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NM_000155.4(GALT):c.512T>C (p.Phe171Ser)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Aug 19, 2021)
Last evaluated:
Jul 30, 2020
Accession:
VCV000003616.14
Variation ID:
3616
Description:
single nucleotide variant
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NM_000155.4(GALT):c.512T>C (p.Phe171Ser)

Allele ID
18655
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9p13.3
Genomic location
9: 34648119 (GRCh38) GRCh38 UCSC
9: 34648116 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P07902:p.Phe171Ser
NC_000009.12:g.34648119T>C
NG_009029.2:g.6531T>C
... more HGVS
Protein change
F171S, F62S
Other names
-
Canonical SPDI
NC_000009.12:34648118:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00013
The Genome Aggregation Database (gnomAD), exomes 0.00000
Exome Aggregation Consortium (ExAC) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
dbSNP: rs111033715
ClinGen: CA340106
UniProtKB: P07902#VAR_002583
OMIM: 606999.0008
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 Jul 30, 2020 RCV000003800.21
Pathogenic 2 criteria provided, multiple submitters, no conflicts Jun 25, 2020 RCV000723392.4
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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
(Dec 12, 2019)
criteria provided, single submitter
Method: clinical testing
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000885500.3
Submitted: (Dec 11, 2020)
Evidence details
Comment:
The GALT c.512T>C; p.Phe171Ser variant (rs111033715) is described in several studies to have reduced or a complete loss of enzymatic activity (Crews 2000, McCorvie 2013, … (more)
Pathogenic
(Sep 22, 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: SCV000695694.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (12)
Comment:
Variant summary: The GALT c.512T>C (p.Phe171Ser) variant is located in the Galactose-1-phosphate uridyl transferase, N-terminal domain causing a missense change involving a conserved nucleotide with … (more)
Pathogenic
(Feb 13, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000110063.8
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (3)
Other databases
http://www.egl-eurofins.com/emvc…
Likely pathogenic
(Nov 15, 2019)
criteria provided, single submitter
Method: clinical testing
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: unknown
Myriad Women's Health, Inc.
Accession: SCV001194025.2
Submitted: (Jun 18, 2020)
Evidence details
Publications
PubMed (7)
Comment:
NM_000155.3(GALT):c.512T>C(F171S) is classified as likely pathogenic in the context of galactosemia. Sources cited for classification include the following: PMID 23583749, 23022339, 22944367, 10811638, 10960497, 11152465 … (more)
Pathogenic
(Jul 30, 2020)
criteria provided, single submitter
Method: clinical testing
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Allele origin: germline
Invitae
Accession: SCV000631393.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (8)
Comment:
This sequence change replaces phenylalanine with serine at codon 171 of the GALT protein (p.Phe171Ser). The phenylalanine residue is highly conserved and there is a … (more)
Pathogenic
(Jun 25, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001792432.1
Submitted: (Aug 19, 2021)
Evidence details
Comment:
Published functional studies demonstrate a significant decrease in GALT enzyme activity (McCorvie et al., 2013; Crews et al., 2000; Riehman et al., 2001); In silico … (more)
Pathogenic
(Jun 23, 1992)
no assertion criteria provided
Method: literature only
GALACTOSEMIA I
Allele origin: germline
OMIM
Accession: SCV000023965.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)

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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Clinical profile and molecular characterization of Galactosemia in Brazil: identification of seven novel mutations. Garcia DF BMC medical genetics 2016 PMID: 27176039
Misfolding of galactose 1-phosphate uridylyltransferase can result in type I galactosemia. McCorvie TJ Biochimica et biophysica acta 2013 PMID: 23583749
Biochemical and molecular characterization of GALT gene from Indian galactosemia patients: identification of 10 novel mutations and their structural and functional implications. Singh R Clinica chimica acta; international journal of clinical chemistry 2012 PMID: 23022339
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
Analysis of galactosemia-linked mutations of GALT enzyme using a computational biology approach. Facchiano A Protein engineering, design & selection : PEDS 2010 PMID: 20008339
Low allelic heterogeneity in a sample of Mexican patients with classical galactosaemia. Velázquez-Aragón J Journal of inherited metabolic disease 2008 PMID: 18956253
Relationship between genotype, activity, and galactose sensitivity in yeast expressing patient alleles of human galactose-1-phosphate uridylyltransferase. Riehman K The Journal of biological chemistry 2001 PMID: 11152465
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
Functional consequence of substitutions at residue 171 in human galactose-1-phosphate uridylyltransferase. Crews C The Journal of biological chemistry 2000 PMID: 10811638
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 and biochemical basis of galactosemia. Wang BB Molecular genetics and metabolism 1998 PMID: 9635294
A common mutation associated with the Duarte galactosemia allele. Elsas LJ American journal of human genetics 1994 PMID: 8198125
Molecular characterization of two galactosemia mutations and one polymorphism: implications for structure-function analysis of human galactose-1-phosphate uridyltransferase. Reichardt JK Biochemistry 1992 PMID: 1610789
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GALT - - - -

Text-mined citations for rs111033715...

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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