VCV002433278.4 - ClinVar

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

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(3)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

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

Variation ID: 2433278 Accession: VCV002433278.4

Type and length

Deletion, 9 bp

Location

Cytogenetic: Xq28 X: 153865459-153865467 (GRCh38) [ NCBI UCSC ] X: 153130914-153130922 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Mar 5, 2023	Oct 26, 2024	Oct 23, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001278116.2:c.2581_2589del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001265045.1:p.His861_Lys863del	inframe deletion
NM_000425.3:c.2581_2589del
NM_000425.5:c.2581_2589del	NP_000416.1:p.His861_Lys863del	inframe deletion
NM_001143963.2:c.2566_2574del	NP_001137435.1:p.His856_Lys858del	inframe deletion
NM_024003.3:c.2581_2589del	NP_076493.1:p.His861_Lys863del	inframe deletion
NC_000023.11:g.153865462_153865470del
NC_000023.10:g.153130917_153130925del
NG_009645.4:g.25707_25715del
LRG_14:g.25707_25715del
LRG_14t1:c.2581_2589del	LRG_14p1:p.His861_Lys863del
LRG_14t2:c.2581_2589del	LRG_14p2:p.His861_Lys863del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000023.11:153865458:CTTGCTGTGCTT:CTT

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
L1CAM		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1266	1531

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Uncertain significance (2)	criteria provided, multiple submitters, no conflicts	Oct 23, 2023	RCV003133966.4
Spastic paraplegia	Uncertain significance (1)	criteria provided, single submitter	May 7, 2023	RCV003778726.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (May 12, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Revvity Omics, Revvity Accession: SCV003812714.2 First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024
Uncertain significance (May 07, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Spastic paraplegia Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004660969.1 First in ClinVar: Feb 28, 2024 Last updated: Feb 28, 2024	Comment: 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 … (more) 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. (less)
Uncertain significance (Oct 23, 2023)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV005377887.1 First in ClinVar: Oct 26, 2024 Last updated: Oct 26, 2024	Comment: 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 … (more) 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 (less)

Comment:

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.

Comment:

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

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Oct 27, 2024

ClinVar Genomic variation as it relates to human health

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

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...