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Gene

WNT1

Wnt family member 1

Summary

Cytogenetic location
12q13.12
Coordinates
Chromosome 12: 48,978,322–48,982,620 (GRCh38)
Exons
4 exons across 4.3 kb
Protein
370 amino acids
Inheritance
Autosomal dominant
Previous symbols
INT1
MANE Select transcript
ENST00000293549.4NM_005430.4
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

  • Monogenic Early-Onset Osteoporosis

    • Early-onset osteoporosis (WNT1-related)Autosomal dominant

      Childhood or young-adult osteoporosis with fractures linked to WNT1 variants.

      • 2 GenCC submitters rate it definitive or strong

  • Osteogenesis Imperfecta

    • A group of inherited connective tissue disorders causing fragile bones that break easily, often with blue sclerae, hearing loss and dental problems.

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

      Cyclic IV bisphosphonates (pamidronate, zoledronate); orthopedic rodding of long bones; physical therapy; denosumab (in clinical use for pediatric OI); romosozumab (in development); hearing monitoring; dental management for dentinogenesis imperfecta

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 WNT1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 12, with a bracket where WNT1 sits. WNT1 and 31 genes near it on chromosome 12, from 48,480,471 to 49,480,470.Chromosome 1212q13.12p13.33p13.32p13.31p13.2p13.1p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11q12q13.11q13.12q13.13q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.11q24.12q24.13q24.21q24.22q24.23q24.31q24.32q24.3348.6 Mb48.8 Mb49 Mb49.2 Mb49.4 MbLYLDT1: 48,482,498–48,496,524, forward strandLYLDT1OR8S1: 48,525,632–48,526,570, forward strandOR8S1OR5BS1: 48,559,882–48,562,956, forward strandOR5BS1LALBA: 48,567,684–48,571,865, reverse strandLALBAKANSL2: 48,653,211–48,682,265, reverse strandKANSL2CCNT1: 48,687,601–48,716,998, reverse strandCCNT1SPMIP11: 48,727,435–48,765,790, forward strandSPMIP11ADCY6: 48,766,191–48,789,906, reverse strandADCY6CACNB3: 48,813,794–48,828,942, forward strandCACNB3DDX23: 48,829,756–48,852,842, reverse strandDDX23RND1: 48,857,134–48,865,870, reverse strandRND1ARF3: 48,903,141–48,957,531, reverse strandARF3: 48,903,503–48,957,365, reverse strandDRC2: 48,904,105–48,931,840, forward strandFKBP11: 48,921,518–48,927,909, reverse strandFKBP11WNT10B: 48,965,185–48,972,669, reverse strandWNT10BWNT1: 48,978,322–48,982,620, forward strandWNT1DDN: 48,995,149–48,999,375, reverse strandDDNPRKAG1: 49,002,272–49,018,820, reverse strandPRKAG1: 49,002,274–49,024,075, reverse strandKMT2D: 49,018,975–49,060,794, reverse strandKMT2DRHEBL1: 49,064,675–49,070,127, reverse strandRHEBL1DHH: 49,086,656–49,094,807, reverse strandDHHLMBR1L: 49,096,550–49,110,900, reverse strandLMBR1LTUBA1B: 49,127,780–49,131,398, reverse strandTUBA1BTUBA1A: 49,184,146–49,189,324, reverse strandTUBA1ATUBA1C: 49,188,736–49,274,600, forward strandTUBA1CPRPH: 49,295,141–49,298,686, forward strandPRPHTROAP: 49,323,165–49,331,735, forward strandTROAPC1QL4: 49,332,409–49,337,227, reverse strandC1QL4DNAJC22: 49,345,607–49,357,546, forward strandDNAJC22SPATS2: 49,366,240–49,528,438, forward strandSPATS2Diagram of WNT1: 4 exons on the forward strand of chromosome 12Exon 2: 3 known disease-causing sitesExon 3: 8 known disease-causing sitesExon 4: 7 known disease-causing sitesExon 1: 48,978,322–48,978,754, 433 basesExon 2: 48,979,468–48,979,721, 254 basesExon 3: 48,980,424–48,980,689, 266 basesExon 4: 48,981,152–48,982,620, 1,469 bases12345′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 2.4 kb of the gene's 4.3 kb; 1,113 of those bases code for the protein.

How a genome test reads WNT1

19

positions in WNT1 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 4.3 kb of WNT1, introns included, not only the 2.4 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.). WNT1 gene: Wnt family member 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/wnt1

Vancouver

Dante Labs. WNT1 gene: Wnt family member 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/wnt1

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