GALT
galactose-1-phosphate uridylyltransferase, the group of Histidine triad superfamily
Basic information
Region (hg38): 9:34638133-34651035
Links
Phenotypes
GenCC
Source:
- 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:
| 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
- Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase (69 variants)
- not provided (20 variants)
- Galactosemia (14 variants)
- GALT-related disorder (2 variants)
- Inborn genetic diseases (2 variants)
- not specified (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.
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 | 127 | 132 | ||||
| missense | 30 | 79 | 109 | 218 | ||
| nonsense | 13 | 26 | 40 | |||
| start loss | 4 | |||||
| frameshift | 15 | 39 | 56 | |||
| inframe indel | 7 | |||||
| splice donor/acceptor (+/-2bp) | 12 | 23 | 36 | |||
| splice region | 1 | 10 | 41 | 52 | ||
| non coding | 20 | 90 | 119 | |||
| Total | 73 | 173 | 140 | 217 | 9 |
Highest pathogenic variant AF is 0.00187
Variants in GALT
This is a list of pathogenic ClinVar variants found in the GALT region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| 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:
- 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