rs1557092050
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001278116.2(L1CAM):c.1358C>T(p.Ala453Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000248 in 1,208,681 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A453A) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000089 ( 0 hom., 1 hem., cov: 24)
Exomes 𝑓: 0.0000018 ( 0 hom. 1 hem. )
Consequence
L1CAM
NM_001278116.2 missense
NM_001278116.2 missense
Scores
6
9
Clinical Significance
Conservation
PhyloP100: 5.22
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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.1358C>T | p.Ala453Val | missense_variant | 12/29 | ENST00000370060.7 | |
L1CAM | NM_000425.5 | c.1358C>T | p.Ala453Val | missense_variant | 11/28 | ||
L1CAM | NM_024003.3 | c.1358C>T | p.Ala453Val | missense_variant | 11/27 | ||
L1CAM | NM_001143963.2 | c.1343C>T | p.Ala448Val | missense_variant | 10/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.1358C>T | p.Ala453Val | missense_variant | 12/29 | 5 | NM_001278116.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000891 AC: 1AN: 112295Hom.: 0 Cov.: 24 AF XY: 0.0000290 AC XY: 1AN XY: 34463
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GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183395Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67863
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GnomAD4 exome AF: 0.00000182 AC: 2AN: 1096386Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 1AN XY: 361812
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Spastic paraplegia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 12, 2021 | 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt L1CAM protein function. ClinVar contains an entry for this variant (Variation ID: 458211). 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 0.001%). This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 453 of the L1CAM protein (p.Ala453Val). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;.;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
0.93, 0.95
.;P;.;P
Vest4
MutPred
0.76
.;Loss of sheet (P = 0.0817);.;Loss of sheet (P = 0.0817);
MVP
MPC
0.68
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at