SYNGAP1

Chr 6AD

synaptic Ras GTPase activating protein 1

Also known as: MRD5, RASA5, SYNGAP

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]

OMIMResearchGenerating clinical summary…
LOFmechanismADLOEUF 0.051 OMIM phenotype
Clinical SummarySYNGAP1
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Gene-Disease Validity (ClinGen)
complex neurodevelopmental disorder · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
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Clinical Trials
4 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint?
0.05LOEUF
pLI 1.000
Z-score 6.97
OE 0.00 (0.000.05)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?
5.60Z-score
OE missense 0.44 (0.400.48)
351 obs / 796.0 exp
Constrained

Extremely missense-constrained (top ~0.01%)

Observed / Expected Ratios?
LoF OE?0.00 (0.000.05)
00.351.4
Missense OE?0.44 (0.400.48)
00.61.4
Synonymous OE?0.88
01.21.6
LoF obs/exp: 0 / 56.5Missense obs/exp: 351 / 796.0Syn Z: 1.65
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveSYNGAP1-related intellectual developmental disorderLOFAD

This gene — mechanism propensity

DN
0.2997th %ile
GOF
0.3887th %ile
LOF
0.87top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · 1 literature citation · LOEUF 0.05 · ClinGen HI: Sufficient evidence for dosage pathogenicity

Literature Evidence

LOFHaploinsufficiency of the SYNGAP1 gene, which codes for a Ras GTPase-activating protein, impairs cognition both in humans and in mice.1

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

References

  1. 1.PMID 27827368

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SYNGAP1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.