12-51721870-G-T

Position:

• chr12-51721870-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2 PP2 PP3_Moderate

The NM_001330260.2(SCN8A):​c.1960G>T​(p.Gly654Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SCN8A NM_001330260.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.58

Genes affected

SCN8A (HGNC:10596): (sodium voltage-gated channel alpha subunit 8) This gene encodes a member of the sodium channel alpha subunit gene family. The encoded protein forms the ion pore region of the voltage-gated sodium channel. This protein is essential for the rapid membrane depolarization that occurs during the formation of the action potential in excitable neurons. Mutations in this gene are associated with cognitive disability, pancerebellar atrophy and ataxia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2010]

SCN8A (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), SCN8A. . Gene score misZ 0.78755 (greater than the threshold 3.09). Trascript score misZ 10.436 (greater than threshold 3.09). GenCC has associacion of gene with myoclonus, familial, 2, infantile convulsions and choreoathetosis, cognitive impairment with or without cerebellar ataxia, undetermined early-onset epileptic encephalopathy, complex neurodevelopmental disorder, developmental and epileptic encephalopathy, 13, benign familial infantile epilepsy, seizures, benign familial infantile, 5.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.857

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCN8A	NM_001330260.2	c.1960G>T	p.Gly654Cys	missense_variant	12/27	ENST00000627620.5	NP_001317189.1
SCN8A	NM_014191.4	c.1960G>T	p.Gly654Cys	missense_variant	12/27	ENST00000354534.11	NP_055006.1
SCN8A	NM_001177984.3	c.1960G>T	p.Gly654Cys	missense_variant	12/26		NP_001171455.1
SCN8A	NM_001369788.1	c.1960G>T	p.Gly654Cys	missense_variant	12/26		NP_001356717.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCN8A	ENST00000354534.11	c.1960G>T	p.Gly654Cys	missense_variant	12/27	1	NM_014191.4	ENSP00000346534.4
SCN8A	ENST00000627620.5	c.1960G>T	p.Gly654Cys	missense_variant	12/27	5	NM_001330260.2	ENSP00000487583.2
SCN8A	ENST00000599343.5	c.1960G>T	p.Gly654Cys	missense_variant	11/26	5		ENSP00000476447.3
SCN8A	ENST00000355133.7	c.1960G>T	p.Gly654Cys	missense_variant	11/25	1		ENSP00000347255.4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1449858 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 721730

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.21
BayesDel_addAF	Pathogenic	0.30	D
BayesDel_noAF	Pathogenic	0.19
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.85	.;D;.;.;.;.;.
Eigen	Uncertain	0.64
Eigen_PC	Uncertain	0.57
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.92	D;D;D;.;D;D;D
M_CAP	Pathogenic	0.65	D
MetaRNN	Pathogenic	0.86	D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.89	D
MutationAssessor	Uncertain	2.2	.;M;M;M;M;M;.
PrimateAI	Uncertain	0.77	T
PROVEAN	Uncertain	-3.8	.;D;D;D;.;.;.
REVEL	Pathogenic	0.75
Sift	Uncertain	0.0010	.;D;D;D;.;.;.
Sift4G	Benign	0.061	.;T;T;T;D;T;D
Polyphen		1.0, 0.99	.;D;.;.;D;.;.
Vest4		0.87, 0.89, 0.87, 0.90, 0.95
MutPred		0.46		Loss of disorder (P = 0.0378);Loss of disorder (P = 0.0378);Loss of disorder (P = 0.0378);Loss of disorder (P = 0.0378);Loss of disorder (P = 0.0378);Loss of disorder (P = 0.0378);.;
MVP		0.86
MPC		2.1
ClinPred		0.99	D
GERP RS		3.9
Varity_R		0.68
gMVP		0.86

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

LitVar

Other links and lift over

dbSNP: rs905574009; hg19: chr12-52115654;