rs782756293

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM1BP6BS2

The NM_001278116.2(L1CAM):​c.1219C>T​(p.Arg407Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,096,695 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 25)
Exomes 𝑓: 0.0000055 ( 0 hom. 2 hem. )

Consequence

L1CAM
NM_001278116.2 missense

Scores

3
10
4

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:2

Conservation

PhyloP100: 0.506
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM1
In a domain Ig-like C2-type 4 (size 87) in uniprot entity L1CAM_HUMAN there are 8 pathogenic changes around while only 0 benign (100%) in NM_001278116.2
BP6
Variant X-153869568-G-A is Benign according to our data. Variant chrX-153869568-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 568459.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BS2
High Hemizygotes in GnomAdExome4 at 2 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
L1CAMNM_001278116.2 linkuse as main transcriptc.1219C>T p.Arg407Cys missense_variant 11/29 ENST00000370060.7 NP_001265045.1 P32004-1
L1CAMNM_000425.5 linkuse as main transcriptc.1219C>T p.Arg407Cys missense_variant 10/28 NP_000416.1 P32004-1
L1CAMNM_024003.3 linkuse as main transcriptc.1219C>T p.Arg407Cys missense_variant 10/27 NP_076493.1 P32004-2
L1CAMNM_001143963.2 linkuse as main transcriptc.1204C>T p.Arg402Cys missense_variant 9/26 NP_001137435.1 P32004-3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
L1CAMENST00000370060.7 linkuse as main transcriptc.1219C>T p.Arg407Cys missense_variant 11/295 NM_001278116.2 ENSP00000359077.1 P32004-1
L1CAMENST00000361699.8 linkuse as main transcriptc.1219C>T p.Arg407Cys missense_variant 10/271 ENSP00000355380.4 P32004-2
L1CAMENST00000361981.7 linkuse as main transcriptc.1204C>T p.Arg402Cys missense_variant 9/261 ENSP00000354712.3 P32004-3
L1CAMENST00000370055.5 linkuse as main transcriptc.1204C>T p.Arg402Cys missense_variant 10/275 ENSP00000359072.1 P32004-3

Frequencies

GnomAD3 genomes
Cov.:
25
GnomAD3 exomes
AF:
0.0000224
AC:
4
AN:
178588
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
64496
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000369
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000147
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000126
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000547
AC:
6
AN:
1096695
Hom.:
0
Cov.:
33
AF XY:
0.00000552
AC XY:
2
AN XY:
362357
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000285
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000663
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000356
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
25
Bravo
AF:
0.0000340
ExAC
AF:
0.0000330
AC:
4

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGeneDxNov 30, 2023In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 25641508) -
Spastic paraplegia Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 02, 2023- -
L1CAM-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesAug 02, 2023This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.74
BayesDel_addAF
Benign
-0.074
T
BayesDel_noAF
Uncertain
-0.080
CADD
Uncertain
24
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.54
.;D;.;.
FATHMM_MKL
Benign
0.15
N
LIST_S2
Uncertain
0.95
D;D;.;D
M_CAP
Pathogenic
0.74
D
MetaRNN
Uncertain
0.65
D;D;D;D
MetaSVM
Uncertain
0.33
D
MutationAssessor
Uncertain
2.5
.;M;.;M
PrimateAI
Uncertain
0.51
T
PROVEAN
Benign
-1.4
N;N;N;N
REVEL
Uncertain
0.49
Sift
Uncertain
0.011
D;D;D;D
Sift4G
Uncertain
0.027
D;D;D;D
Polyphen
1.0
.;D;.;D
Vest4
0.39
MutPred
0.64
.;Loss of disorder (P = 0.0986);.;Loss of disorder (P = 0.0986);
MVP
0.76
MPC
1.7
ClinPred
0.48
T
GERP RS
4.5
Varity_R
0.48
gMVP
0.94

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs782756293; hg19: chrX-153135023; COSMIC: COSV62830614; COSMIC: COSV62830614; API