Skip to content
Use your HSA or FSA funds

Gene

SYN1

synapsin I

Summary

Cytogenetic location
Xp11.3-p11.23
Coordinates
Chromosome X: 47,571,901–47,619,857 (GRCh38)
Exons
13 exons across 48 kb
Protein
705 amino acids
Previous symbols
MRX50
MANE Select transcript
ENST00000295987.13NM_006950.3
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)

    • X-Linked Complex Neurodevelopmental Disorder

      A complex neurodevelopmental disorder that is transmitted via X-linked inheritance, and is characterized by intellectual disability, autism and epilepsy.

      • ClinGen rates the link definitive
      • 1 GenCC submitter rates it definitive or strong
    • 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.

      • 2 GenCC submitters rate it definitive or strong

Broader groupings

How SYN1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome X, with a bracket where SYN1 sits. SYN1 and 17 genes near it on chromosome X, from 47,095,879 to 48,095,878.Chromosome XXp11.3-p11.23p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2847.2 Mb47.4 Mb47.6 Mb47.8 Mb48 MbRGN: 47,061,388–47,096,431, forward strandRGNNDUFB11: 47,142,071–47,145,507, reverse strandNDUFB11RBM10: 47,144,284–47,186,814, forward strandRBM10UBA1: 47,190,713–47,215,173, forward strandUBA1CDK16: 47,217,860–47,230,000, forward strandCDK16USP11: 47,232,866–47,248,328, forward strandUSP11ZNF157: 47,366,479–47,414,624, forward strandZNF157ZNF41: 47,444,693–47,483,247, reverse strandZNF41ARAF: 47,561,043–47,571,921, forward strandARAFSYN1: 47,571,901–47,619,857, reverse strandSYN1TIMP1: 47,582,227–47,586,793, forward strandTIMP1CFP: 47,621,537–47,630,305, reverse strandCFPELK1: 47,631,617–47,650,604, reverse strandELK1UXT: 47,651,792–47,659,301, reverse strandUXTZNF81: 47,836,471–48,003,066, forward strandZNF81ZNF182: 47,974,851–48,004,375, reverse strandZNF182ZNF630: 47,983,356–48,071,893, reverse strandZNF630SPACA5: 48,004,336–48,009,735, forward strandSPACA5Diagram of SYN1: 13 exons on the reverse strand of chromosome XExon 13: 1 known disease-causing siteExon 12: 13 known disease-causing sitesExon 11: 2 known disease-causing sitesExon 10: 7 known disease-causing sitesExon 9: 2 known disease-causing sitesExon 8: 3 known disease-causing sitesExon 7: 2 known disease-causing sitesExon 5: 3 known disease-causing sitesExon 4: 2 known disease-causing sitesExon 2: 1 known disease-causing siteExon 1: 8 known disease-causing sitesExon 13: 47,571,901–47,572,999, 1,099 basesExon 12: 47,574,002–47,574,590, 589 basesExon 11: 47,574,688–47,574,775, 88 basesExon 10: 47,575,128–47,575,274, 147 basesExon 9: 47,576,131–47,576,233, 103 basesExon 8: 47,576,332–47,576,406, 75 basesExon 7: 47,576,498–47,576,640, 143 basesExon 6: 47,577,439–47,577,501, 63 basesExon 5: 47,604,978–47,605,067, 90 basesExon 4: 47,605,223–47,605,379, 157 basesExon 3: 47,606,945–47,607,036, 92 basesExon 2: 47,607,141–47,607,198, 58 basesExon 1: 47,619,352–47,619,857, 506 bases1310515′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 3.2 kb of the gene's 48 kb; 2,118 of those bases code for the protein.

How a genome test reads SYN1

50

positions in SYN1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 48 kb of SYN1, introns included, not only the 3.2 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.). SYN1 gene: synapsin I. Retrieved 16 October 2026, from https://dantelabs.com/genes/syn1

Vancouver

Dante Labs. SYN1 gene: synapsin I [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/syn1

One test. A lifetime of answers.

From $449Free shipping · Results in 6–8 weeks

Get my Genome Test