6-33441184-A-G

Position:

• chr6-33441184-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP2

The NM_006772.3(SYNGAP1):​c.1925A>G​(p.Lys642Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: SYNGAP1 NM_006772.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.30

Genes affected

SYNGAP1 (HGNC:11497): (synaptic Ras GTPase activating protein 1) This gene encodes a Ras GTPase activating protein that is a member of the N-methyl-D-aspartate receptor complex. The N-terminal domain of the protein contains a Ras-GAP domain, a pleckstrin homology domain, and a C2 domain that may be involved in binding of calcium and phospholipids. The C-terminal domain consists of a ten histidine repeat region, serine and tyrosine phosphorylation sites, and a T/SXV motif required for postsynaptic scaffold protein interaction. The encoded protein negatively regulates Ras, Rap and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor trafficking to the postsynaptic membrane to regulate synaptic plasticity and neuronal homeostasis. Allelic variants of this gene are associated with intellectual disability and autism spectrum disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]

SYNGAP1 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 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), SYNGAP1. . Gene score misZ 5.6047 (greater than the threshold 3.09). Trascript score misZ 7.6762 (greater than threshold 3.09). GenCC has associacion of gene with autosomal dominant non-syndromic intellectual disability, complex neurodevelopmental disorder, intellectual disability, autosomal dominant 5, SYNGAP1-related developmental and epileptic encephalopathy, myoclonic-astatic epilepsy.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYNGAP1	NM_006772.3	c.1925A>G	p.Lys642Arg	missense_variant	12/19	ENST00000646630.1	NP_006763.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYNGAP1	ENST00000646630.1	c.1925A>G	p.Lys642Arg	missense_variant	12/19		NM_006772.3	ENSP00000496007.1
SYNGAP1	ENST00000644458.1	c.1925A>G	p.Lys642Arg	missense_variant	12/19			ENSP00000495541.1
SYNGAP1	ENST00000449372.7	c.1925A>G	p.Lys642Arg	missense_variant	12/18	5		ENSP00000416519.4
SYNGAP1	ENST00000418600.7	c.1925A>G	p.Lys642Arg	missense_variant	12/19	5		ENSP00000403636.3
SYNGAP1	ENST00000645250.1	c.1748A>G	p.Lys583Arg	missense_variant	10/17			ENSP00000494861.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Uncertain	0.099	D
BayesDel_noAF	Benign	-0.10
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.66	D;D;.;.;.;.;.;.
Eigen	Uncertain	0.31
Eigen_PC	Uncertain	0.41
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.92	.;D;D;D;D;D;D;D
M_CAP	Benign	0.011	T
MetaRNN	Uncertain	0.48	T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Uncertain	2.1	M;M;.;.;M;M;.;.
PrimateAI	Uncertain	0.78	T
PROVEAN	Uncertain	-2.7	.;.;.;D;.;D;D;.
REVEL	Uncertain	0.32
Sift	Uncertain	0.013	.;.;.;D;.;D;D;.
Sift4G	Uncertain	0.035	.;D;.;D;D;D;D;.
Polyphen		0.0010	B;B;.;.;B;B;.;.
Vest4		0.74, 0.88, 0.70, 0.82
MutPred		0.37		Loss of ubiquitination at K642 (P = 0.0092);Loss of ubiquitination at K642 (P = 0.0092);Loss of ubiquitination at K642 (P = 0.0092);Loss of ubiquitination at K642 (P = 0.0092);Loss of ubiquitination at K642 (P = 0.0092);Loss of ubiquitination at K642 (P = 0.0092);.;.;
MVP		0.74
MPC		0.92
ClinPred		0.97	D
GERP RS		4.8
Varity_R		0.35
gMVP		0.87

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: rs1485749468; hg19: chr6-33408961;