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 (3 variants)
• Galactosemia 4 (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.

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				10	3	13
missense			29	3	2	34
nonsense	3					3
start loss						0
frameshift			1			1
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region			1		2	3
non coding					16	16
Total	3	0	32	13	21

Highest pathogenic variant AF is 0.0000526

Variants in GALM

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

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

Position	Type	Phenotype	Significance	ClinVar
2-38666166-C-T		Inborn genetic diseases	Likely benign (Jan 31, 2024)
2-38666169-C-T		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
2-38666174-A-G		Inborn genetic diseases	Uncertain significance (Dec 13, 2021)
2-38666174-A-T			Uncertain significance (Oct 17, 2022)
2-38666183-G-A			Uncertain significance (Aug 14, 2021)
2-38666190-G-C			Uncertain significance (Oct 13, 2022)
2-38666196-T-C			Uncertain significance (Oct 05, 2022)
2-38666197-G-A			Likely benign (Nov 21, 2023)
2-38666223-A-G		GALM-related disorder	Uncertain significance (May 26, 2024)
2-38666238-C-T		Inborn genetic diseases	Uncertain significance (Apr 08, 2024)
2-38666255-G-T		Inborn genetic diseases	Uncertain significance (Feb 01, 2023)
2-38666258-A-G		Inborn genetic diseases	Uncertain significance (Dec 03, 2024)
2-38666274-G-A		Inborn genetic diseases	Uncertain significance (Oct 04, 2022)
2-38666283-C-T			Uncertain significance (Nov 24, 2022)
2-38666308-G-A		GALM-related disorder	Benign (Jan 26, 2024)
2-38666311-G-A			Likely benign (Dec 30, 2023)
2-38666325-T-C		Inborn genetic diseases	Uncertain significance (Oct 27, 2021)
2-38666335-C-A			Likely benign (Dec 13, 2023)
2-38666518-A-G			Benign (May 12, 2021)
2-38666535-G-A			Benign (May 12, 2021)
2-38675784-T-C			Benign (May 12, 2021)
2-38675812-G-T			Benign (May 25, 2021)
2-38675880-T-A			Benign (May 13, 2021)
2-38675909-C-G			Uncertain significance (Apr 10, 2023)
2-38675916-C-A			Pathogenic (Feb 27, 2022)

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