NM_000155.4(GALT):c.813G>C (p.Glu271Asp) AND Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 4, 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:: RCV003062205.3

Allele description [Variation Report for NM_000155.4(GALT):c.813G>C (p.Glu271Asp)]

NM_000155.4(GALT):c.813G>C (p.Glu271Asp)

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.813G>C (p.Glu271Asp)

HGVS:

NC_000009.12:g.34648887G>C
NG_009029.2:g.7299G>C
NG_028966.1:g.1703G>C
NM_000155.4:c.813G>CMANE SELECT
NM_001258332.2:c.486G>C
NP_000146.2:p.Glu271Asp
NP_001245261.1:p.Glu162Asp
NC_000009.11:g.34648884G>C

Protein change:

E162D

Molecular consequence:

NM_000155.4:c.813G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001258332.2:c.486G>C - missense variant - [Sequence Ontology: SO:0001583]

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

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Uncultured Helicobacter sp. clone B9 23S ribosomal RNA gene, partial sequence
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003440886	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 4, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 34030713, 25592817, 29252199, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003440886

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 4, 2023)

germline

clinical testing

PubMed (4)
[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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The genetic basis of classical galactosaemia in Polish patients.

Jezela-Stanek A, Bauer A, Wertheim-Tysarowska K, Bal J, Rygiel AM, Sykut-Cegielska J.

Orphanet J Rare Dis. 2021 May 24;16(1):239. doi: 10.1186/s13023-021-01869-3.

PubMed [citation]

PMID:: 34030713
PMCID:: PMC8142503

Clinical and molecular spectra in galactosemic patients from neonatal screening in northeastern Italy: structural and functional characterization of new variations in the galactose-1-phosphate uridyltransferase (GALT) gene.

Viggiano E, Marabotti A, Burlina AP, Cazzorla C, D'Apice MR, Giordano L, Fasan I, Novelli G, Facchiano A, Burlina AB.

Gene. 2015 Apr 1;559(2):112-8. doi: 10.1016/j.gene.2015.01.013. Epub 2015 Jan 13.

PubMed [citation]

PMID:: 25592817

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003440886.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 271 of the GALT protein (p.Glu271Asp). This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Glu271 amino acid residue in GALT. Other variant(s) that disrupt this residue have been observed in individuals with GALT-related conditions (PMID: 34030713), which suggests that this may be a clinically significant amino acid residue. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GALT protein function. ClinVar contains an entry for this variant (Variation ID: 2136758). This missense change has been observed in individual(s) with clinical features of galactosemia (PMID: 25592817, 29252199).

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

Last Updated: Sep 29, 2024

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