NM_000425.4(L1CAM):c.1828+5G>T AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Apr 6, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000480495.1

Allele description

NM_000425.4(L1CAM):c.1828+5G>T

Gene:
L1CAM:L1 cell adhesion molecule [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_000425.4(L1CAM):c.1828+5G>T
HGVS:
  • NC_000023.11:g.153867993C>A
  • NG_009645.3:g.46231G>T
  • NM_000425.4:c.1828+5G>T
  • NC_000023.10:g.153133448C>A
  • NM_000425.3:c.1828+5G>T
Links:
dbSNP: rs1064793164
NCBI 1000 Genomes Browser:
rs1064793164
Molecular consequence:
  • NM_000425.4:c.1828+5G>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000565104GeneDxcriteria provided, single submitter
Likely pathogenic
(Apr 6, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000565104.3

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

Description

The c.1828+5 G>T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The 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 benign variant in these populations. It is predicted to damage or destroy the natural splice donor site and 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. Therefore, based on the available evidence, this variant is likely pathogenic.

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

Last Updated: Sep 8, 2018