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NM_000154.2(GALK1):c.593C>T (p.Ala198Val)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Dec 28, 2020)
Last evaluated:
Nov 12, 2019
Accession:
VCV000005633.7
Variation ID:
5633
Description:
single nucleotide variant
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NM_000154.2(GALK1):c.593C>T (p.Ala198Val)

Allele ID
20672
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.1
Genomic location
17: 75763032 (GRCh38) GRCh38 UCSC
17: 73759113 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.73759113G>A
NC_000017.11:g.75763032G>A
NM_000154.2:c.593C>T MANE Select NP_000145.1:p.Ala198Val missense
... more HGVS
Protein change
A198V
Other names
-
Canonical SPDI
NC_000017.11:75763031:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00300 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00107
1000 Genomes Project 0.00300
The Genome Aggregation Database (gnomAD), exomes 0.00124
Links
ClinGen: CA117661
UniProtKB: P51570#VAR_015746
OMIM: 604313.0006
dbSNP: rs80084721
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 6 criteria provided, conflicting interpretations Nov 12, 2019 RCV000005987.11
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GALK1 - - GRCh38
GRCh37
203 351

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Dec 20, 2017)
criteria provided, single submitter
Method: clinical testing
Deficiency of galactokinase
Allele origin: unknown
Counsyl
Accession: SCV000800800.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (3)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Deficiency of galactokinase
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001285771.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (5)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Uncertain significance
(Nov 12, 2019)
criteria provided, single submitter
Method: clinical testing
Deficiency of galactokinase
Allele origin: germline
Invitae
Accession: SCV000631404.4
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces alanine with valine at codon 198 of the GALK1 protein (p.Ala198Val). The alanine residue is highly conserved and there is a … (more)
Uncertain significance
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Deficiency of galactokinase
Allele origin: unknown
Mendelics
Accession: SCV001140835.1
Submitted: (Oct 22, 2019)
Evidence details
Pathogenic
(Apr 01, 2001)
no assertion criteria provided
Method: literature only
GALACTOSEMIA II
Allele origin: germline
OMIM
Accession: SCV000026169.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Jan 07, 2020)
no assertion criteria provided
Method: clinical testing
Deficiency of galactokinase
Allele origin: germline
Natera, Inc.
Accession: SCV001459342.1
Submitted: (Dec 28, 2020)
Evidence details

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
Galactokinase deficiency induced cataracts in Indian infants: identification of 4 novel mutations in GALK gene. Singh R Current eye research 2012 PMID: 22632133
Features and outcome of galactokinase deficiency in children diagnosed by newborn screening. Hennermann JB Journal of inherited metabolic disease 2011 PMID: 21290184
The effect of a Pro²⁸Thr point mutation on the local structure and stability of human galactokinase enzyme-a theoretical study. Jójárt B Journal of molecular modeling 2011 PMID: 21264483
Galactokinase gene mutations and age-related cataract. Lack of association in an Italian population. Maraini G Molecular vision 2003 PMID: 12942049
Functional analysis of disease-causing mutations in human galactokinase. Timson DJ European journal of biochemistry 2003 PMID: 12694189
A genetic factor for age-related cataract: identification and characterization of a novel galactokinase variant, "Osaka," in Asians. Okano Y American journal of human genetics 2001 PMID: 11231902

Text-mined citations for rs80084721...

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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 Aug 27, 2021