rs1553463586

chr2-165389080-T-A

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1 PM2 PP2 PP3_Strong PP5_Moderate

The NM_001040142.2(SCN2A):c.5274T>A(p.Ser1758Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SCN2A NM_001040142.2 missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: -0.0650

Genes affected

SCN2A (HGNC:10588): (sodium voltage-gated channel alpha subunit 2) Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with four repeat domains, each of which is composed of six membrane-spanning segments, and one or more regulatory beta subunits. Voltage-gated sodium channels function in the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family. Allelic variants of this gene are associated with seizure disorders and autism spectrum disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PM1: In a helix (size 35) in uniprot entity SCN2A_HUMAN there are 15 pathogenic changes around while only 0 benign (100%) in NM_001040142.2
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, SCN2A
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.97
• PP5: Variant 2-165389080-T-A is Pathogenic according to our data. Variant chr2-165389080-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 521745.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCN2A	NM_001040142.2	c.5274T>A	p.Ser1758Arg	missense_variant	27/27	ENST00000375437.7
SCN2A	NM_001371246.1	c.5274T>A	p.Ser1758Arg	missense_variant	27/27	ENST00000631182.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN2A	ENST00000375437.7	c.5274T>A	p.Ser1758Arg	missense_variant	27/27	5	NM_001040142.2	P1
SCN2A	ENST00000631182.3	c.5274T>A	p.Ser1758Arg	missense_variant	27/27	5	NM_001371246.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Inborn genetic diseases Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 19, 2020

The alteration results in an amino acid change:_x000D_ _x000D_ The c.5274T>A (p.S1758R) alteration is located in exon 27 (coding exon 26) of the SCN2A gene. This alteration results from a T to A substitution at nucleotide position 5274, causing the serine (S) at amino acid position 1758 to be replaced by an arginine (R). The alteration is not observed in population databases: _x000D_ _x000D_ Based on data from the Genome Aggregation Database (gnomAD), the SCN2A c.5274T>A alteration was not observed, with coverage at this position. The amino acid alteration has been observed in affected individuals:_x000D_ _x000D_ This amino acid substitution, resulting from a different nucleotide change (c.5274T>G), was reported de novo in an individual with autism spectrum disorder, intellectual disability, motor and speech delays, gastrointestinal disturbances, hypotonia, and a history of feeding problems (Guo, 2018). The altered amino acid is conserved throughout evolution:_x000D_ _x000D_ The p.S1758 amino acid is conserved in available vertebrate species. The amino acid is located in a functionally important protein domain:_x000D_ _x000D_ The p.S1758 amino acid is located in the S6 transmembrane segment of domain IV of Nav1.2 neuronal voltage gated sodium channel. The S5 and S6 segments from each of the four domains form the inner portion of the ion channel pore; the four S6 segments form the wider intracellular end of the pore (Yu, 2003). The alteration is predicted deleterious by in silico modeling:_x000D_ _x000D_ The p.S1758R alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.49	D
BayesDel_noAF	Pathogenic	0.46
Cadd	Benign	21
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.98	D;.;T;.;D;D;.
Eigen	Uncertain	0.53
Eigen_PC	Uncertain	0.39
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Uncertain	0.96	D;.;D;.;.;.;D
M_CAP	Pathogenic	0.88	D
MetaRNN	Pathogenic	0.97	D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	4.2	H;H;.;H;H;H;H
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.93	D
PROVEAN	Uncertain	-4.0	D;.;.;.;.;D;D
REVEL	Pathogenic	0.91
Sift	Pathogenic	0.0	D;.;.;.;.;D;D
Sift4G	Pathogenic	0.0010	D;.;.;D;.;D;D
Polyphen		1.0	D;D;.;D;D;D;D
Vest4		0.84
MutPred		0.89		Gain of methylation at S1758 (P = 0.054);Gain of methylation at S1758 (P = 0.054);.;Gain of methylation at S1758 (P = 0.054);Gain of methylation at S1758 (P = 0.054);Gain of methylation at S1758 (P = 0.054);Gain of methylation at S1758 (P = 0.054);
MVP		1.0
ClinPred		1.0	D
GERP RS		3.1
Varity_R		0.98
gMVP		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs1553463586; hg19: chr2-166245590;