NM_000155.4(GALT):c.611G>C (p.Arg204Pro) AND Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 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:: RCV003504547.2

Allele description [Variation Report for NM_000155.4(GALT):c.611G>C (p.Arg204Pro)]

NM_000155.4(GALT):c.611G>C (p.Arg204Pro)

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.611G>C (p.Arg204Pro)

HGVS:

NC_000009.12:g.34648380G>C
NG_009029.2:g.6792G>C
NG_028966.1:g.1196G>C
NM_000155.4:c.611G>CMANE SELECT
NM_001258332.2:c.284G>C
NP_000146.2:p.Arg204Pro
NP_001245261.1:p.Arg95Pro
NC_000009.11:g.34648377G>C
P07902:p.Arg204Pro

Protein change:

R95P

Links:

UniProtKB: P07902#VAR_008045; dbSNP: rs111033740

NCBI 1000 Genomes Browser:

rs111033740

Molecular consequence:

NM_000155.4:c.611G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001258332.2:c.284G>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004294298	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (May 4, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 20213376, 34030713, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004294298

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(May 4, 2023)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Molecular and clinical analysis of patients with classic and Duarte galactosemia in western Hungary.

Milánkovics I, Schuler A, Kámory E, Csókay B, Fodor F, Somogyi C, Németh K, Fekete G.

Wien Klin Wochenschr. 2010 Feb;122(3-4):95-102. doi: 10.1007/s00508-010-1311-7.

PubMed [citation]

PMID:: 20213376

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

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004294298.1

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

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. 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. This missense change has been observed in individual(s) with galactose-1-phosphate uridylyltransferase deficiency (PMID: 20213376, 34030713). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 204 of the GALT protein (p.Arg204Pro).

#	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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