rs1557090220

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePM2PP5_Moderate

The NM_001278116.2(L1CAM):​c.3046+1G>C variant causes a splice donor, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).

Frequency

Genomes: not found (cov: 24)

Consequence

L1CAM
NM_001278116.2 splice_donor, intron

Scores

1
3
1
Splicing: ADA: 1.000
2

Clinical Significance

Likely pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 4.18
Variant links:
Genes affected
L1CAM (HGNC:6470): (L1 cell adhesion molecule) The protein encoded by this gene is an axonal glycoprotein belonging to the immunoglobulin supergene family. The ectodomain, consisting of several immunoglobulin-like domains and fibronectin-like repeats (type III), is linked via a single transmembrane sequence to a conserved cytoplasmic domain. This cell adhesion molecule plays an important role in nervous system development, including neuronal migration and differentiation. Mutations in the gene cause X-linked neurological syndromes known as CRASH (corpus callosum hypoplasia, retardation, aphasia, spastic paraplegia and hydrocephalus). Alternative splicing of this gene results in multiple transcript variants, some of which include an alternate exon that is considered to be specific to neurons. [provided by RefSeq, May 2013]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.045839958 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.7, offset of -31, new splice context is: atcGTacgg. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant X-153864820-C-G is Pathogenic according to our data. Variant chrX-153864820-C-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 527976.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
L1CAMNM_001278116.2 linkuse as main transcriptc.3046+1G>C splice_donor_variant, intron_variant ENST00000370060.7 NP_001265045.1 P32004-1
L1CAMNM_000425.5 linkuse as main transcriptc.3046+1G>C splice_donor_variant, intron_variant NP_000416.1 P32004-1
L1CAMNM_024003.3 linkuse as main transcriptc.3046+1G>C splice_donor_variant, intron_variant NP_076493.1 P32004-2
L1CAMNM_001143963.2 linkuse as main transcriptc.3031+1G>C splice_donor_variant, intron_variant NP_001137435.1 P32004-3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
L1CAMENST00000370060.7 linkuse as main transcriptc.3046+1G>C splice_donor_variant, intron_variant 5 NM_001278116.2 ENSP00000359077.1 P32004-1
L1CAMENST00000361699.8 linkuse as main transcriptc.3046+1G>C splice_donor_variant, intron_variant 1 ENSP00000355380.4 P32004-2
L1CAMENST00000361981.7 linkuse as main transcriptc.3031+1G>C splice_donor_variant, intron_variant 1 ENSP00000354712.3 P32004-3
L1CAMENST00000370055.5 linkuse as main transcriptc.3031+1G>C splice_donor_variant, intron_variant 5 ENSP00000359072.1 P32004-3

Frequencies

GnomAD3 genomes
Cov.:
24
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
24

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Spastic paraplegia Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMay 02, 2019In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in L1CAM are known to be pathogenic (PMID: 19846429). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with L1CAM-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change affects a donor splice site in intron 22 of the L1CAM gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.21
D
BayesDel_noAF
Uncertain
0.060
CADD
Pathogenic
29
DANN
Uncertain
0.99
FATHMM_MKL
Uncertain
0.96
D
GERP RS
5.2

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
1.0
dbscSNV1_RF
Pathogenic
0.93
SpliceAI score (max)
1.0
Details are displayed if max score is > 0.2
DS_DL_spliceai
1.0
Position offset: 1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1557090220; hg19: chrX-153130275; API