GALM

galactose mutarotase

Basic information

Region (hg38): 2:38666081-38741237

Links

ENSG00000143891 ∙ NCBI:130589 ∙ OMIM:137030 ∙ HGNC:24063 ∙ Uniprot:Q96C23 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• galactosemia 4 (Moderate), mode of inheritance: AR
• galactosemia 4 (Strong), mode of inheritance: AR
• galactosemia 4 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Galactosemia IV	AR	Biochemical	Dietary management (with a galactose-free diet) has been reported as resulting in normal galactose levels; some have been reported as resuming a normal diet in childhood and maintaining normal galactose levels	Biochemical; Ophthalmologic	30451973; 30910422

ClinVar

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

• not_provided (48 variants)
• Inborn_genetic_diseases (37 variants)
• GALM-related_disorder (8 variants)
• Galactosemia_4 (6 variants)
• not_specified (1 variants)
• Schizophrenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALM gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138801.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				13	3	16
missense		1	52	3	1	57
nonsense	4					4
start loss						0
frameshift	1		1			2
splice donor/acceptor (+/-2bp)						0
Total	5	1	53	16	4

Highest pathogenic variant AF is 0.000369863

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALM	protein_coding	protein_coding	ENST00000272252	7	75328

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.88e-11	0.0581	125578	0	170	125748	0.000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.146	194	188	1.03	0.00000979	2201
Missense in Polyphen		74	82.866	0.89301		947
Synonymous	-0.826	89	79.6	1.12	0.00000442	694
Loss of Function	0.0512	16	16.2	0.986	7.73e-7	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000852	0.000852
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000924	0.000925
Finnish	0.00286	0.00282
European (Non-Finnish)	0.000535	0.000528
Middle Eastern	0.000924	0.000925
South Asian	0.0000653	0.0000653
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mutarotase converts alpha-aldose to the beta-anomer. It is active on D-glucose, L-arabinose, D-xylose, D-galactose, maltose and lactose (By similarity). {ECO:0000250, ECO:0000269|PubMed:12753898, ECO:0000269|PubMed:15026423}.
• Pathway: Glycolysis / Gluconeogenesis - Homo sapiens (human);Galactose metabolism - Homo sapiens (human);Glycolysis;Glycogenosis, Type VII. Tarui disease;Gluconeogenesis;Glycogenosis, Type IA. Von gierke disease;Glycogenosis, Type IC;Fanconi-bickel syndrome;Glycogen Storage Disease Type 1A (GSD1A) or Von Gierke Disease;Triosephosphate isomerase;Fructose-1,6-diphosphatase deficiency;Phosphoenolpyruvate carboxykinase deficiency 1 (PEPCK1);Glycogenosis, Type IB;NOTCH-Ncore;D-galactose degradation V (Leloir pathway);trehalose degradation;sucrose degradation (Consensus)

Recessive Scores

• pRec: 0.189

Intolerance Scores

• loftool: 0.826
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.350
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Galm

Gene ontology

• Biological process: glucose metabolic process;galactose metabolic process;galactose catabolic process via UDP-galactose
• Cellular component: cytoplasm;extracellular exosome
• Molecular function: aldose 1-epimerase activity;carbohydrate binding