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Gene

SLC5A7

solute carrier family 5 member 7

Summary

Cytogenetic location
2q12.3
Coordinates
Chromosome 2: 107,986,524–108,013,994 (GRCh38)
Exons
9 exons across 27.5 kb
Protein
580 amino acids
Also known as
hCHT, CHT1, ChT
MANE Select transcript
ENST00000264047.3NM_021815.5
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

  • Charcot-Marie-Tooth Disease

    • Distal Hereditary Motor Neuropathy

      Inherited neuropathies that mainly affect motor nerves, causing weakness and wasting of the hands and feet, including SORD-related neuropathy.

      • ClinGen rates the link moderate
      • 2 GenCC submitters rate it definitive or strong

  • Congenital Myasthenic Syndrome

    • Congenital Myasthenic Syndrome (All Types)

      Umbrella term covering all congenital myasthenic syndromes, including the common CHRNE, RAPSN, DOK7 and MUSK forms.

      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Many forms respond to specific medications such as pyridostigmine, salbutamol or ephedrine, and the right choice depends on the gene involved.

  • Spinal Muscular Atrophy

    • A group of disorders characterised by degeneration of spinal cord anterior horn cells, leading to progressive muscle weakness and atrophy.

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

      Gene therapy (onasemnogene abeparvovec), antisense oligonucleotide therapy (nusinersen), oral splicing modifier (risdiplam), supportive care

How SLC5A7 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where SLC5A7 sits. SLC5A7 and 5 genes near it on chromosome 2, from 107,500,259 to 108,500,258.Chromosome 22q12.3p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3107.6 Mb107.8 Mb108 Mb108.2 Mb108.4 MbRGPD4: 107,826,892–107,892,544, forward strandRGPD4SLC5A7: 107,986,524–108,013,994, forward strandSLC5A7SULT1C3: 108,239,968–108,266,254, forward strandSULT1C3SULT1C2: 108,288,639–108,310,568, forward strandSULT1C2SULT1C4: 108,377,911–108,388,990, forward strandSULT1C4GCC2: 108,449,107–108,509,415, forward strandGCC2Diagram of SLC5A7: 9 exons on the forward strand of chromosome 2Exon 2: 4 known disease-causing sitesExon 4: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 7: 2 known disease-causing sitesExon 8: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 1: 107,986,524–107,986,763, 240 basesExon 2: 107,988,105–107,988,333, 229 basesExon 3: 107,992,106–107,992,219, 114 basesExon 4: 107,992,972–107,993,127, 156 basesExon 5: 107,997,838–107,997,986, 149 basesExon 6: 108,001,897–108,002,040, 144 basesExon 7: 108,006,049–108,006,202, 154 basesExon 8: 108,008,465–108,008,682, 218 basesExon 9: 108,010,232–108,013,994, 3,763 bases1234567895′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 5.2 kb of the gene's 27.5 kb; 1,743 of those bases code for the protein.

How a genome test reads SLC5A7

14

positions in SLC5A7 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 27.5 kb of SLC5A7, introns included, not only the 5.2 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.). SLC5A7 gene: solute carrier family 5 member 7. Retrieved 17 October 2026, from https://dantelabs.com/genes/slc5a7

Vancouver

Dante Labs. SLC5A7 gene: solute carrier family 5 member 7 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/slc5a7

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