rs1555229539
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 9P and 2B. PM1PM2PP2PP3_StrongBP6_Moderate
The NM_014191.4(SCN8A):c.4742T>A(p.Phe1581Tyr) 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. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. F1581F) has been classified as Likely benign.
Frequency
Consequence
NM_014191.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN8A | NM_001330260.2 | c.4742T>A | p.Phe1581Tyr | missense_variant | 26/27 | ENST00000627620.5 | |
SCN8A | NM_014191.4 | c.4742T>A | p.Phe1581Tyr | missense_variant | 26/27 | ENST00000354534.11 | |
SCN8A | NM_001177984.3 | c.4619T>A | p.Phe1540Tyr | missense_variant | 25/26 | ||
SCN8A | NM_001369788.1 | c.4619T>A | p.Phe1540Tyr | missense_variant | 25/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN8A | ENST00000354534.11 | c.4742T>A | p.Phe1581Tyr | missense_variant | 26/27 | 1 | NM_014191.4 | P4 | |
SCN8A | ENST00000627620.5 | c.4742T>A | p.Phe1581Tyr | missense_variant | 26/27 | 5 | NM_001330260.2 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 31, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at