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Gene

SYNGAP1

synaptic Ras GTPase activating protein 1

Summary

Cytogenetic location
6p21.32
Coordinates
Chromosome 6: 33,420,065–33,453,689 (GRCh38)
Exons
19 exons across 33.6 kb
Protein
1,343 amino acids
Also known as
SYNGAP, RASA5, KIAA1938
MANE Select transcript
ENST00000646630.1NM_006772.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

    • Epilepsy (Full Panel)

      • Epilepsy

        One of 171 genes linked to it

        A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.

        • 3 GenCC submitters rate it definitive or strong

    • Intellectual Disability

      • One of 233 genes linked to it

        • 3 GenCC submitters rate it definitive or strong

    How SYNGAP1 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 6, with a bracket where SYNGAP1 sits. SYNGAP1 and 33 genes near it on chromosome 6, from 32,936,877 to 33,936,876.Chromosome 66p21.32p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12q13q14.1q14.2q14.3q15q16.1q16.2q16.3q21q22.1q22.2q22.31q22.32q22.33q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q26q2733 Mb33.2 Mb33.4 Mb33.6 Mb33.8 MbHLA-DMB: 32,929,338–32,941,490, reverse strandHLA-DMB: 32,937,364–32,953,122, reverse strandHLA-DMA: 32,948,613–32,969,094, reverse strandHLA-DMABRD2: 32,968,564–32,981,505, forward strandBRD2HLA-DOA: 33,004,178–33,009,617, reverse strandHLA-DOAHLA-DPA1: 33,064,569–33,080,781, reverse strandHLA-DPA1HLA-DPB1: 33,073,786–33,091,655, forward strandHLA-DPB1COL11A2: 33,162,681–33,192,802, reverse strandRXRB: 33,193,585–33,200,693, reverse strandRXRBSLC39A7: 33,200,305–33,204,439, forward strandSLC39A7HSD17B8: 33,204,631–33,206,831, forward strandHSD17B8RING1: 33,208,033–33,212,722, forward strandRING1VPS52: 33,250,272–33,272,047, reverse strandVPS52RPS18: 33,271,730–33,276,513, forward strandB3GALT4: 33,277,123–33,284,832, forward strandWDR46: 33,279,103–33,289,523, reverse strandPFDN6: 33,288,680–33,298,441, forward strandRGL2: 33,291,180–33,299,534, reverse strandTAPBP: 33,299,694–33,314,284, reverse strandZBTB22: 33,314,406–33,318,021, reverse strandZBTB22DAXX: 33,318,558–33,323,259, reverse strandDAXX: 33,321,386–33,329,286, reverse strandSMIM40: 33,323,628–33,329,279, reverse strandSMIM40KIFC1: 33,391,429–33,410,441, forward strandKIFC1PHF1: 33,410,360–33,416,453, forward strandPHF1CUTA: 33,416,442–33,418,381, reverse strandCUTASYNGAP1: 33,420,065–33,453,689, forward strandSYNGAP1ZBTB9: 33,453,970–33,457,544, forward strandZBTB9BAK1: 33,568,791–33,580,305, reverse strandBAK1ITPR3: 33,620,331–33,696,575, forward strandITPR3UQCC2: 33,690,635–33,711,748, reverse strandUQCC2IP6K3: 33,721,314–33,750,520, reverse strandIP6K3LEMD2: 33,771,202–33,789,173, reverse strandLEMD2MLN: 33,794,673–33,804,006, reverse strandMLNDiagram of SYNGAP1: 19 exons on the forward strand of chromosome 6Exon 1: 2 known disease-causing sitesExon 2: 6 known disease-causing sitesExon 3: 5 known disease-causing sitesExon 4: 7 known disease-causing sitesExon 5: 13 known disease-causing sitesExon 6: 7 known disease-causing sitesExon 7: 8 known disease-causing sitesExon 8: 52 known disease-causing sitesExon 9: 12 known disease-causing sitesExon 10: 14 known disease-causing sitesExon 11: 20 known disease-causing sitesExon 12: 12 known disease-causing sitesExon 13: 12 known disease-causing sitesExon 15: 74 known disease-causing sitesExon 16: 8 known disease-causing sitesExon 17: 17 known disease-causing sitesExon 18: 2 known disease-causing sitesExon 19: 1 known disease-causing siteExon 1: 33,420,065–33,420,331, 267 basesExon 2: 33,423,477–33,423,598, 122 basesExon 3: 33,425,798–33,425,903, 106 basesExon 4: 33,432,161–33,432,252, 92 basesExon 5: 33,432,685–33,432,806, 122 basesExon 6: 33,435,152–33,435,305, 154 basesExon 7: 33,435,515–33,435,613, 99 basesExon 8: 33,437,668–33,438,291, 624 basesExon 9: 33,438,419–33,438,563, 145 basesExon 10: 33,438,775–33,438,919, 145 basesExon 11: 33,440,729–33,440,965, 237 basesExon 12: 33,441,173–33,441,374, 202 basesExon 13: 33,441,581–33,441,759, 179 basesExon 14: 33,442,453–33,442,494, 42 basesExon 15: 33,442,889–33,443,960, 1,072 basesExon 16: 33,444,444–33,444,617, 174 basesExon 17: 33,446,575–33,446,786, 212 basesExon 18: 33,447,843–33,447,933, 91 basesExon 19: 33,451,760–33,453,689, 1,930 bases124681012141618195′3′

    Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

    Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

    Nearby genes from Ensembl release 116, on GRCh38.

    Exons make up 6 kb of the gene's 33.6 kb; 4,032 of those bases code for the protein.

    How a genome test reads SYNGAP1

    304

    positions in SYNGAP1 where ClinVar classes a change as pathogenic or likely pathogenic

    304 of them (100%) fall in regions short reads find hard.

    • MHC (304 sites)The major histocompatibility complex (HLA genes), highly polymorphic and poorly represented by a single reference.

    A whole genome covers all 33.6 kb of SYNGAP1, introns included, not only the 6 kb of exons.

    Where this comes from

    • HGNC: the gene's symbol, name, other symbols and location.
    • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
    • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
    • The ACMG secondary findings list, SF v3.2.
    • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
    • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
    • Data release 2026.10.16-c6eea6bf.

    Cite this page

    APA

    Dante Labs. (n.d.). SYNGAP1 gene: synaptic Ras GTPase activating protein 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/syngap1

    Vancouver

    Dante Labs. SYNGAP1 gene: synaptic Ras GTPase activating protein 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/syngap1

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