VCV000039372.29 - ClinVar

NM_000155.4(GALT):c.652C>T (p.Leu218=)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(14)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Benign; other

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

This variant is part of a Haplotype

NM_000155.3(GALT):c.[652C>T;c.940A>G]

Identifiers

NM_000155.4(GALT):c.652C>T (p.Leu218=)

Variation ID: 39372 Accession: VCV000039372.29

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 9p13.3 9: 34648421 (GRCh38) [ NCBI UCSC ] 9: 34648418 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Apr 4, 2013	Sep 29, 2024	Feb 1, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_000155.4:c.652C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000146.2:p.Leu218=	synonymous
NM_001258332.2:c.325C>T	NP_001245261.1:p.Leu109=	synonymous
NC_000009.12:g.34648421C>T
NC_000009.11:g.34648418C>T
NG_009029.2:g.6833C>T
NG_028966.1:g.1237C>T

... more HGVS ... less HGVS

Protein change

Other names

L218L

Canonical SPDI

NC_000009.12:34648420:C:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.03095 (T)

Allele frequency Help The frequency of the allele represented by this VCV record.

The Genome Aggregation Database (gnomAD), exomes 0.03735

Exome Aggregation Consortium (ExAC) 0.03832

Trans-Omics for Precision Medicine (TOPMed) 0.02333

The Genome Aggregation Database (gnomAD) 0.02537

1000 Genomes Project 30x 0.02983

1000 Genomes Project 0.03095

Links

ClinGen: CA220423 Genetic Testing Registry (GTR): GTR000500512 OMIM: 606999.0012 dbSNP: rs2070075 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
GALT		-	-	GRCh38 GRCh37	718	882

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase	Benign (7)	criteria provided, multiple submitters, no conflicts	Feb 1, 2024	RCV000032587.29
not provided	Benign; other (4)	criteria provided, multiple submitters, no conflicts	Jul 15, 2021	RCV000078233.23
Galactosemia	Likely benign (1)	no assertion criteria provided	Mar 29, 2017	RCV001826537.9
not specified	Benign (2)	no assertion criteria provided	-	RCV001701572.11

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Benign (Jul 15, 2021)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001988713.2 First in ClinVar: Nov 06, 2021 Last updated: Mar 04, 2023
Benign (Nov 29, 2023)	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024) Method: clinical testing	Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase Affected status: unknown Allele origin: germline	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories Accession: SCV000885499.4 First in ClinVar: Dec 06, 2016 Last updated: Feb 20, 2024
Benign (May 18, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase Affected status: no Allele origin: germline	Genome-Nilou Lab Accession: SCV001623031.1 First in ClinVar: May 23, 2021 Last updated: May 23, 2021	Sex: mixed
Benign (Feb 11, 2015)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not provided Affected status: not provided Allele origin: germline	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics Accession: SCV000281539.1 First in ClinVar: Jun 08, 2016 Last updated: Jun 08, 2016
other (Feb 05, 2015)	criteria provided, single submitter (EGL Classification Definitions 2015) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Eurofins Ntd Llc (ga) Accession: SCV000110071.8 First in ClinVar: Jan 17, 2014 Last updated: Dec 06, 2016	Other databases http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GALT Number of individuals with the variant: 90 Sex: mixed
benign (Aug 18, 2011)	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) Method: curation, clinical testing	Galactosemia (autosomal unknown) Affected status: yes, unknown Allele origin: germline	Women's Health and Genetics/Laboratory Corporation of America, LabCorp Accession: SCV000052472.2 First in ClinVar: Apr 04, 2013 Last updated: Apr 11, 2022	Publications: PubMed (2) PubMed: 10408771‚ 10424825 Comment: Converted during submission to Benign. Observation 1: Tissue: Blood Observation 2: Tissue: Blood
Benign (Feb 01, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000631395.6 First in ClinVar: Dec 26, 2017 Last updated: Feb 20, 2024
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005272555.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024
Benign (Mar 06, 2018)	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000479763.3 First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020	Comment: This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more) This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
Benign (Jul 19, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase Affected status: unknown Allele origin: unknown	Fulgent Genetics, Fulgent Genetics Accession: SCV002805435.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022
Likely benign (Mar 29, 2017)	no assertion criteria provided Method: clinical testing	Galactosemia Affected status: unknown Allele origin: germline	Natera, Inc. Accession: SCV002085227.1 First in ClinVar: Feb 13, 2022 Last updated: Feb 13, 2022
Benign (Sep 23, 2014)	no assertion criteria provided Method: literature only	Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase Affected status: yes Allele origin: germline	GeneReviews Accession: SCV000257444.1 First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013	Publications: PubMed (2) PubMed: 9012409‚ 11286503 Other databases http://www.ncbi.nlm.nih.gov/book… http://www.ncbi.nlm.nih.gov/books/NBK258640/
Benign (-)	no assertion criteria provided Method: clinical testing	not specified Affected status: yes Allele origin: germline	Genome Diagnostics Laboratory, University Medical Center Utrecht Additional submitter: Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV001930366.1 First in ClinVar: Sep 26, 2021 Last updated: Sep 26, 2021
Benign (-)	no assertion criteria provided Method: clinical testing	not specified Affected status: yes Allele origin: germline	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ Additional submitter: Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV001952222.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021
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Comment:

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Duarte Variant Galactosemia.	Adam MP	-	2020	PMID: 25473725
Functional analysis of the human galactose-1-phosphate uridyltransferase promoter in Duarte and LA variant galactosemia.	Elsas LJ	Molecular genetics and metabolism	2001	PMID: 11286503
Presence of a deletion in the 5' upstream region of the GALT gene in Duarte (D2) alleles.	Kozák L	Journal of medical genetics	1999	PMID: 10424825
Classical galactosemia and mutations at the galactose-1-phosphate uridyl transferase (GALT) gene.	Tyfield L	Human mutation	1999	PMID: 10408771
Molecular basis for Duarte and Los Angeles variant galactosemia.	Langley SD	American journal of human genetics	1997	PMID: 9012409
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GALT	-	-	-	-

Text-mined citations for rs2070075 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 27, 2024

ClinVar Genomic variation as it relates to human health

NM_000155.4(GALT):c.652C>T (p.Leu218=)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs2070075 ...