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Gene

SLC6A9

solute carrier family 6 member 9

Summary

Cytogenetic location
1p34.1
Coordinates
Chromosome 1: 43,996,483–44,031,462 (GRCh38)
Exons
14 exons across 35 kb
Protein
633 amino acids
Inheritance
Autosomal recessive
Also known as
GLYT1, GlyT-1
MANE Select transcript
ENST00000372310.8NM_001024845.3
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 report relevant to this gene

  • Disorders of Glycine & Serine Metabolism

    • Glycine Encephalopathy (Non-Ketotic Hyperglycinemia)Autosomal recessive

      Caused by variants in GLDC, AMT or GCSH (and, in an atypical form, SLC6A9), which cause high glycine in the brain and can lead to seizures, low muscle tone and developmental problems.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing allows treatment with sodium benzoate and dextromethorphan, which can reduce seizures in some forms.

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How SLC6A9 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where SLC6A9 sits. SLC6A9 and 15 genes near it on chromosome 1, from 43,513,973 to 44,513,972.Chromosome 11p34.1p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q4443.6 Mb43.8 Mb44 Mb44.2 Mb44.4 MbPTPRF: 43,525,086–43,626,579, forward strandPTPRFKDM4A: 43,649,256–43,705,518, forward strandKDM4A: 43,650,149–43,931,014, forward strandST3GAL3: 43,705,824–43,931,167, forward strandST3GAL3ARTN: 43,933,272–43,937,244, forward strandARTNIPO13: 43,946,672–43,968,024, forward strandDPH2: 43,969,975–43,973,373, forward strandATP6V0B: 43,974,487–43,978,299, forward strandATP6V0BB4GALT2: 43,978,943–43,991,173, forward strandB4GALT2CCDC24: 43,991,352–43,996,529, forward strandCCDC24SLC6A9: 43,996,483–44,031,462, reverse strandSLC6A9KLF17: 44,118,821–44,135,387, forward strandKLF17KLF18: 44,137,821–44,141,631, reverse strandKLF18DMAP1: 44,213,427–44,230,038, forward strandDMAP1ERI3: 44,221,070–44,355,267, reverse strandERI3RNF220: 44,405,142–44,651,724, forward strandRNF220Diagram of SLC6A9: 14 exons on the reverse strand of chromosome 1Exon 8: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 6: 2 known disease-causing sitesExon 4: 1 known disease-causing siteExon 14: 43,996,483–43,997,739, 1,257 basesExon 13: 43,997,855–43,998,025, 171 basesExon 12: 44,000,767–44,000,867, 101 basesExon 11: 44,000,956–44,001,055, 100 basesExon 10: 44,001,164–44,001,298, 135 basesExon 9: 44,001,390–44,001,627, 238 basesExon 8: 44,002,313–44,002,416, 104 basesExon 7: 44,002,512–44,002,646, 135 basesExon 6: 44,002,853–44,002,985, 133 basesExon 5: 44,008,353–44,008,623, 271 basesExon 4: 44,009,965–44,010,096, 132 basesExon 3: 44,010,726–44,010,882, 157 basesExon 2: 44,024,248–44,024,362, 115 basesExon 1: 44,031,306–44,031,462, 157 bases1410515′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 35 kb; 1,902 of those bases code for the protein.

How a genome test reads SLC6A9

10

positions in SLC6A9 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 35 kb of SLC6A9, 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.). SLC6A9 gene: solute carrier family 6 member 9. Retrieved 16 October 2026, from https://dantelabs.com/genes/slc6a9

Vancouver

Dante Labs. SLC6A9 gene: solute carrier family 6 member 9 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/slc6a9

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