chrX-153865088-G-T

Position:

• chrX-153865088-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001278116.2(L1CAM):​c.2872C>A​(p.Leu958Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000912 in 1,096,806 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 9.1e-7 (0 hom. 0 hem.)
• Consequence: L1CAM NM_001278116.2 missense, splice_region
• Scores: Splicing: ADA: 0.00001634
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58

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]

L1CAM (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.22138783).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
L1CAM	NM_001278116.2	c.2872C>A	p.Leu958Met	missense_variant, splice_region_variant	22/29	ENST00000370060.7	NP_001265045.1
L1CAM	NM_000425.5	c.2872C>A	p.Leu958Met	missense_variant, splice_region_variant	21/28		NP_000416.1
L1CAM	NM_024003.3	c.2872C>A	p.Leu958Met	missense_variant, splice_region_variant	21/27		NP_076493.1
L1CAM	NM_001143963.2	c.2857C>A	p.Leu953Met	missense_variant, splice_region_variant	20/26		NP_001137435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
L1CAM	ENST00000370060.7	c.2872C>A	p.Leu958Met	missense_variant, splice_region_variant	22/29	5	NM_001278116.2	ENSP00000359077.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 9.12e-7 AC: 1 AN: 1096806 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 362640

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000119

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.011
DANN	Benign	0.90
DEOGEN2	Benign	0.38	.;T;.;.
FATHMM_MKL	Benign	0.0084	N
LIST_S2	Benign	0.84	T;T;.;T
M_CAP	Pathogenic	0.49	D
MetaRNN	Benign	0.22	T;T;T;T
MetaSVM	Benign	-0.88	T
MutationAssessor	Benign	1.1	.;L;.;L
PrimateAI	Benign	0.34	T
PROVEAN	Benign	-0.66	N;N;N;N
REVEL	Benign	0.074
Sift	Uncertain	0.0020	D;D;D;D
Sift4G	Benign	0.12	T;T;T;D
Polyphen		0.33, 0.24	.;B;.;B
Vest4		0.26
MutPred		0.36		.;Gain of phosphorylation at Y955 (P = 0.0815);.;Gain of phosphorylation at Y955 (P = 0.0815);
MVP		0.31
MPC		1.3
ClinPred		0.73	D
GERP RS		-9.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.41
gMVP		0.45

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000016
dbscSNV1_RF	Benign	0.016
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-153130543;