NM_000155.4(GALT):c.893T>C (p.Met298Thr) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely pathogenic(1);Uncertain significance(1) (Last evaluated: Dec 22, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000433820.2

Allele description [Variation Report for NM_000155.4(GALT):c.893T>C (p.Met298Thr)]

NM_000155.4(GALT):c.893T>C (p.Met298Thr)

Gene:
GALT:galactose-1-phosphate uridylyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9p13.3
Genomic location:
Preferred name:
NM_000155.4(GALT):c.893T>C (p.Met298Thr)
HGVS:
  • NC_000009.12:g.34649070T>C
  • NG_009029.2:g.7482T>C
  • NG_028966.1:g.1886T>C
  • NM_000155.4:c.893T>CMANE SELECT
  • NM_001258332.1:c.566T>C
  • NP_000146.2:p.Met298Thr
  • NP_001245261.1:p.Met189Thr
  • NC_000009.11:g.34649067T>C
  • NM_000155.2:c.893T>C
Protein change:
M189T
Links:
dbSNP: rs886042064
NCBI 1000 Genomes Browser:
rs886042064
Molecular consequence:
  • NM_000155.4:c.893T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258332.1:c.566T>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000330957EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Sep 29, 2015)
germlineclinical testing

Citation Link,

SCV000534681GeneDxcriteria provided, single submitter
Likely pathogenic
(Dec 22, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown2not providednot providednot providednot providedclinical testing

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000330957.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided2not providednot providednot provided

From GeneDx, SCV000534681.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The M298T variant in the GALT gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The M298T variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The M298T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. The M298T variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 27, 2021

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