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NM_000155.4(GALT):c.289_291del (p.Asn97del) AND GALT-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 1, 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:
RCV003974957.1

Allele description [Variation Report for NM_000155.4(GALT):c.289_291del (p.Asn97del)]

NM_000155.4(GALT):c.289_291del (p.Asn97del)

Gene:
GALT:galactose-1-phosphate uridylyltransferase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9p13.3
Genomic location:
Preferred name:
NM_000155.4(GALT):c.289_291del (p.Asn97del)
HGVS:
  • NC_000009.12:g.34647528_34647530del
  • NG_009029.2:g.5940_5942del
  • NG_028966.1:g.344_346del
  • NM_000155.4:c.289_291delMANE SELECT
  • NM_001258332.2:c.50+270_50+272del
  • NP_000146.2:p.Asn97del
  • NC_000009.11:g.34647523_34647525del
  • NC_000009.11:g.34647525_34647527del
  • NM_000155.3:c.289_291del
  • NM_000155.3:c.289_291delAAC
Protein change:
N97del
Links:
dbSNP: rs398123179
NCBI 1000 Genomes Browser:
rs398123179
Molecular consequence:
  • NM_000155.4:c.289_291del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001258332.2:c.50+270_50+272del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV004787309PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Nov 1, 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, SCV004787309.1

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

Description

The GALT c.289_291delAAC variant is predicted to result in an in-frame deletion (p.Asn97del). This variant has been reported in the homozygous state or heterozygous state with a second pathogenic GALT variant in individuals with galactosemia (Boutron et al. 2012. PubMed ID: 22944367; Schadewaldt et al. 2014. PubMed ID: 25268296; Garcia et al. 2016. PubMed ID: 27176039). It was also reported in a cohort of Swedish galactosemia patients, although no additional clinical or genetic information was reported about the patient in that cohort (Ohlsson et al. 2019. PubMed ID: 31194895). The p.Asn97 amino acid is involved in Hydrogen bonding with UDP-alpha-D-glucose, and disruption of this amino acid is predicted to impact both the enzyme active site and intersubunit interactions (Boutron et al. 2012. PubMed ID: 22944367; https://www.uniprot.org/uniprotkb/P07902). Several substitutions of the p.Asn97 amino acid (p.Asn97Asp, p.Asn97Ser, p.Asn97Ile) have been reported in patients with galactosemia (Boutron et al. 2012. PubMed ID: 22944367; Shin. 2004. PubMed ID: 15633893; ClinVar ID #811178). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. In summary, this variant is interpreted as pathogenic.

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

Last Updated: Jul 15, 2024