NM_000155.4(GALT):c.289_291del (p.Asn97del) AND Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 13, 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:: RCV001389960.8

Allele description [Variation Report for NM_000155.4(GALT):c.289_291del (p.Asn97del)]

NM_000155.4(GALT):c.289_291del (p.Asn97del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

9p13.3

Genomic location:

Preferred name:

NM_000155.4(GALT):c.289_291del (p.Asn97del)

HGVS:

NC_000009.12:g.34647528_34647530del
NG_009029.2:g.5940_5942del
NG_028966.1:g.344_346del
NM_000155.4:c.289_291delMANE SELECT
NM_001258332.2:c.50+270_50+272del
NP_000146.2:p.Asn97del
NC_000009.11:g.34647523_34647525del
NC_000009.11:g.34647525_34647527del
NM_000155.3:c.289_291del
NM_000155.3:c.289_291delAAC

Protein change:

N97del

Links:

dbSNP: rs398123179

NCBI 1000 Genomes Browser:

rs398123179

Molecular consequence:

NM_000155.4:c.289_291del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001258332.2:c.50+270_50+272del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV001591521	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 13, 2024)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 25268296, 27176039, 7550229, 15633893, 22944367, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001591521

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 13, 2024)

germline

clinical testing

PubMed (6)
[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

Endogenous galactose formation in galactose-1-phosphate uridyltransferase deficiency.

Schadewaldt P, Kamalanathan L, Hammen HW, Kotzka J, Wendel U.

Arch Physiol Biochem. 2014 Dec;120(5):228-39. doi: 10.3109/13813455.2014.962547. Epub 2014 Sep 30.

PubMed [citation]

PMID:: 25268296

Clinical profile and molecular characterization of Galactosemia in Brazil: identification of seven novel mutations.

Garcia DF, Camelo JS Jr, Molfetta GA, Turcato M, Souza CF, Porta G, Steiner CE, Silva WA Jr.

BMC Med Genet. 2016 May 12;17(1):39. doi: 10.1186/s12881-016-0300-8.

PubMed [citation]

PMID:: 27176039
PMCID:: PMC4866286

See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001591521.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This variant, c.289_291del, results in the deletion of 1 amino acid(s) of the GALT protein (p.Asn97del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs770349232, gnomAD 0.0009%). This variant has been observed in individuals with galactosemia (PMID: 22944367, 25268296, 27176039; Invitae). ClinVar contains an entry for this variant (Variation ID: 92515). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant disrupts the p.Asn97 amino acid residue in GALT. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7550229, 15633893, 22944367). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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