NM_000155.4(GALT):c.752_753delinsCT (p.Tyr251Ser) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 22, 2024
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:: RCV004586664.1

Allele description [Variation Report for NM_000155.4(GALT):c.752_753delinsCT (p.Tyr251Ser)]

NM_000155.4(GALT):c.752_753delinsCT (p.Tyr251Ser)

Gene:

GALT:galactose-1-phosphate uridylyltransferase [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

9p13.3

Genomic location:

Preferred name:

NM_000155.4(GALT):c.752_753delinsCT (p.Tyr251Ser)

HGVS:

NC_000009.12:g.34648826_34648827delinsCT
NG_009029.2:g.7238_7239delinsCT
NG_028966.1:g.1642_1643delinsCT
NM_000155.4:c.752_753delinsCTMANE SELECT
NM_001258332.2:c.425_426delinsCT
NP_000146.2:p.Tyr251Ser
NP_001245261.1:p.Tyr142Ser
NC_000009.11:g.34648823_34648824delACinsCT
NC_000009.11:g.34648823_34648824delinsCT

Protein change:

Y142S

Links:

dbSNP: rs886043390

NCBI 1000 Genomes Browser:

rs886043390

Molecular consequence:

NM_000155.4:c.752_753delinsCT - missense variant - [Sequence Ontology: SO:0001583]
NM_001258332.2:c.425_426delinsCT - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005077063	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Apr 22, 2024)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11754113, 11397328 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005077063

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Apr 22, 2024)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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 analysis in newborns from Texas affected with galactosemia.

Yang YP, Corley N, Garcia-Heras J.

Hum Mutat. 2002 Jan;19(1):82-3.

PubMed [citation]

PMID:: 11754113

Outcomes analysis of verbal dyspraxia in classic galactosemia.

Robertson A, Singh RH, Guerrero NV, Hundley M, Elsas LJ.

Genet Med. 2000 Mar-Apr;2(2):142-8.

PubMed [citation]

PMID:: 11397328

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005077063.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: GALT c.752_753delinsCT (p.Tyr251Ser) results in a non-conservative amino acid change located in the Galactose-1-phosphate uridyl transferase, C-terminal (IPR005850) of the encoded protein sequence. Three of three in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 1613432 control chromosomes (gnomAD v4.0.0). This frequency is not significantly higher than estimated for a pathogenic variant in GALT causing Galactosemia (1.2e-05 vs 0.0029), allowing no conclusion about variant significance. c.752_753delinsCT has been reported in the literature in individuals affected with Galactosemia (Yang_2002, Robertson_2000). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 11397328, 11754113). ClinVar contains an entry for this variant (Variation ID: 286433). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

#	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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