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NM_000533.5(PLP1):c.762+2T>C AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 23, 2016
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV000255182.1

Allele description [Variation Report for NM_000533.5(PLP1):c.762+2T>C]

NM_000533.5(PLP1):c.762+2T>C

Genes:
RAB9B:RAB9B, member RAS oncogene family [Gene - OMIM - HGNC]
PLP1:proteolipid protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq22.2
Genomic location:
Preferred name:
NM_000533.5(PLP1):c.762+2T>C
HGVS:
  • NC_000023.11:g.103789400T>C
  • NG_008863.2:g.17890T>C
  • NG_016452.2:g.47883A>G
  • NM_000533.5:c.762+2T>CMANE SELECT
  • NM_001128834.3:c.762+2T>C
  • NM_001305004.1:c.597+2T>C
  • NM_199478.3:c.657+2T>C
  • NC_000023.10:g.103044329T>C
  • NM_000533.3:c.762+2T>C
Links:
dbSNP: rs886039487
NCBI 1000 Genomes Browser:
rs886039487
Molecular consequence:
  • NM_000533.5:c.762+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001128834.3:c.762+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001305004.1:c.597+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_199478.3:c.657+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000322132GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Feb 23, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000322132.7

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

Description

The c.762+2T>C variant in the PLP1 gene has been reported previously in association with Pelizaeus-Merzbacher disease (Mimault et al., 1999). This splice site variant destroys the canonical splice donor site in intron 6. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. The c.762+2T>C variant 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 variant in these populations. We interpret c.762+2T>C as a pathogenic variant.

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

Last Updated: Jun 10, 2023