NM_133642.5(LARGE1):c.178C>T (p.Arg60Trp) AND not provided

Germline classification:: Uncertain significance (4 submissions)
Last evaluated:: Jul 17, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001579427.6

Allele description [Variation Report for NM_133642.5(LARGE1):c.178C>T (p.Arg60Trp)]

NM_133642.5(LARGE1):c.178C>T (p.Arg60Trp)

Gene:

LARGE1:LARGE xylosyl- and glucuronyltransferase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q12.3

Genomic location:

Preferred name:

NM_133642.5(LARGE1):c.178C>T (p.Arg60Trp)

HGVS:

NC_000022.11:g.33650597G>A
NG_009929.2:g.274832C>T
NM_001362949.2:c.178C>T
NM_001362951.2:c.178C>T
NM_001362953.2:c.178C>T
NM_001378624.1:c.178C>T
NM_001378625.1:c.178C>T
NM_001378626.1:c.178C>T
NM_001378627.1:c.178C>T
NM_001378628.1:c.178C>T
NM_001378629.1:c.178C>T
NM_004737.6:c.178C>T
NM_004737.7:c.178C>T
NM_133642.5:c.178C>TMANE SELECT
NP_001349878.1:p.Arg60Trp
NP_001349880.1:p.Arg60Trp
NP_001349882.1:p.Arg60Trp
NP_001365553.1:p.Arg60Trp
NP_001365554.1:p.Arg60Trp
NP_001365555.1:p.Arg60Trp
NP_001365556.1:p.Arg60Trp
NP_001365557.1:p.Arg60Trp
NP_001365558.1:p.Arg60Trp
NP_004728.1:p.Arg60Trp
NP_598397.1:p.Arg60Trp
LRG_856t1:c.178C>T
LRG_856t2:c.178C>T
LRG_856:g.274832C>T
LRG_856p1:p.Arg60Trp
LRG_856p2:p.Arg60Trp
NC_000022.10:g.34046583G>A
NM_004737.4:c.178C>T

Protein change:

R60W

Links:

dbSNP: rs142135345

NCBI 1000 Genomes Browser:

rs142135345

Molecular consequence:

NM_001362949.2:c.178C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001362951.2:c.178C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001362953.2:c.178C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001378624.1:c.178C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001378625.1:c.178C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001378626.1:c.178C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001378627.1:c.178C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001378628.1:c.178C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001378629.1:c.178C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_004737.7:c.178C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_133642.5:c.178C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001807207	Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus	no assertion criteria provided	Uncertain significance	germline	clinical testing
SCV001970759	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Uncertain significance	germline	clinical testing
SCV002577020	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Sep 19, 2022)	germline	clinical testing	Citation Link,
SCV003816473	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 17, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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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
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001807207.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001970759.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

From GeneDx, SCV002577020.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 24709677, 25279699)

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

From Revvity Omics, Revvity, SCV003816473.2

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

#	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: May 1, 2024

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