rs1064795331
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP2PP3_ModeratePP5
The NM_006772.3(SYNGAP1):c.1717C>T(p.Arg573Trp) 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006772.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNGAP1 | NM_006772.3 | c.1717C>T | p.Arg573Trp | missense_variant | Exon 11 of 19 | ENST00000646630.1 | NP_006763.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNGAP1 | ENST00000646630.1 | c.1717C>T | p.Arg573Trp | missense_variant | Exon 11 of 19 | NM_006772.3 | ENSP00000496007.1 | |||
SYNGAP1 | ENST00000644458.1 | c.1717C>T | p.Arg573Trp | missense_variant | Exon 11 of 19 | ENSP00000495541.1 | ||||
SYNGAP1 | ENST00000449372.7 | c.1717C>T | p.Arg573Trp | missense_variant | Exon 11 of 18 | 5 | ENSP00000416519.4 | |||
SYNGAP1 | ENST00000418600.7 | c.1717C>T | p.Arg573Trp | missense_variant | Exon 11 of 19 | 5 | ENSP00000403636.3 | |||
SYNGAP1 | ENST00000645250.1 | c.1540C>T | p.Arg514Trp | missense_variant | Exon 9 of 17 | ENSP00000494861.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 39
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Intellectual disability, autosomal dominant 5 Pathogenic:3Uncertain:1
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The variant has been previously reported as de novo in a similarly affected individual (PS2_S). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000421734, PMID:30581057, PS1_S).A different missense change at the same codon (p.Arg573Leu, p.Arg573Gln) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000521291,VCV001176819, PM5_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.758, 3CNET: 0.862, PP3_P). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 573 of the SYNGAP1 protein (p.Arg573Trp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with SYNGAP1-related conditions (PMID: 30581057). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 421734). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SYNGAP1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
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not provided Pathogenic:3
Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30581057) -
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Intellectual disability Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at