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NM_133642.5(LARGE1):c.2255C>G (p.Ala752Gly) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Apr 27, 2019
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:
RCV000149996.6

Allele description [Variation Report for NM_133642.5(LARGE1):c.2255C>G (p.Ala752Gly)]

NM_133642.5(LARGE1):c.2255C>G (p.Ala752Gly)

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.2255C>G (p.Ala752Gly)
Other names:
p.A752G:GCC>GGC
HGVS:
  • NC_000022.11:g.33274443G>C
  • NG_009929.2:g.650986C>G
  • NM_001362949.2:c.2255C>G
  • NM_001362951.2:c.2255C>G
  • NM_001362953.2:c.2255C>G
  • NM_001378624.1:c.2255C>G
  • NM_001378625.1:c.2255C>G
  • NM_001378626.1:c.2255C>G
  • NM_001378627.1:c.2108C>G
  • NM_001378628.1:c.2108C>G
  • NM_001378629.1:c.2099C>G
  • NM_001378630.1:c.1652C>G
  • NM_001378631.1:c.1349C>G
  • NM_004737.7:c.2255C>G
  • NM_133642.5:c.2255C>GMANE SELECT
  • NP_001349878.1:p.Ala752Gly
  • NP_001349880.1:p.Ala752Gly
  • NP_001349882.1:p.Ala752Gly
  • NP_001365553.1:p.Ala752Gly
  • NP_001365554.1:p.Ala752Gly
  • NP_001365555.1:p.Ala752Gly
  • NP_001365556.1:p.Ala703Gly
  • NP_001365557.1:p.Ala703Gly
  • NP_001365558.1:p.Ala700Gly
  • NP_001365559.1:p.Ala551Gly
  • NP_001365560.1:p.Ala450Gly
  • NP_004728.1:p.Ala752Gly
  • NP_598397.1:p.Ala752Gly
  • LRG_856t1:c.2255C>G
  • LRG_856t2:c.2255C>G
  • LRG_856:g.650986C>G
  • LRG_856p1:p.Ala752Gly
  • LRG_856p2:p.Ala752Gly
  • NC_000022.10:g.33670429G>C
  • NM_004737.4:c.2255C>G
Protein change:
A450G
Links:
dbSNP: rs200024875
NCBI 1000 Genomes Browser:
rs200024875
Molecular consequence:
  • NM_001362949.2:c.2255C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001362951.2:c.2255C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001362953.2:c.2255C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378624.1:c.2255C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378625.1:c.2255C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378626.1:c.2255C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378627.1:c.2108C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378628.1:c.2108C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378629.1:c.2099C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378630.1:c.1652C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378631.1:c.1349C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004737.7:c.2255C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_133642.5:c.2255C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000196855GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Aug 14, 2017) 		germlineclinical testing

Citation Link,

SCV003816437Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Apr 27, 2019) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 GeneDx, SCV000196855.12

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The A752G variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This substitution occurs at a position that is conserved across species. However, the A752G variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV003816437.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 16, 2024