6-33438440-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP2PP3
The NM_006772.3(SYNGAP1):c.1408A>G(p.Met470Val) 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 Uncertain significance (★).
Frequency
Consequence
NM_006772.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNGAP1 | NM_006772.3 | c.1408A>G | p.Met470Val | missense_variant | Exon 9 of 19 | ENST00000646630.1 | NP_006763.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNGAP1 | ENST00000646630.1 | c.1408A>G | p.Met470Val | missense_variant | Exon 9 of 19 | NM_006772.3 | ENSP00000496007.1 | |||
SYNGAP1 | ENST00000644458.1 | c.1408A>G | p.Met470Val | missense_variant | Exon 9 of 19 | ENSP00000495541.1 | ||||
SYNGAP1 | ENST00000449372.7 | c.1408A>G | p.Met470Val | missense_variant | Exon 9 of 18 | 5 | ENSP00000416519.4 | |||
SYNGAP1 | ENST00000418600.7 | c.1408A>G | p.Met470Val | missense_variant | Exon 9 of 19 | 5 | ENSP00000403636.3 | |||
SYNGAP1 | ENST00000645250.1 | c.1231A>G | p.Met411Val | missense_variant | Exon 7 of 17 | ENSP00000494861.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 35
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1408A>G (p.M470V) alteration is located in coding exon 9 of the SYNGAP1 gene. This alteration results from a A to G substitution at nucleotide position 1408, causing the methionine (M) at amino acid position 470 to be replaced by a valine (V). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. The in silico prediction for this alteration is inconclusive. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.