NM_133642.5(LARGE1):c.1949G>A (p.Arg650Gln) AND not specified

Germline classification:: Benign/Likely benign (5 submissions)
Last evaluated:: Jun 11, 2024
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:: RCV000081176.30

Allele description [Variation Report for NM_133642.5(LARGE1):c.1949G>A (p.Arg650Gln)]

NM_133642.5(LARGE1):c.1949G>A (p.Arg650Gln)

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.1949G>A (p.Arg650Gln)

Other names:

p.R650Q:CGG>CAG

HGVS:

NC_000022.11:g.33277184C>T
NG_009929.2:g.648245G>A
NM_001362949.2:c.1949G>A
NM_001362951.2:c.1949G>A
NM_001362953.2:c.1949G>A
NM_001378624.1:c.1949G>A
NM_001378625.1:c.1949G>A
NM_001378626.1:c.1949G>A
NM_001378627.1:c.1802G>A
NM_001378628.1:c.1802G>A
NM_001378629.1:c.1793G>A
NM_001378630.1:c.1346G>A
NM_001378631.1:c.1043G>A
NM_004737.7:c.1949G>A
NM_133642.5:c.1949G>AMANE SELECT
NP_001349878.1:p.Arg650Gln
NP_001349880.1:p.Arg650Gln
NP_001349882.1:p.Arg650Gln
NP_001365553.1:p.Arg650Gln
NP_001365554.1:p.Arg650Gln
NP_001365555.1:p.Arg650Gln
NP_001365556.1:p.Arg601Gln
NP_001365557.1:p.Arg601Gln
NP_001365558.1:p.Arg598Gln
NP_001365559.1:p.Arg449Gln
NP_001365560.1:p.Arg348Gln
NP_004728.1:p.Arg650Gln
NP_598397.1:p.Arg650Gln
LRG_856t1:c.1949G>A
LRG_856t2:c.1949G>A
LRG_856:g.648245G>A
LRG_856p1:p.Arg650Gln
LRG_856p2:p.Arg650Gln
NC_000022.10:g.33673170C>T
NM_004737.4:c.1949G>A

Protein change:

R348Q

Links:

dbSNP: rs73399520

NCBI 1000 Genomes Browser:

rs73399520

Molecular consequence:

NM_001362949.2:c.1949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001362951.2:c.1949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001362953.2:c.1949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378624.1:c.1949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378625.1:c.1949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378626.1:c.1949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378627.1:c.1802G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378628.1:c.1802G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378629.1:c.1793G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378630.1:c.1346G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378631.1:c.1043G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004737.7:c.1949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_133642.5:c.1949G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000113084	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Nov 15, 2012)	germline	clinical testing	Citation Link,
SCV000170082	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jun 9, 2014)	germline	clinical testing	Citation Link,
SCV000193508	Genetic Services Laboratory, University of Chicago	no assertion criteria provided	Likely benign	germline	clinical testing
SCV000310638	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001144422	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	benign (Jun 11, 2024)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22426012, 26467025

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	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

Assessment of target enrichment platforms using massively parallel sequencing for the mutation detection for congenital muscular dystrophy.

Valencia CA, Rhodenizer D, Bhide S, Chin E, Littlejohn MR, Keong LM, Rutkowski A, Bonnemann C, Hegde M.

J Mol Diagn. 2012 May-Jun;14(3):233-46. doi: 10.1016/j.jmoldx.2012.01.009. Epub 2012 Mar 16.

PubMed [citation]

PMID:: 22426012
PMCID:: PMC3349841

See all PubMed Citations (3)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000113084.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	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	unknown	not provided	not provided	not provided		2	not provided	not provided	not provided

From GeneDx, SCV000170082.10

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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 Genetic Services Laboratory, University of Chicago, SCV000193508.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000310638.1

#	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

From Athena Diagnostics, SCV001144422.2

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

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

Last Updated: Apr 20, 2025

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