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NM_001278116.2(L1CAM):c.925G>A (p.Glu309Lys) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 5, 2023
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:
RCV001545171.3

Allele description [Variation Report for NM_001278116.2(L1CAM):c.925G>A (p.Glu309Lys)]

NM_001278116.2(L1CAM):c.925G>A (p.Glu309Lys)

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.925G>A (p.Glu309Lys)
HGVS:
  • NC_000023.11:g.153870122C>T
  • NG_009645.3:g.44102G>A
  • NM_000425.5:c.925G>A
  • NM_001143963.2:c.910G>A
  • NM_001278116.2:c.925G>AMANE SELECT
  • NM_024003.3:c.925G>A
  • NP_000416.1:p.Glu309Lys
  • NP_001137435.1:p.Glu304Lys
  • NP_001265045.1:p.Glu309Lys
  • NP_076493.1:p.Glu309Lys
  • LRG_14t1:c.925G>A
  • LRG_14t2:c.925G>A
  • LRG_14p1:p.Glu309Lys
  • LRG_14p2:p.Glu309Lys
  • NC_000023.10:g.153135577C>T
  • NM_000425.3:c.925G>A
  • NM_000425.4:c.925G>A
  • NM_001278116.1:c.925G>A
Protein change:
E304K
Links:
dbSNP: rs367665974
NCBI 1000 Genomes Browser:
rs367665974
Molecular consequence:
  • NM_000425.5:c.925G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001143963.2:c.910G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001278116.2:c.925G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024003.3:c.925G>A - 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
SCV001764448GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Jun 5, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001764448.2

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

Description

Published functional studies demonstrate a damaging effect, as this variant led to decreased cell-matrix adhesion, decreased cell migration, loss of axon guidance, and loss of proper synapse formation (Tagliavacca et al., 2013); Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; In silico analysis suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 15555929, 9610803, 11438988, 24155914, 22973895, 11772994, 16760466, 7920660, 7762552)

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

Last Updated: Oct 8, 2024