GALT

galactose-1-phosphate uridylyltransferase, the group of Histidine triad superfamily

Basic information

Region (hg38): 9:34638133-34651035

Links

ENSG00000213930

∙ NCBI:2592 ∙ OMIM:606999 ∙ HGNC:4135 ∙ Uniprot:P07902 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

galactosemia (Definitive), mode of inheritance: AR
classic galactosemia (Definitive), mode of inheritance: AR
classic galactosemia (Supportive), mode of inheritance: AR
classic galactosemia (Strong), mode of inheritance: AR
galactosemia (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Galactosemia I	AR	Biochemical	Although there is some controversy related to treatment of individuals with various enzymatic activities, dietary measures (eg,lactose-free and galactose-restricted diet, with vitamin supplementation aimed to prevent decreased bone mineralization) can be effective	Biochemical; Endocrine; Gastrointestinal; Hematologic; Neurologic; Obstetric; Ophthalmologic; Renal	1610789; 1766867; 7927329; 8040766; 8051928; 8112740; 8499924; 8522334; 8956044; 1897530; 1373122; 2011574; 5337683; 4926707; 4136146; 90818; 6290834; 2512439; 1706789; 8444204; 8198125; 7887416; 8692963; 8943248; 8969739; 9012409; 11261429; 10472536; 10424825; 10604151; 12595586; 16838075; 19224951; 19793842; 20075179; 20222886; 20301691; 20978943; 21059483; 21321007; 21735606; 21779791; 22461411; 22483615; 22944367; 23022339

ClinVar

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

Deficiency_of_UDPglucose-hexose-1-phosphate_uridylyltransferase (689 variants)
not_provided (205 variants)
Galactosemia (175 variants)
not_specified (94 variants)
GALT-related_disorder (22 variants)
Inborn_genetic_diseases (21 variants)
Premature_ovarian_failure (1 variants)
See_cases (1 variants)
GALT_POLYMORPHISM (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALT gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000155.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous		5 clinvar	25 clinvar	140 clinvar	1 clinvar	171
missense	37 clinvar	136 clinvar	157 clinvar	5 clinvar	1 clinvar	336
nonsense	25 clinvar	21 clinvar	1 clinvar			47
start loss	3	1	1			5
frameshift	23 clinvar	42 clinvar	2 clinvar			67
splice donor/acceptor (+/-2bp)	14 clinvar	25 clinvar	1 clinvar			40
Total	102	230	187	145	2

Highest pathogenic variant AF is 0.0025412473

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALT	protein_coding	protein_coding	ENST00000378842	11	12903

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000205	0.975	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.915	177	215	0.824	0.0000128	2460
Missense in Polyphen		72	98.645	0.72989		1116
Synonymous	0.476	75	80.4	0.933	0.00000444	753
Loss of Function	2.07	13	23.9	0.543	0.00000116	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000853	0.000853
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000149	0.000149
Middle Eastern	0.000381	0.000381
South Asian	0.000327	0.000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays an important role in galactose metabolism. {ECO:0000269|PubMed:22461411, ECO:0000269|PubMed:27005423}.;
Disease: DISEASE: Galactosemia (GALCT) [MIM:230400]: Inherited disorder of galactose metabolism that causes jaundice, cataracts, and mental retardation. {ECO:0000269|PubMed:10220154, ECO:0000269|PubMed:11754113, ECO:0000269|PubMed:11919338, ECO:0000269|PubMed:1373122, ECO:0000269|PubMed:1427861, ECO:0000269|PubMed:15841485, ECO:0000269|PubMed:1610789, ECO:0000269|PubMed:17041746, ECO:0000269|PubMed:17876724, ECO:0000269|PubMed:18956253, ECO:0000269|PubMed:1897530, ECO:0000269|PubMed:2011574, ECO:0000269|PubMed:22461411, ECO:0000269|PubMed:23022339, ECO:0000269|PubMed:25592817, ECO:0000269|PubMed:25614870, ECO:0000269|PubMed:27005423, ECO:0000269|PubMed:7550229, ECO:0000269|PubMed:7887416, ECO:0000269|PubMed:7887417, ECO:0000269|PubMed:8112740, ECO:0000269|PubMed:8499924, ECO:0000269|PubMed:8598637, ECO:0000269|PubMed:8741038, ECO:0000269|PubMed:8869397, ECO:0000269|PubMed:8956044, ECO:0000269|PubMed:9222760}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Prolactin signaling pathway - Homo sapiens (human);Galactose metabolism - Homo sapiens (human);Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Galactosemia III;Galactosemia II (GALK);Galactose Metabolism;GLUT-1 deficiency syndrome;Congenital disorder of glycosylation CDG-IId;Nucleotide Sugars Metabolism;Lactose Synthesis;Galactosemia;Metabolism of carbohydrates;Metabolism;D-galactose degradation V (Leloir pathway);Galactose catabolism;Galactose metabolism (Consensus)

Recessive Scores

pRec: 0.0956

Intolerance Scores

loftool: 0.0408
rvis_EVS: -0.14
rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

pHI: 0.103
hipred: Y
hipred_score: 0.575
ghis: 0.515

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Galt
Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; liver/biliary system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process: UDP-glucose metabolic process;galactose metabolic process;UDP-glucose catabolic process;galactose catabolic process;galactose catabolic process via UDP-galactose
Cellular component: cytoplasm;Golgi apparatus;cytosol
Molecular function: protein binding;UDP-glucose:hexose-1-phosphate uridylyltransferase activity;zinc ion binding