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NM_000155.4(GALT):c.508-2_509del AND Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 7, 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:
RCV001378380.6

Allele description [Variation Report for NM_000155.4(GALT):c.508-2_509del]

NM_000155.4(GALT):c.508-2_509del

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.508-2_509del
HGVS:
  • NC_000009.12:g.34648113_34648116del
  • NG_009029.2:g.6525_6528del
  • NG_028966.1:g.929_932del
  • NM_000155.4:c.508-2_509delMANE SELECT
  • NM_001258332.2:c.181-2_182del
  • NC_000009.11:g.34648107_34648110del
  • NC_000009.11:g.34648110_34648113del
Links:
dbSNP: rs2132343638
NCBI 1000 Genomes Browser:
rs2132343638
Molecular consequence:
  • NM_000155.4:c.508-2_509del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001258332.2:c.181-2_182del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase
Synonyms:
GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE DEFICIENCY; Galactose-1-phosphate uridyltransferase deficiency; Transferase Deficiency Galactosemia; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009258; MedGen: C0268151; Orphanet: 352; Orphanet: 79239; OMIM: 230400

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001575932Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 7, 2023) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Mutation spectrum in the French cohort of galactosemic patients and structural simulation of 27 novel missense variations.

Boutron A, Marabotti A, Facchiano A, Cheillan D, Zater M, Oliveira C, Costa C, Labrune P, Brivet M; French Galactosemia Working Group..

Mol Genet Metab. 2012 Nov;107(3):438-47. doi: 10.1016/j.ymgme.2012.07.025. Epub 2012 Aug 6.

PubMed [citation]
PMID:
22944367
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001575932.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This variant results in the deletion of part of exon 6 (c.508-2_509del) of the GALT gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in GALT are known to be pathogenic (PMID: 22944367). This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with classic galactosemia (PMID: 31194895). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 1067186). Studies have shown that this variant is associated with inconclusive levels of altered splicing (PMID: 31194895). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Feb 28, 2024