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NM_133642.5(LARGE1):c.1599C>T (p.Ile533=) AND not specified

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
May 19, 2017
Review status:
criteria provided, conflicting classifications
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:
RCV000193827.12

Allele description [Variation Report for NM_133642.5(LARGE1):c.1599C>T (p.Ile533=)]

NM_133642.5(LARGE1):c.1599C>T (p.Ile533=)

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.1599C>T (p.Ile533=)
HGVS:
  • NC_000022.11:g.33304360G>A
  • NG_009929.2:g.621069C>T
  • NM_001362949.2:c.1599C>T
  • NM_001362951.2:c.1599C>T
  • NM_001362953.2:c.1599C>T
  • NM_001378624.1:c.1599C>T
  • NM_001378625.1:c.1599C>T
  • NM_001378626.1:c.1599C>T
  • NM_001378627.1:c.1599C>T
  • NM_001378628.1:c.1599C>T
  • NM_001378629.1:c.1443C>T
  • NM_001378630.1:c.996C>T
  • NM_001378631.1:c.840C>T
  • NM_004737.7:c.1599C>T
  • NM_133642.5:c.1599C>TMANE SELECT
  • NP_001349878.1:p.Ile533=
  • NP_001349880.1:p.Ile533=
  • NP_001349882.1:p.Ile533=
  • NP_001365553.1:p.Ile533=
  • NP_001365554.1:p.Ile533=
  • NP_001365555.1:p.Ile533=
  • NP_001365556.1:p.Ile533=
  • NP_001365557.1:p.Ile533=
  • NP_001365558.1:p.Ile481=
  • NP_001365559.1:p.Ile332=
  • NP_001365560.1:p.Ile280=
  • NP_004728.1:p.Ile533=
  • NP_598397.1:p.Ile533=
  • LRG_856t1:c.1599C>T
  • LRG_856t2:c.1599C>T
  • LRG_856:g.621069C>T
  • LRG_856p1:p.Ile533=
  • LRG_856p2:p.Ile533=
  • NC_000022.10:g.33700346G>A
  • NM_004737.4:c.1599C>T
Links:
dbSNP: rs12627793
NCBI 1000 Genomes Browser:
rs12627793
Molecular consequence:
  • NM_001362949.2:c.1599C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001362951.2:c.1599C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001362953.2:c.1599C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378624.1:c.1599C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378625.1:c.1599C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378626.1:c.1599C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378627.1:c.1599C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378628.1:c.1599C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378629.1:c.1443C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378630.1:c.996C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001378631.1:c.840C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004737.7:c.1599C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_133642.5:c.1599C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000247833Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Mar 11, 2015)
germlineclinical testing

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

SCV000708545Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Likely benign
(May 19, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not 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 Genetic Services Laboratory, University of Chicago, SCV000247833.1

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

From Eurofins Ntd Llc (ga), SCV000708545.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 17, 2024