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Gene

LEF1

lymphoid enhancer binding factor 1

Summary

Cytogenetic location
4q25
Coordinates
Chromosome 4: 108,047,548–108,168,932 (GRCh38)
Exons
12 exons across 121.4 kb
Protein
399 amino acids
Inheritance
Autosomal dominant
Also known as
TCF1ALPHA, TCF10, TCF7L3
MANE Select transcript
ENST00000265165.6NM_016269.5
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 report relevant to this gene

  • Ectodermal Dysplasias

    • Ectodermal dysplasia 17 with or without limb malformationsAutosomal dominant

      A LEF1 disorder with sparse hair, dental anomalies and sometimes limb differences.

      • 1 GenCC submitter rates it definitive or strong

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How LEF1 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 LEF1 sits. LEF1 and 4 genes near it on chromosome 4, from 107,608,240 to 108,608,239.Chromosome 44q25p16.3p16.2p16.1p15.33p15.32p15.31p15.2p15.1p14p13p12p11q11q12q13.1q13.2q13.3q21.1q21.21q21.22q21.23q21.3q22.1q22.2q22.3q23q24q25q26q27q28.1q28.2q28.3q31.1q31.21q31.22q31.23q31.3q32.1q32.2q32.3q33q34.1q34.2q34.3q35.1q35.2107.8 Mb108 Mb108.2 Mb108.4 Mb108.6 MbPAPSS1: 107,590,276–107,720,395, reverse strandPAPSS1SGMS2: 107,824,563–107,915,047, forward strandSGMS2CYP2U1: 107,931,324–107,953,465, forward strandCYP2U1HADH: 107,989,683–108,035,241, forward strandHADHLEF1: 108,047,548–108,168,932, reverse strandLEF1Diagram of LEF1: 12 exons on the reverse strand of chromosome 4Exon 4: 2 known disease-causing sitesExon 12: 108,047,548–108,048,751, 1,204 basesExon 11: 108,063,623–108,063,663, 41 basesExon 10: 108,064,336–108,064,384, 49 basesExon 9: 108,070,663–108,070,770, 108 basesExon 8: 108,078,220–108,078,382, 163 basesExon 7: 108,079,492–108,079,614, 123 basesExon 6: 108,081,586–108,081,669, 84 basesExon 5: 108,083,356–108,083,446, 91 basesExon 4: 108,089,125–108,089,257, 133 basesExon 3: 108,163,568–108,163,701, 134 basesExon 2: 108,165,097–108,165,163, 67 basesExon 1: 108,167,555–108,168,932, 1,378 bases1210864215′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 3.6 kb of the gene's 121.4 kb; 1,200 of those bases code for the protein.

How a genome test reads LEF1

2

positions in LEF1 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 121.4 kb of LEF1, introns included, not only the 3.6 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.). LEF1 gene: lymphoid enhancer binding factor 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/lef1

Vancouver

Dante Labs. LEF1 gene: lymphoid enhancer binding factor 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/lef1

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