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SYNGAP1

Synonyms
MRD5, RASA1, RASA5, SYNGAP
External resources
Summary
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.

Variant Counts

Variant classification counts, according to ACMG guideline on all identified variants among our tested samples, are listed. The variants with over 5% variant frequency in population genome databases ( gnomAD, dbSNP, etc.) are excluded.

Pathogenic
551
Likely pathogenic
3
VUS
5,569
Likely benign
14,243
Benign
1,011

Patient Phenotypes

Proportions of phenotypes among 523 patients carrying pathogenic or likely pathogenic variants on SYNGAP1 gene are displayed below. The following symptoms were found in patients with a variant in SYNGAP1. However, patients may have been diagnosed with a different variant.

Phenotype class
Patients in 3billion (%)
Abnormality of the nervous system
44.2%
Abnormality of the eye
34%
Abnormality of the musculoskeletal system
33.1%
Abnormality of head or neck
27.9%
Abnormality of the cardiovascular system
17.4%
Abnormality of the integument
16.4%
Growth abnormality
16.4%
Abnormality of limbs
16.3%
Abnormality of the ear
15.7%
Abnormality of metabolism homeostasis
12.6%
Abnormality of the genitourinary system
11.3%
Abnormality of the digestive system
9.6%
Abnormality of the immune system
8.8%
Abnormality of the respiratory system
5.7%
Abnormality of blood and blood forming tissues
5.4%
Abnormality of prenatal development or birth
4.6%
Abnormality of the endocrine system
4.4%
Neoplasm
4.4%
Abnormal cellular phenotype
1.3%
Abnormality of the breast
1.3%
Constitutional symptom
1%
Abnormality of the voice
0.4%
Abnormality of the thoracic cavity
0%

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