MGAM2

protein-coding

maltase-glucoamylase 2 (putative), the group of Glycoside hydrolase family 31

Gene summary

Predicted to enable alpha-1,4-glucosidase activity. Predicted to be involved in disaccharide catabolic process. Predicted to be located in several cellular components, including apical part of cell; endomembrane system; and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001293626.2

Inheritance

—

ClinVar variants

U:1B:1

Top phenotype

Aganglionic megacolon

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr7:142,111,718-142,222,324

External References & Databases

Ensembl (ENSG00000257743)

Transcript & Mutation Effects

hg38 • Region Span ~110.6 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 MGAM2 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 1

Aganglionic megacolonTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001293626.2. 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			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	1	1	0	2

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001293626.2	RefSeq	NP_001280555.1	47	MANE Select
ENST00000477922.4	Ensembl	ENSP00000420449.3	47	MANE Select
ENST00000550469.6	Ensembl	ENSP00000447431.2	12	Standard
ENST00000550469.7	Ensembl	ENSP00000447431.2	12	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)
Galactose metabolism - Homo sapiens (human)

Biological Process

carbohydrate metabolic process

Molecular Function

glucan 1,4-alpha-glucosidase activity
carbohydrate binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000550469
Coding exons: 12
Length: 110576
Individuals with no LoFs: 114598
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 114604
p: 0.0000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.22	190	243	0.780	0.0000130	3174
Missense (PolyPhen)		70	94.269	0.74255		1213
Synonymous	0.0396	92	92.5	0.995	0.00000524	884
Loss of Function	3.43	5	22.6	0.221	0.00000111	292

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000063	0.000059	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00012	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.000067	0.000067	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (gene trap): N