MGAM2

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

Basic information

Region (hg38): 7:142111718-142222324

Links

ENSG00000257743 ∙ NCBI:93432 ∙ ∙ HGNC:28101 ∙ Uniprot:Q2M2H8 ∙ 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 MGAM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGAM2 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in MGAM2

This is a list of pathogenic ClinVar variants found in the MGAM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-142167474-G-T		Aganglionic megacolon	Uncertain significance (May 16, 2019)
7-142199898-A-G			Likely benign (Mar 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGAM2	protein_coding	protein_coding	ENST00000550469	12	110576

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.410	0.590	114598	0	6	114604	0.0000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	190	243	0.780	0.0000130	3174
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000628	0.0000628
Ashkenazi Jewish	0.00	0.00
East Asian	0.000123	0.000115
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000123	0.000115
South Asian	0.0000672	0.0000669
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Starch and sucrose metabolism - Homo sapiens (human);Carbohydrate digestion and absorption - Homo sapiens (human);Galactose metabolism - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• ghis: 0.441

Essentials

• essential_gene_gene_trap: N

Gene ontology

• Biological process: carbohydrate metabolic process
• Cellular component: integral component of membrane
• Molecular function: glucan 1,4-alpha-glucosidase activity;carbohydrate binding