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NM_000155.4(GALT):c.253-2A>G

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 30, 2020
Accession:
VCV000025142.11
Variation ID:
25142
Description:
single nucleotide variant
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NM_000155.4(GALT):c.253-2A>G

Allele ID
36476
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9p13.3
Genomic location
9: 34647490 (GRCh38) GRCh38 UCSC
9: 34647487 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.34647487A>G
NC_000009.12:g.34647490A>G
NG_009029.2:g.5902A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000009.12:34647489:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00005
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA312562
Genetic Testing Registry (GTR): GTR000500512
dbSNP: rs111033661
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, multiple submitters, no conflicts Sep 30, 2020 RCV000022073.15
Pathogenic 2 criteria provided, multiple submitters, no conflicts Apr 26, 2017 RCV000185912.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GALT - - GRCh38
GRCh37
447 522

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Oct 23, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000228800.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Apr 26, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000238865.8
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.253-2A>G splice site mutation in the GALT gene has been previously reported in Hispanic individuals with galactosemia (Yang et al., 2002). This mutation destroys … (more)
Pathogenic
(Sep 30, 2020)
criteria provided, single submitter
Method: clinical testing
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: germline
Invitae
Accession: SCV000631390.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects an acceptor splice site in intron 2 of the GALT gene. It is expected to disrupt RNA splicing and likely results … (more)
Pathogenic
(Jun 13, 2016)
criteria provided, single submitter
Method: clinical testing
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000695685.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (9)
Comment:
Variant summary: The GALT c.253-2A>G variant involves the alteration of a conserved intronic nucleotide. One in silico tool predicts a damaging outcome for this variant. … (more)
Pathogenic
(Dec 04, 2019)
criteria provided, single submitter
Method: clinical testing
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: unknown
Myriad Women's Health, Inc.
Accession: SCV001193839.2
Submitted: (Jun 18, 2020)
Evidence details
Publications
PubMed (4)
Comment:
NM_000155.3(GALT):c.253-2A>G(aka IVS2-2A>G) is classified as pathogenic in the context of galactosemia. Sources cited for classification include the following: PMID 22944367, 18956253, 19375122 and 11754113. Classification … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Novel GALT variations and mutation spectrum in the Korean population with decreased galactose-1-phosphate uridyltransferase activity. Choi R BMC medical genetics 2014 PMID: 25124065
Mutational analysis of the GALT gene in Filipino patients. Estrada SC The Kobe journal of medical sciences 2013 PMID: 24045215
Mutation spectrum in the French cohort of galactosemic patients and structural simulation of 27 novel missense variations. Boutron A Molecular genetics and metabolism 2012 PMID: 22944367
An update on the molecular analysis of classical galactosaemia patients diagnosed in Spain and Portugal: 7 new mutations in 17 new families. Gort L Medicina clinica 2009 PMID: 19375122
Low allelic heterogeneity in a sample of Mexican patients with classical galactosaemia. Velázquez-Aragón J Journal of inherited metabolic disease 2008 PMID: 18956253
Simultaneous amplification, detection, and analysis of common mutations in the galactose-1-phosphate uridyl transferase gene. Jama M The Journal of molecular diagnostics : JMD 2007 PMID: 17884932
Combination of enzyme analysis, allele-specific PCR and sequencing to detect mutations in the GALT gene. Calderon FR Journal of inherited metabolic disease 2007 PMID: 17876724
Characterization of an unusual deletion of the galactose-1-phosphate uridyl transferase (GALT) gene. Coffee B Genetics in medicine : official journal of the American College of Medical Genetics 2006 PMID: 17079880
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
Molecular analysis in newborns from Texas affected with galactosemia. Yang YP Human mutation 2002 PMID: 11754113
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GALT - - - -

Text-mined citations for rs111033661...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021