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NM_000155.2(GALT):c.-119_-116delGTCA

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Interpretation:
Pathogenic/Likely pathogenic, other​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Sep 20, 2021)
Last evaluated:
Jul 15, 2021
Accession:
VCV000025111.12
Variation ID:
25111
Description:
4bp deletion
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NM_000155.2(GALT):c.-119_-116delGTCA

Allele ID
36445
Variant type
Deletion
Variant length
4 bp
Cytogenetic location
9p13.3
Genomic location
9: 34646576-34646579 (GRCh38) GRCh38 UCSC
9: 34646583-34646586 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_000155.3:c.-119_-116delGTCA
NM_000155.4:c.-119_-116delGTCA MANE Select
NC_000009.12:g.34646578_34646581GTCA[2]
NG_009029.2:g.4990_4993GTCA[2]
Protein change
-
Other names
-
Canonical SPDI
NC_000009.12:34646575:CAGTCAGTCAGTCA:CAGTCAGTCA
Functional consequence
effect on promoter activity [Variation Ontology VariO:0153]
Global minor allele frequency (GMAF)
0.04173 (CAGTCAGTCA)

Allele frequency
-
Links
ClinGen: CA252850
OMIM: 606999.0017
dbSNP: rs111033640
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 5 criteria provided, multiple submitters, no conflicts May 18, 2021 RCV000022037.11
Pathogenic, other 3 criteria provided, multiple submitters, no conflicts Jul 15, 2021 RCV000185922.6
Pathogenic 1 no assertion criteria provided May 1, 2009 RCV000003809.4
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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
(Sep 26, 2019)
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: SCV000052459.3
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (7)
Comment:
Variant summary: GALT c.-119_-116delGTCA involves the deletion of a stretch of four nucleotides located in the GALT promoter region. The variant allele was found at … (more)
Pathogenic
(Jul 15, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000238877.12
Submitted: (Sep 20, 2021)
Evidence details
Comment:
The c.-119_-116delGTCA promoter variant (Duarte 2 variant) causes a reduction in GALT transcription resulting in approximately 50% of normal galactose-1-phosphate uridyltransferase (GALT) activity in individuals … (more)
other
(Jul 23, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000858734.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely pathogenic
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: unknown
Mendelics
Accession: SCV001137799.1
Submitted: (Oct 22, 2019)
Evidence details
Pathogenic
(Nov 02, 2020)
criteria provided, single submitter
Method: clinical testing
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: germline
Invitae
Accession: SCV000959727.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change deletes 4 nucleotides (-119_-116delGTCA) in the GALT promoter without disrupting the protein coding sequence. This variant is present in population databases (rs111033640, … (more)
Pathogenic
(Mar 23, 2021)
criteria provided, single submitter
Method: clinical testing
Not provided
Allele origin: germline
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV001713482.1
Submitted: (May 26, 2021)
Evidence details
Publications
Bookshelf: NBK258640
Likely pathogenic
(May 18, 2021)
criteria provided, single submitter
Method: clinical testing
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: germline
Pars Genome Lab
Accession: SCV001736818.1
Submitted: (Jun 12, 2021)
Evidence details
Pathogenic
(May 01, 2009)
no assertion criteria provided
Method: literature only
GALACTOSEMIA, DUARTE VARIANT
Allele origin: germline
OMIM
Accession: SCV000023974.3
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (4)
Benign
(Sep 23, 2014)
no assertion criteria provided
Method: literature only
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: germline
GeneReviews
Accession: SCV000257439.1
Submitted: (Dec 08, 2015)
Comment:
Reduces promoter function
Evidence details
Publications
PubMed (4)
Other databases
http://www.ncbi.nlm.nih.gov/book…

Functional evidence

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Functional consequence Method Result Submitter Supporting information
effect on promoter activity
GeneReviews
Accession: SCV000257439.1
Submitted: (Dec 08, 2015)
Evidence details
Publications
PubMed (4)
Other databases
http://www.ncbi.nlm.nih.gov/book…

Citations for this variant

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Title Author Journal Year Link
Duarte Variant Galactosemia Fridovich-Keil JL - 2020 PMID: 25473725
Duarte Variant Galactosemia Fridovich-Keil JL - 2020 BookShelf: NBK258640
Laboratory diagnosis of galactosemia: a technical standard and guideline of the American College of Medical Genetics and Genomics (ACMG). Pasquali M Genetics in medicine : official journal of the American College of Medical Genetics 2018 PMID: 29261178
Origins, distribution and expression of the Duarte-2 (D2) allele of galactose-1-phosphate uridylyltransferase. Carney AE Human molecular genetics 2009 PMID: 19224951
Molecular analysis in newborns from Texas affected with galactosemia. Yang YP Human mutation 2002 PMID: 11754113
Galactosemia: deletion in the 5' upstream region of the GALT gene reduces promoter efficiency. Trbusek M Human genetics 2001 PMID: 11479743
Functional analysis of the human galactose-1-phosphate uridyltransferase promoter in Duarte and LA variant galactosemia. Elsas LJ Molecular genetics and metabolism 2001 PMID: 11286503
Presence of a deletion in the 5' upstream region of the GALT gene in Duarte (D2) alleles. Kozák L Journal of medical genetics 1999 PMID: 10424825
The molecular biology of galactosemia. Elsas LJ 2nd Genetics in medicine : official journal of the American College of Medical Genetics 1998 PMID: 11261429
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GALT - - - -
http://www.ncbi.nlm.nih.gov/books/NBK258640/ - - - -

Text-mined citations for rs111033640...

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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