NC_000009.11:g.(?_34646573)_(34649581_?)del AND Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 17, 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:: RCV004581873.2

Allele description [Variation Report for NC_000009.11:g.(?_34646573)_(34649581_?)del]

NC_000009.11:g.(?_34646573)_(34649581_?)del

Gene:: GALT:galactose-1-phosphate uridylyltransferase [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 9p13.3
Genomic location:: Chr9: 34646573 - 34649581 (on Assembly GRCh37)
Preferred name:: NC_000009.11:g.(?_34646573)_(34649581_?)del
HGVS:: NC_000009.11:g.(?_34646573)_(34649581_?)del
This HGVS expression did not pass validation

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

Recent activity

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mitochondrial adenyl nucleotide antiporter SLC25A23 isoform X17 [Homo sapiens]
mitochondrial adenyl nucleotide antiporter SLC25A23 isoform X17 [Homo sapiens]
gi|2462567614|ref|XP_054178075.1|

Protein
DNA-dependemt RNA polymerase beta subunit, partial [Pasteurellaceae bacterium]
DNA-dependemt RNA polymerase beta subunit, partial [Pasteurellaceae bacterium]
gi|1134677065|gb|APX42648.1|

Protein
Lonepinella sp. strain BR2474 DNA repair protein (recN) gene, partial cds
Lonepinella sp. strain BR2474 DNA repair protein (recN) gene, partial cds
gi|1938963814|gb|MT024712.1|

Nucleotide
PREDICTED: Homo sapiens ADAM metallopeptidase with thrombospondin type 1 motif 1...
PREDICTED: Homo sapiens ADAM metallopeptidase with thrombospondin type 1 motif 14 (ADAMTS14), transcript variant X6, mRNA
gi|2217275603|ref|XM_011539307.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005067214	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 17, 2023)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22944367, 30231941, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005067214

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 17, 2023)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Fertility in classical galactosaemia, a study of N-glycan, hormonal and inflammatory gene interactions.

Colhoun HO, Rubio Gozalbo EM, Bosch AM, Knerr I, Dawson C, Brady J, Galligan M, Stepien K, O'Flaherty R, Catherine Moss C, Peter Barker P, Fitzgibbon M, Doran PP, Treacy EP.

Orphanet J Rare Dis. 2018 Sep 19;13(1):164. doi: 10.1186/s13023-018-0906-3.

PubMed [citation]

PMID:: 30231941
PMCID:: PMC6146524

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005067214.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 1-10 of the GALT gene, which includes the initiator codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GALT are known to be pathogenic (PMID: 22944367). A similar copy number variant has been observed in individual(s) with clinical features of GALT-related disorders (PMID: 30231941). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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