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Gene

LETM1

leucine zipper and EF-hand containing transmembrane protein 1

Summary

Cytogenetic location
4p16.3
Coordinates
Chromosome 4: 1,811,479–1,856,156 (GRCh38)
Exons
14 exons across 44.7 kb
Protein
739 amino acids
Also known as
SLC55A1, Mdm38
MANE Select transcript
ENST00000302787.3NM_012318.3
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated reports relevant to this gene

No Genome Test report reads LETM1 yet. The test sequences your whole genome, so your data includes it all the same.

How LETM1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 4, with a bracket where LETM1 sits. LETM1 and 17 genes near it on chromosome 4, from 1,333,818 to 2,333,817.Chromosome 44p16.3p16.3p16.2p16.1p15.33p15.32p15.31p15.2p15.1p14p13p12p11q11q12q13.1q13.2q13.3q21.1q21.21q21.22q21.23q21.3q22.1q22.2q22.3q23q24q25q26q27q28.1q28.2q28.3q31.1q31.21q31.22q31.23q31.3q32.1q32.2q32.3q33q34.1q34.2q34.3q35.1q35.21.4 Mb1.6 Mb1.8 Mb2 Mb2.2 MbMAEA: 1,289,839–1,340,148, forward strandMAEAUVSSA: 1,345,691–1,395,989, forward strandUVSSANKX1-1: 1,402,932–1,406,442, reverse strandNKX1-1FAM53A: 1,617,915–1,684,356, reverse strandFAM53ASLBP: 1,692,731–1,712,344, reverse strandSLBPTACC3: 1,712,858–1,745,178, forward strandTACC3TMEM129: 1,715,951–1,721,367, reverse strandTMEM129FGFR3: 1,793,286–1,808,873, forward strandFGFR3LETM1: 1,811,479–1,856,156, reverse strandLETM1NSD2: 1,870,559–1,982,207, forward strandNSD2NELFA: 1,982,715–2,041,903, reverse strandNELFANICOL1: 2,040,628–2,043,964, forward strandNICOL1ASPNAT: 2,058,662–2,069,089, forward strandASPNATPOLN: 2,071,918–2,242,138, reverse strandPOLN: 2,078,998–2,242,276, reverse strandHAUS3: 2,227,462–2,242,190, reverse strandHAUS3MXD4: 2,247,431–2,262,144, reverse strandMXD4ZFYVE28: 2,269,578–2,418,794, reverse strandZFYVE28Diagram of LETM1: 14 exons on the reverse strand of chromosome 4Exon 12: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 14: 1,811,479–1,814,573, 3,095 basesExon 13: 1,815,664–1,815,802, 139 basesExon 12: 1,816,727–1,816,914, 188 basesExon 11: 1,819,338–1,819,472, 135 basesExon 10: 1,822,181–1,822,312, 132 basesExon 9: 1,822,988–1,823,131, 144 basesExon 8: 1,823,644–1,823,775, 132 basesExon 7: 1,825,564–1,825,683, 120 basesExon 6: 1,832,744–1,832,947, 204 basesExon 5: 1,834,845–1,834,982, 138 basesExon 4: 1,836,429–1,836,572, 144 basesExon 3: 1,841,347–1,841,797, 451 basesExon 2: 1,849,149–1,849,209, 61 basesExon 1: 1,855,869–1,856,156, 288 bases141210864215′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 5.4 kb of the gene's 44.7 kb; 2,220 of those bases code for the protein.

Sequencing LETM1

18Moderate

How hard LETM1 is to sequence with short reads, out of 100

  • Mappability2%
  • Homology50%
  • Repeats6.3%
  • GC content13%
  • Reference coverage0%

3

positions in LETM1 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 44.7 kb of LETM1, introns included, not only the 5.4 kb of exons.

Traits linked to LETM1

The Human Phenotype Ontology lists these as features of the rare conditions LETM1 can cause. Each trait's page lists the other genes linked to it.

External links

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.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.17-8666dff2.

Cite this page

APA

Dante Labs. (n.d.). LETM1 gene: leucine zipper and EF-hand containing transmembrane protein 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/letm1

Vancouver

Dante Labs. LETM1 gene: leucine zipper and EF-hand containing transmembrane protein 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/letm1

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