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Gene

GRHL3

grainyhead like transcription factor 3

Summary

Cytogenetic location
1p36.11
Coordinates
Chromosome 1: 24,319,357–24,355,318 (GRCh38)
Exons
16 exons across 36 kb
Protein
602 amino acids
Inheritance
Autosomal dominant
Also known as
SOM
Previous symbols
TFCP2L4
MANE Select transcript
ENST00000361548.9NM_198173.3
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

  • Hereditary Orofacial Clefting

    • GRHL3-related Orofacial CleftingAutosomal dominant

      Cleft palate, sometimes with other features of van der Woude syndrome, caused by variants in the GRHL3 gene.

      • ClinGen rates the link definitive
      • 1 GenCC submitter rates it definitive or strong
    • Van der Woude SyndromeAutosomal dominant

      Cleft lip and/or palate together with pits in the lower lip, usually caused by IRF6 variants and less often by GRHL3 variants, with incomplete penetrance and variable features.

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

      Knowing can inform recurrence risk, which is up to 50% for each child, and support early surgical and dental planning.

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 GRHL3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 1, with a bracket where GRHL3 sits. GRHL3 and 14 genes near it on chromosome 1, from 23,837,338 to 24,837,337.Chromosome 11p36.11p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q4424 Mb24.2 Mb24.4 Mb24.6 Mb24.8 MbHMGCL: 23,801,877–23,838,620, reverse strandHMGCLFUCA1: 23,845,077–23,868,361, reverse strandFUCA1CNR2: 23,870,515–23,913,396, reverse strandCNR2PNRC2: 23,956,839–23,963,776, forward strandPNRC2SRSF10: 23,962,474–23,980,927, reverse strandSRSF10MYOM3: 24,054,822–24,112,190, reverse strandMYOM3IL22RA1: 24,119,769–24,143,301, reverse strandIL22RA1IFNLR1: 24,154,168–24,187,959, reverse strandIFNLR1GRHL3: 24,319,357–24,355,318, forward strandGRHL3STPG1: 24,355,830–24,416,934, reverse strandSTPG1NIPAL3: 24,413,515–24,476,735, forward strandNIPAL3RCAN3: 24,502,320–24,541,040, forward strandRCAN3NCMAP: 24,556,061–24,609,328, forward strandNCMAPSRRM1: 24,631,716–24,673,281, forward strandSRRM1CLIC4: 24,745,342–24,844,324, forward strandCLIC4Diagram of GRHL3: 16 exons on the forward strand of chromosome 1Exon 4: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 9: 2 known disease-causing sitesExon 10: 1 known disease-causing siteExon 1: 24,319,357–24,319,568, 212 basesExon 2: 24,331,426–24,331,612, 187 basesExon 3: 24,334,645–24,334,706, 62 basesExon 4: 24,336,482–24,336,827, 346 basesExon 5: 24,337,078–24,337,151, 74 basesExon 6: 24,337,636–24,337,789, 154 basesExon 7: 24,337,992–24,338,103, 112 basesExon 8: 24,339,668–24,339,762, 95 basesExon 9: 24,342,115–24,342,273, 159 basesExon 10: 24,342,694–24,342,772, 79 basesExon 11: 24,342,892–24,343,025, 134 basesExon 12: 24,344,897–24,344,931, 35 basesExon 13: 24,346,553–24,346,641, 89 basesExon 14: 24,347,468–24,347,553, 86 basesExon 15: 24,350,058–24,350,122, 65 basesExon 16: 24,354,374–24,355,318, 945 bases12468101214165′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 2.8 kb of the gene's 36 kb; 1,809 of those bases code for the protein.

How a genome test reads GRHL3

7

positions in GRHL3 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 36 kb of GRHL3, introns included, not only the 2.8 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.). GRHL3 gene: grainyhead like transcription factor 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/grhl3

Vancouver

Dante Labs. GRHL3 gene: grainyhead like transcription factor 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/grhl3

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