GeneBe

GALT

protein-coding

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

Gene summary

Galactose-1-phosphate uridyl transferase (GALT) catalyzes the second step of the Leloir pathway of galactose metabolism, namely the conversion of UDP-glucose + galactose-1-phosphate to glucose-1-phosphate + UDP-galactose. The absence of this enzyme results in classic galactosemia in humans and can be fatal in the newborn period if lactose is not removed from the diet. The pathophysiology of galactosemia has not been clearly defined. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

MANE transcript

NM_000155.4

Inheritance

AR

ClinVar variants

P:379U:226B:148

Top phenotype

Galactosemia I

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr9:34,638,133-34,651,035

External References & Databases

Ensembl (ENSG00000213930)NCBI Gene (2592)OMIM (606999)HGNC:4135GenCCUniProt (P07902)AlphaFoldClinVar (GALT)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~12.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

classic galactosemiaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009258

Submitter: Labcorp Genetics (formerly Invitae)

classic galactosemiaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009258

Submitter: Orphanet

classic galactosemiaDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009258

Submitter: Natera

galactosemiaDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0018116

Submitter: Myriad Women's Health

classic galactosemiaDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009258

Submitter: G2P

classic galactosemiaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009258

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Galactosemia IAR

Manifestation: Biochemical; Endocrine; Gastrointestinal; Hematologic; Neurologic; Obstetric; Ophthalmologic; Renal

Intervention: Biochemical

Rationale: 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

Refs: 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; 23022339Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GALT variants in ClinVar

10 Conditions Cataloged
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferaseTotal: 732
GalactosemiaTotal: 341
not providedTotal: 231
not specifiedTotal: 120
GALT-related disorderTotal: 51
Inborn genetic diseasesTotal: 25
Fetal anomalies with a likely genetic causeTotal: 2
Premature ovarian failureTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000155.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
5
clinvar
27
clinvar
142
clinvar
1
clinvar
 175
missense
34
clinvar
148
clinvar
190
clinvar
4
clinvar
1
clinvar
 377
nonsense
25
clinvar
31
clinvar
1
clinvar
 57
start loss
1
clinvar
4
clinvar
1
clinvar
 6
frameshift
22
clinvar
59
clinvar
1
clinvar
 82
splice donor/acceptor (+/-2bp)
11
clinvar
39
clinvar
6
clinvar
 56
Total932862261462753

Highest pathogenic variant AF is 0.0025412473

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 87 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000155.4RefSeqNP_000146.211MANE Select
ENST00000378842.8EnsemblENSP00000368119.411MANE Select
NM_001258332.2RefSeqNP_001245261.18Standard
ENST00000450095.6EnsemblENSP00000401956.28Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • 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)

Biological Process

  • UDP-glucose metabolic process
  • galactose metabolic process
  • UDP-glucose catabolic process
  • galactose catabolic process
  • galactose catabolic process via UDP-galactose

Molecular Function

  • protein binding
  • UDP-glucose:hexose-1-phosphate uridylyltransferase activity
  • zinc ion binding

Cellular Component

  • cytoplasm
  • Golgi apparatus
  • cytosol

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000378842
Coding exons
11
Length
12903
Individuals with no LoFs
125689
Homozygous LoFs
0
Heterozygous LoFs
59
Defined
125748
p
0.000235
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.9151772150.8240.00001282460
Missense (PolyPhen)7298.6450.729891116
Synonymous0.4767580.40.9330.00000444753
Loss of Function2.071323.90.5430.00000116249

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.000610.00055rare
Ashkenazi Jewish00.0absent
East Asian0.000380.00038rare
Finnish00.0absent
European (Non-Finnish)0.000150.00015rare
South Asian0.000330.00033rare
Other0.000330.00033rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec
0.0956

Intolerance Scores

LoFtool
0.0408
RVIS EVS
-0.14
RVIS percentile EVS
43.77

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.990

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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