOD-81547	yes	23.44
E-GEOD-100618	no	310.75
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• It was concluded that the genetic variant determining starch metabolism influences the response to weight-loss dietary intervention. Overweight and obese individuals carrying the AMY1-AMY2 rs11185098 genotype associated with higher amylase activity may have greater loss of adiposity during low-calorie diet interventions. (PMID:28659346)
• A significant link between serum amylase activity and ABO blood type in Chinese subjects. (PMID:30938472)
• alpha-Amylase expressed in human small intestinal epithelial cells is essential for cell proliferation and differentiation. (PMID:31478242)

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), AMY1B (ENSG00000174876), AMY1C (ENSG00000187733), AMY1A (ENSG00000237763), AMY2A (ENSG00000243480)

Protein

Protein identifiers

Alpha-amylase 2B — P19961 (reviewed: P19961)

Alternative names: 1,4-alpha-D-glucan glucanohydrolase 2B, Carcinoid alpha-amylase

All UniProt accessions (3): P19961, C9J2Z5, C9JWK7

UniProt curated annotations — full annotation on UniProt →

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.

Isoforms (2)

UniProt ID	Names	Canonical?
P19961-1	1	yes
P19961-2	2

RefSeq proteins (3): NP_001373038, NP_001374366, NP_066188 (=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 (20 total): binding site 7, disulfide bond 5, splice variant 2, active site 2, signal peptide 1, chain 1, site 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P19961-F1	96.70	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 (1): 16

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

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: 55 (showing top): MODULE_92, WANG_CLIM2_TARGETS_UP, MODULE_255, REACTOME_DIGESTION_OF_DIETARY_CARBOHYDRATE, MODULE_317, NKX61_01, FREAC3_01, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, TGANTCA_AP1_C, KEGG_STARCH_AND_SUCROSE_METABOLISM, MODULE_88, AACTTT_UNKNOWN, CUI_TCF21_TARGETS_2_DN

GO Biological Process (1): carbohydrate metabolic process (GO:0005975)

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
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

1728 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
AMY2B	MGAM	O43451	986
AMY2B	MGAM2	Q2M2H8	986
AMY2B	SI	P14410	924
AMY2B	GYG1	P46976	838
AMY2B	CTRB1	P17538	835
AMY2B	CTRB2	Q6GPI1	834
AMY2B	GYG2	O15488	828
AMY2B	HAO1	Q9UJM8	825
AMY2B	ALB	P02768	737
AMY2B	PNLIP	P16233	729
AMY2B	INS	P01308	692
AMY2B	MANBA	O00462	686
AMY2B	BCHE	P06276	676
AMY2B	BPI	P17213	666
AMY2B	ATP1A1	P05023	653

IntAct

13 interactions, top by confidence:

A	B	Type	Score
DUSP4	MYO1C	psi-mi:“MI:0914”(association)	0.350
DUSP4	PSMD11	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
ORF10	HSPA5	psi-mi:“MI:0914”(association)	0.350
ZBTB18	CBR3	psi-mi:“MI:0914”(association)	0.350
AMY2A	GYG2	psi-mi:“MI:0914”(association)	0.350
AMY1A	GYG2	psi-mi:“MI:0914”(association)	0.350
AMY2A	GYS1	psi-mi:“MI:0914”(association)	0.350
ZNF843	AMY2A	psi-mi:“MI:0914”(association)	0.350
AMY2B	FOS	psi-mi:“MI:0915”(physical association)	0.000
tkt1	AMY2B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (9): AMY2B (Affinity Capture-MS), AMY2B (Affinity Capture-RNA), AMY2B (Affinity Capture-MS), AMY2B (Affinity Capture-MS), AMY2B (Affinity Capture-MS), AMY2B (Affinity Capture-MS), AMY2B (Affinity Capture-MS), AMY2B (Affinity Capture-MS), AMY2B (Affinity Capture-MS)

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	98
Likely benign	10
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1840 predictions. Top by Δscore:

Variant	Effect	Δscore
1:103565899:T:TA	acceptor_gain	1.0000
1:103573062:GGTTC:G	acceptor_gain	1.0000
1:103573257:TCAG:T	donor_loss	1.0000
1:103573258:CAG:C	donor_loss	1.0000
1:103573259:AGGTA:A	donor_loss	1.0000
1:103573260:GGTAA:G	donor_loss	1.0000
1:103573261:GTAA:G	donor_loss	1.0000
1:103573895:G:GG	donor_gain	1.0000
1:103573912:GGAA:G	donor_gain	1.0000
1:103573913:G:GT	donor_gain	1.0000
1:103573913:G:T	donor_gain	1.0000
1:103573936:G:GT	donor_gain	1.0000
1:103574256:CTAGG:C	acceptor_loss	1.0000
1:103574257:TAG:T	acceptor_loss	1.0000
1:103574258:A:T	acceptor_loss	1.0000
1:103574259:G:GT	acceptor_loss	1.0000
1:103574392:AAGT:A	donor_loss	1.0000
1:103574393:AGT:A	donor_loss	1.0000
1:103574394:G:GG	donor_gain	1.0000
1:103575338:GATGC:G	donor_gain	1.0000
1:103575342:C:G	donor_gain	1.0000
1:103575439:A:AG	acceptor_gain	1.0000
1:103575440:G:GG	acceptor_gain	1.0000
1:103575440:GGCT:G	acceptor_gain	1.0000
1:103577483:A:AG	acceptor_gain	1.0000
1:103577717:TA:T	acceptor_loss	1.0000
1:103577718:A:AG	acceptor_gain	1.0000
1:103577718:AG:A	acceptor_gain	1.0000
1:103577718:AGGAA:A	acceptor_loss	1.0000
1:103577719:G:GG	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000077186 (1:103575013 GGTGT>G,GGT,GGTGTGT), RS1000260855 (1:103569589 G>C), RS1000381755 (1:103557418 A>G,T), RS1000515817 (1:103564242 A>C), RS1000549551 (1:103574810 T>C), RS1000589493 (1:103563958 A>G), RS1000653370 (1:103565508 A>G), RS1000837823 (1:103563614 C>G,T), RS1001017611 (1:103574066 C>G,T), RS1001151037 (1:103569675 G>A,C), RS1001227350 (1:103568732 T>A), RS1001246377 (1:103561216 G>A), RS1001341358 (1:103556525 G>A), RS1001395237 (1:103556266 A>G), RS1001435343 (1:103569828 G>A)

Disease associations

OMIM: gene MIM:104660 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST006585_2389	Blood protein levels	3.000000e-36

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	3
Tetrachlorodibenzodioxin	decreases expression	2
Cyclosporine	decreases expression, increases methylation	2
Aflatoxin B1	decreases expression, decreases methylation	2
aristolochic acid I	increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	affects expression	1
jinfukang	decreases expression	1
Resveratrol	increases expression, affects cotreatment	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Cisplatin	increases expression	1
Estradiol	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	decreases expression	1
Okadaic Acid	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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