AMY2B

amylase alpha 2B, the group of Amylases alpha

Basic information

Region (hg38): 1:103553814-103579534

Previous symbols: [ "AMY2" ]

Links

ENSG00000240038 ∙ NCBI:280 ∙ OMIM:104660 ∙ HGNC:478 ∙ Uniprot:P19961 ∙ 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 AMY2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMY2B 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	2
missense			46	4		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	5	1

Variants in AMY2B

This is a list of pathogenic ClinVar variants found in the AMY2B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-103571609-T-C		not specified	Uncertain significance (Nov 22, 2023)
1-103571616-T-G		not specified	Uncertain significance (Nov 22, 2023)
1-103571630-A-G		not specified	Uncertain significance (Feb 28, 2024)
1-103571630-A-T		not specified	Uncertain significance (Apr 25, 2022)
1-103571676-G-A		not specified	Uncertain significance (Dec 16, 2022)
1-103571688-T-C		not specified	Uncertain significance (Aug 01, 2022)
1-103571693-C-A		not specified	Uncertain significance (Feb 03, 2022)
1-103571693-C-T			Benign (Dec 20, 2017)
1-103571736-G-C		not specified	Uncertain significance (Feb 16, 2023)
1-103571747-C-A		not specified	Uncertain significance (Sep 17, 2021)
1-103571747-C-T		not specified	Uncertain significance (Jul 19, 2023)
1-103571754-G-A		not specified	Uncertain significance (Jun 22, 2021)
1-103572134-G-A		not specified	Uncertain significance (Feb 10, 2022)
1-103572137-A-G		not specified	Likely benign (Dec 07, 2023)
1-103572207-G-C		not specified	Uncertain significance (Apr 22, 2022)
1-103572216-A-G		not specified	Uncertain significance (Jul 14, 2023)
1-103573100-C-G		not specified	Likely benign (Sep 29, 2023)
1-103573226-G-C		not specified	Uncertain significance (Sep 07, 2022)
1-103573720-C-T		not specified	Uncertain significance (May 13, 2024)
1-103573753-A-C		not specified	Uncertain significance (May 08, 2023)
1-103573781-A-T		not specified	Uncertain significance (Jul 14, 2022)
1-103573805-T-A		not specified	Uncertain significance (Dec 03, 2021)
1-103573808-G-C		not specified	Uncertain significance (Oct 05, 2023)
1-103573840-C-A		not specified	Uncertain significance (Aug 30, 2022)
1-103573843-A-T		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMY2B	protein_coding	protein_coding	ENST00000361355	10	25720

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.88e-30	0.00000150	125565	0	167	125732	0.000664

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.52	388	271	1.43	0.0000144	3394
Missense in Polyphen		135	107.19	1.2594		1392
Synonymous	-1.55	104	85.7	1.21	0.00000425	919
Loss of Function	-1.64	39	29.4	1.33	0.00000181	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00157	0.00157
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000761	0.000761
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000424	0.000422
Middle Eastern	0.000761	0.000761
South Asian	0.00167	0.00167
Other	0.000818	0.000815

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: 0.387

Intolerance Scores

• loftool: 0.232
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.146
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.273

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 exosome
• Molecular function: alpha-amylase activity;metal ion binding;alpha-amylase activity (releasing maltohexaose)