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NM_000155.4(GALT):c.626A>G (p.Tyr209Cys)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Apr 13, 2021)
Last evaluated:
Aug 29, 2020
Accession:
VCV000025231.11
Variation ID:
25231
Description:
single nucleotide variant
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NM_000155.4(GALT):c.626A>G (p.Tyr209Cys)

Allele ID
36565
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9p13.3
Genomic location
9: 34648395 (GRCh38) GRCh38 UCSC
9: 34648392 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P07902:p.Tyr209Cys
NC_000009.11:g.34648392A>G
NC_000009.12:g.34648395A>G
... more HGVS
Protein change
Y100C
Other names
p.Y209C:TAT>TGT
Canonical SPDI
NC_000009.12:34648394:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00001
Links
ClinGen: CA312567
Genetic Testing Registry (GTR): GTR000500512
UniProtKB: P07902#VAR_002596
dbSNP: rs111033744
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 Aug 29, 2020 RCV000022167.16
Pathogenic 3 criteria provided, multiple submitters, no conflicts Apr 13, 2018 RCV000185918.4
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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
445 520

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
pathogenic
(Aug 18, 2011)
criteria provided, single submitter
Method: curation, clinical testing
Galactosemia
(autosomal recessive)
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000052471.1
Submitted: (Aug 18, 2011)
Evidence details
Publications
PubMed (3)
Comment:
Converted during submission to Pathogenic.
Pathogenic
(May 06, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000110069.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Sep 14, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000281374.1
Submitted: (May 19, 2016)
Evidence details
Pathogenic
(Apr 13, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000238871.9
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The Y209C variant is a common pathogenic variant in the Caucasian population and has been reported in several unrelated individuals with galactosemia (Elsas et al., … (more)
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: germline
Baylor Genetics
Accession: SCV001163243.1
Submitted: (Sep 27, 2019)
Evidence details
Likely pathogenic
(Dec 13, 2019)
criteria provided, single submitter
Method: clinical testing
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: unknown
Myriad Women's Health, Inc.
Accession: SCV001193851.2
Submitted: (Jun 18, 2020)
Evidence details
Publications
PubMed (6)
Comment:
NM_000155.3(GALT):c.626A>G(Y209C) is classified as likely pathogenic in the context of galactosemia. Sources cited for classification include the following: PMID 12595586, 10960497, 22693313, 11261429, 10399107 and … (more)
Pathogenic
(Aug 29, 2020)
criteria provided, single submitter
Method: clinical testing
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: germline
Invitae
Accession: SCV000952487.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change replaces tyrosine with cysteine at codon 209 of the GALT protein (p.Tyr209Cys). The tyrosine residue is moderately conserved and there is a … (more)
Pathogenic
(Mar 09, 2021)
no assertion criteria provided
Method: literature only
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: germline
GeneReviews
Accession: SCV000147998.3
Submitted: (Apr 13, 2021)
Evidence details
Publications
PubMed (1)
BookShelf: NBK1518
Comment:
Severe classic pathogenic variant

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
Classic Galactosemia and Clinical Variant Galactosemia Berry GT - 2021 PMID: 20301691
N- and O-linked glycosylation of total plasma glycoproteins in galactosemia. Liu Y Molecular genetics and metabolism 2012 PMID: 22743281
Problems with the new born screen for galactosaemia. Malone JI BMJ case reports 2011 PMID: 22693313
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
Prevention of a molecular misdiagnosis in galactosemia. Barbouth D Genetics in medicine : official journal of the American College of Medical Genetics 2006 PMID: 16540753
Verbal dyspraxia and galactosemia. Webb AL Pediatric research 2003 PMID: 12595586
Molecular detection of galactosemia mutations by PCR-ELISA. Muralidharan K Methods in molecular biology (Clifton, N.J.) 2003 PMID: 12491926
Outcomes analysis of verbal dyspraxia in classic galactosemia. Robertson A Genetics in medicine : official journal of the American College of Medical Genetics 2000 PMID: 11397328
Galactose breath testing distinguishes variant and severe galactose-1-phosphate uridyltransferase genotypes. Berry GT Pediatric research 2000 PMID: 10960497
Urine and plasma galactitol in patients with galactose-1-phosphate uridyltransferase deficiency galactosemia. Palmieri M Metabolism: clinical and experimental 1999 PMID: 10535394
Classical galactosemia and mutations at the galactose-1-phosphate uridyl transferase (GALT) gene. Tyfield L Human mutation 1999 PMID: 10408771
Molecular characterization of Polish patients with classical galactosaemia. Zekanowski C Journal of inherited metabolic disease 1999 PMID: 10399107
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 - - - -

Text-mined citations for rs111033744...

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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 20, 2021