NM_001278116.2(L1CAM):c.2581_2589del (p.His861_Lys863del) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Oct 23, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV003133966.4

Allele description [Variation Report for NM_001278116.2(L1CAM):c.2581_2589del (p.His861_Lys863del)]

NM_001278116.2(L1CAM):c.2581_2589del (p.His861_Lys863del)

Gene:

L1CAM:L1 cell adhesion molecule [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_001278116.2(L1CAM):c.2581_2589del (p.His861_Lys863del)

HGVS:

NC_000023.11:g.153865462_153865470del
NG_009645.4:g.25707_25715del
NM_000425.5:c.2581_2589del
NM_001143963.2:c.2566_2574del
NM_001278116.2:c.2581_2589delMANE SELECT
NM_024003.3:c.2581_2589del
NP_000416.1:p.His861_Lys863del
NP_001137435.1:p.His856_Lys858del
NP_001265045.1:p.His861_Lys863del
NP_076493.1:p.His861_Lys863del
LRG_14t1:c.2581_2589del
LRG_14t2:c.2581_2589del
LRG_14:g.25707_25715del
LRG_14p1:p.His861_Lys863del
LRG_14p2:p.His861_Lys863del
NC_000023.10:g.153130914_153130922del
NC_000023.10:g.153130917_153130925del
NM_000425.3:c.2581_2589del

Molecular consequence:

NM_000425.5:c.2581_2589del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001143963.2:c.2566_2574del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001278116.2:c.2581_2589del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_024003.3:c.2581_2589del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003812714	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 12, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005377887	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Oct 23, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003812714

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(May 12, 2022)

germline

clinical testing

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

SCV005377887

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Oct 23, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Revvity Omics, Revvity, SCV003812714.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV005377887.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Not observed at significant frequency in large population cohorts (gnomAD); In-frame deletion of 3 amino acids in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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