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NM_001278116.2(L1CAM):c.1828+5G>T AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 6, 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:
RCV000480495.1

Allele description

NM_001278116.2(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_001278116.2(L1CAM):c.1828+5G>T
HGVS:
  • NC_000023.11:g.153867993C>A
  • NG_009645.3:g.46231G>T
  • NM_000425.5:c.1828+5G>T
  • NM_001143963.2:c.1813+5G>T
  • NM_001278116.2:c.1828+5G>TMANE SELECT
  • NM_024003.3:c.1828+5G>T
  • LRG_14t1:c.1828+5G>T
  • LRG_14t2: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_000425.5:c.1828+5G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001143963.2:c.1813+5G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001278116.2:c.1828+5G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_024003.3:c.1828+5G>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

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
SCV000565104GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Apr 6, 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, 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: Feb 27, 2021