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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 7, 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:: RCV003778726.2

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)

Name:: Spastic paraplegia
Identifiers:: MedGen: C0037772; Human Phenotype Ontology: HP:0001258

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004660969	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004660969

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 7, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004660969.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 2433278). This variant has not been reported in the literature in individuals affected with L1CAM-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.02%). This variant, c.2581_2589del, results in the deletion of 3 amino acid(s) of the L1CAM protein (p.His861_Lys863del), but otherwise preserves the integrity of the reading frame.

#	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

Last Updated: Oct 26, 2024

ClinVar

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