NM_000155.4(GALT):c.821-7A>G AND Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase

Clinical significance:Pathogenic (Last evaluated: Oct 23, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000804257.4

Allele description [Variation Report for NM_000155.4(GALT):c.821-7A>G]

NM_000155.4(GALT):c.821-7A>G

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.821-7A>G
HGVS:
  • NC_000009.12:g.34648991A>G
  • NG_009029.2:g.7403A>G
  • NG_028966.1:g.1807A>G
  • NM_000155.4:c.821-7A>GMANE SELECT
  • NM_001258332.2:c.494-7A>G
  • NC_000009.11:g.34648988A>G
  • NM_000155.3:c.821-7A>G
Links:
dbSNP: rs767337193
NCBI 1000 Genomes Browser:
rs767337193
Molecular consequence:
  • NM_000155.4:c.821-7A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258332.2:c.494-7A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase (GALAC1)
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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000944157Invitaecriteria provided, single submitter
Pathogenic
(Oct 23, 2020)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV001163246Baylor Geneticscriteria provided, single submitter
Pathogenicgermlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Novel GALT variations and mutation spectrum in the Korean population with decreased galactose-1-phosphate uridyltransferase activity.

Choi R, Jo KI, Ko DH, Lee DH, Song J, Jin DK, Ki CS, Lee SY, Kim JW, Lee YW, Park HD.

BMC Med Genet. 2014 Aug 15;15:94. doi: 10.1186/s12881-014-0094-5.

PubMed [citation]
PMID:
25124065
PMCID:
PMC4236512

Molecular and biochemical characterization of the GALT gene in Korean patients with galactose-1-phosphate uridyltransferase deficiency.

Ko DH, Chang HE, Song SH, Park KU, Kim JQ, Kim MC, Song YH, Hong YH, Lee DH, Song J.

Clin Chim Acta. 2010 Oct 9;411(19-20):1506-10. doi: 10.1016/j.cca.2010.06.008. Epub 2010 Jun 11.

PubMed [citation]
PMID:
20547145
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV000944157.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change falls in intron 8 of the GALT gene. It does not directly change the encoded amino acid sequence of the GALT protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs767337193, ExAC 0.08%). This variant has been observed on the opposite chromosome (in trans) from other pathogenic variants in individuals with GALT-related conditions (PMID: 20547145, 25124065). This finding is consistent with autosomal recessive inheritance, and suggests that this variant contributes to disease. ClinVar contains an entry for this variant (Variation ID: 649344). Studies have shown that this variant is associated with skipping of exon 9 but is expected to preserve the integrity of the reading frame (PMID: 20547145) For these reasons, this variant has been classified as Pathogenic.

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

From Baylor Genetics, SCV001163246.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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