chrX-153872676-G-T

Variant names:

• chrX-153872676-G-T
• NM_001278116.2:c.113C>A

Variant summary

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

The NM_001278116.2(L1CAM):​c.113C>A​(p.Thr38Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000913 in 1,095,511 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 22)
  • Exomes 𝑓: 9.1e-7 (0 hom. 0 hem.)
• Consequence: L1CAM NM_001278116.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.50

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]

ENSG00000284987 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
L1CAM	NM_001278116.2	c.113C>A	p.Thr38Lys	missense_variant	Exon 4 of 29	ENST00000370060.7	NP_001265045.1
L1CAM	NM_000425.5	c.113C>A	p.Thr38Lys	missense_variant	Exon 3 of 28		NP_000416.1
L1CAM	NM_024003.3	c.113C>A	p.Thr38Lys	missense_variant	Exon 3 of 27		NP_076493.1
L1CAM	NM_001143963.2	c.98C>A	p.Thr33Lys	missense_variant	Exon 2 of 26		NP_001137435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
L1CAM	ENST00000370060.7	c.113C>A	p.Thr38Lys	missense_variant	Exon 4 of 29	5	NM_001278116.2	ENSP00000359077.1
ENSG00000284987	ENST00000646191.1	n.*155C>A		non_coding_transcript_exon_variant	Exon 4 of 5			ENSP00000493873.1
ENSG00000284987	ENST00000646191.1	n.*155C>A		3_prime_UTR_variant	Exon 4 of 5			ENSP00000493873.1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome AF: 9.13e-7 AC: 1 AN: 1095511 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 360899

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.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Benign	0.0067	T
BayesDel_noAF	Benign	-0.23
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.59	.;D;.;.;T;T;T;T
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.88	D;D;.;D;T;D;D;D
M_CAP	Uncertain	0.12	D
MetaRNN	Uncertain	0.72	D;D;D;D;D;D;D;D
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.0	.;M;.;M;.;.;.;.
PrimateAI	Uncertain	0.64	T
PROVEAN	Pathogenic	-4.7	D;D;D;D;D;D;D;D
REVEL	Benign	0.24
Sift	Uncertain	0.020	D;D;D;D;D;D;D;D
Sift4G	Uncertain	0.0030	D;D;D;D;.;.;D;.
Polyphen		1.0, 0.94	.;D;.;P;.;.;.;.
Vest4		0.62
MutPred		0.67		.;Gain of methylation at T38 (P = 0.0148);.;Gain of methylation at T38 (P = 0.0148);Gain of methylation at T38 (P = 0.0148);.;.;Gain of methylation at T38 (P = 0.0148);
MVP		0.77
MPC		1.6
ClinPred		0.99	D
GERP RS		4.7
Varity_R		0.87
gMVP		0.97

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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-153138131;