AMY2A

protein-coding

amylase alpha 2A, the group of Amylases alpha

Gene summary

This gene encodes a member of the alpha-amylase family of proteins. Amylases are secreted proteins that hydrolyze 1,4-alpha-glucoside bonds in oligosaccharides and polysaccharides, catalyzing the first step in digestion of dietary starch and glycogen. This gene and several family members are present in a gene cluster on chromosome 1. This gene encodes an amylase isoenzyme produced by the pancreas. [provided by RefSeq, Jan 2015]

Previous symbols:

AMY2

MANE transcript

NM_000699.4

Inheritance

—

ClinVar variants

U:67B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.12

Max pathogenic AF

—

Genomic locus

chr1:103,617,427-103,625,780

External References & Databases

Ensembl (ENSG00000243480)

Transcript & Mutation Effects

hg38 • Region Span ~8.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AMY2A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000699.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			67 clinvar		1 clinvar	68
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	1	1	69

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_000699.4	RefSeq	NP_000690.1	10	MANE Select
ENST00000414303.7	Ensembl	ENSP00000397582.2	10	MANE Select
ENST00000423678.2	Ensembl	ENSP00000390832.2	4	Standard
XM_047418085.1	RefSeq	XP_047274041.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

carbohydrate metabolic process
carbohydrate catabolic process
polysaccharide digestion

Molecular Function

alpha-amylase activity
calcium ion binding
chloride ion binding
alpha-amylase activity (releasing maltohexaose)

Cellular Component

extracellular region
extracellular space
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000414303
Coding exons: 10
Length: 8404
Individuals with no LoFs: 125187
Homozygous LoFs: 0
Heterozygous LoFs: 58
Defined: 125245
p: 0.000232

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.02	175	141	1.24	0.00000705	3301
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00043	0.00042	rare
South Asian	0.00013	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.489

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.842

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium