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NM_000155.4(GALT):c.568T>C (p.Trp190Arg) AND GALT-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 6, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003398667.4

Allele description [Variation Report for NM_000155.4(GALT):c.568T>C (p.Trp190Arg)]

NM_000155.4(GALT):c.568T>C (p.Trp190Arg)

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.568T>C (p.Trp190Arg)
HGVS:
  • NC_000009.12:g.34648337T>C
  • NG_009029.2:g.6749T>C
  • NG_028966.1:g.1153T>C
  • NM_000155.4:c.568T>CMANE SELECT
  • NM_001258332.2:c.241T>C
  • NP_000146.2:p.Trp190Arg
  • NP_000146.2:p.Trp190Arg
  • NP_001245261.1:p.Trp81Arg
  • NC_000009.11:g.34648334T>C
  • NM_000155.3:c.568T>C
Protein change:
W190R
Links:
dbSNP: rs398123184
NCBI 1000 Genomes Browser:
rs398123184
Molecular consequence:
  • NM_000155.4:c.568T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258332.2:c.241T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
GALT-related disorder
Synonyms:
GALT-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004112151PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jul 6, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004112151.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The GALT c.568T>C variant is predicted to result in the amino acid substitution p.Trp190Arg. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as likely pathogenic by a single submitter in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/92520/). Internally, this variant was observed in a patient with enzymatically confirmed reduced galactose-1-phosphate uridylyltransferase activity and parental studies in that patient confirmed the c.568T>C (p.Trp190Arg) variant was in trans with a pathogenic GALT variant. Taken together, we interpret this variant as likely pathogenic.

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

Last Updated: Nov 10, 2024