AMY1A

amylase alpha 1A, the group of Amylases alpha

Basic information

Region (hg38): 1:103655760-103664554

Previous symbols: [ "AMY1" ]

Links

ENSG00000237763 ∙ NCBI:276 ∙ OMIM:104700 ∙ HGNC:474 ∙ Uniprot:P0DUB6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AMY1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMY1A 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				1		1
missense			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	2	0

Variants in AMY1A

This is a list of pathogenic ClinVar variants found in the AMY1A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-103660368-G-A		not specified	Uncertain significance (Jul 16, 2024)
1-103660401-C-T			Likely benign (Jun 26, 2018)
1-103660431-A-G		not specified	Uncertain significance (Nov 21, 2023)
1-103660444-C-T			Benign/Likely benign (Jul 01, 2024)
1-103660445-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-103660451-G-A		not specified	Uncertain significance (Nov 11, 2024)
1-103660479-C-T		not specified	Uncertain significance (May 26, 2024)
1-103660593-G-A		not specified	Uncertain significance (Mar 22, 2023)
1-103660611-C-T		not specified	Uncertain significance (Oct 29, 2021)
1-103660648-G-A		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMY1A	protein_coding	protein_coding	ENST00000370083	10	9262

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000323	0.378	110315	1	30	110346	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0522	32	31.2	1.03	0.00000151	3401
Missense in Polyphen		20	16.41	1.2188		1546
Synonymous	0.151	8	8.56	0.934	3.66e-7	923
Loss of Function	-0.124	5	4.71	1.06	3.59e-7	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000261	0.000261
Ashkenazi Jewish	0.000386	0.000361
East Asian	0.000118	0.000117
Finnish	0.000105	0.000104
European (Non-Finnish)	0.000112	0.0000992
Middle Eastern	0.000118	0.000117
South Asian	0.000247	0.000235
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Starch and sucrose metabolism - Homo sapiens (human);Carbohydrate digestion and absorption - Homo sapiens (human);Salivary secretion - Homo sapiens (human);Glycogen synthetase deficiency;Glycogenosis, Type III. Cori disease, Debrancher glycogenosis;Mucopolysaccharidosis VI. Sly syndrome;Sucrase-isomaltase deficiency;Glycogenosis, Type IV. Amylopectinosis, Anderson disease;Glycogenosis, Type VI. Hers disease;Starch and Sucrose Metabolism;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: 0.481

Haploinsufficiency Scores

• pHI: 0.151
• hipred: N
• hipred_score: 0.258

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.755

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

Gene ontology

• Biological process: carbohydrate metabolic process
• Cellular component: extracellular space;extracellular exosome
• Molecular function: alpha-amylase activity;protein binding;metal ion binding;alpha-amylase activity (releasing maltohexaose)