MGAM

maltase-glucoamylase, the group of Glycoside hydrolase family 31

Basic information

Region (hg38): 7:141907812-142106747

Links

ENSG00000257335 ∙ NCBI:8972 ∙ OMIM:154360 ∙ HGNC:7043 ∙ Uniprot:O43451 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

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

• Inborn genetic diseases (77 variants)
• not provided (19 variants)
• MGAM-related condition (4 variants)
• Gestational diabetes mellitus uncontrolled (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGAM 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				6	4	10
missense			74	9	3	86
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	75	15	7

Variants in MGAM

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

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

Position	Type	Phenotype	Significance	ClinVar
7-141919044-C-G		not specified	Uncertain significance (Jan 03, 2024)
7-141919062-G-A		not specified	Uncertain significance (Jan 10, 2023)
7-141919151-A-G		not specified	Uncertain significance (Sep 20, 2023)
7-141919153-A-G		not specified	Uncertain significance (Feb 15, 2023)
7-141919153-A-T		not specified	Uncertain significance (Feb 28, 2024)
7-141919204-C-T		not specified	Uncertain significance (Jun 13, 2023)
7-141919248-G-A		not specified	Uncertain significance (Feb 23, 2023)
7-141919327-T-C		not specified	Uncertain significance (Dec 22, 2023)
7-141919417-G-C		not specified	Uncertain significance (Apr 27, 2023)
7-141919474-T-A		not specified	Uncertain significance (Feb 13, 2024)
7-141919488-T-C		not specified	Uncertain significance (Apr 04, 2023)
7-141919548-A-G		not specified	Uncertain significance (Dec 02, 2021)
7-141919575-C-G		not specified	Uncertain significance (Nov 14, 2023)
7-141919602-T-C		not specified	Uncertain significance (Nov 18, 2022)
7-141919602-T-G		not specified	Uncertain significance (Jul 16, 2021)
7-141919663-A-G		not specified	Uncertain significance (Dec 21, 2023)
7-141919764-G-A		not specified	Uncertain significance (Feb 16, 2023)
7-141919795-G-T		not specified	Uncertain significance (Aug 02, 2021)
7-141919814-G-C		not specified	Uncertain significance (Jun 06, 2023)
7-141930133-G-A		not specified	Uncertain significance (Nov 10, 2022)
7-141930200-C-G		not specified	Uncertain significance (Mar 16, 2022)
7-141935833-A-G		not specified	Uncertain significance (Aug 17, 2022)
7-141935837-T-C		not specified	Uncertain significance (Oct 27, 2022)
7-141935897-A-T		not specified	Uncertain significance (Feb 16, 2023)
7-141943898-G-T		not specified	Uncertain significance (May 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGAM	protein_coding	protein_coding	ENST00000549489	47	198935

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.04e-35	0.796	124145	3	732	124880	0.00295

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.761	1095	1.03e+3	1.07	0.0000558	12185
Missense in Polyphen		327	323.05	1.0122		3637
Synonymous	-1.06	403	377	1.07	0.0000206	3506
Loss of Function	2.93	72	104	0.691	0.00000518	1203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00952	0.00923
Ashkenazi Jewish	0.00269	0.00269
East Asian	0.00787	0.00783
Finnish	0.000514	0.000510
European (Non-Finnish)	0.00211	0.00206
Middle Eastern	0.00787	0.00783
South Asian	0.00191	0.00177
Other	0.00136	0.00132

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May serve as an alternate pathway for starch digestion when luminal alpha-amylase activity is reduced because of immaturity or malnutrition. May play a unique role in the digestion of malted dietary oligosaccharides used in food manufacturing.
• Pathway: Starch and sucrose metabolism - Homo sapiens (human);Carbohydrate digestion and absorption - Homo sapiens (human);Galactose metabolism - 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;Glucocorticoid Receptor Pathway;Neutrophil degranulation;Digestion of dietary carbohydrate;Innate Immune System;Immune System;Galactose metabolism;Digestion;Digestion and absorption (Consensus)

Recessive Scores

• pRec: 0.575

Intolerance Scores

• loftool: 0.104
• rvis_EVS: 2.36
• rvis_percentile_EVS: 98.45

Haploinsufficiency Scores

• pHI: 0.410
• hipred: N
• hipred_score: 0.431
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Mgam
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: maltose metabolic process;starch catabolic process;neutrophil degranulation;polysaccharide digestion
• Cellular component: plasma membrane;integral component of membrane;apical plasma membrane;extracellular exosome;tertiary granule membrane;ficolin-1-rich granule membrane
• Molecular function: catalytic activity;glucan 1,4-alpha-glucosidase activity;alpha-1,4-glucosidase activity;amylase activity;carbohydrate binding;maltose alpha-glucosidase activity