Trait

Central cleft upper lip

Clinical name: Median cleft upper lip

A type of cleft lip presenting as a midline (median) gap in the upper lip.

HPO HP:0000161

Also called: Midline cleft lip
Body system: Abnormality of head or neck

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39 genes linked to Central cleft upper lip

Changes in these genes cause rare conditions in which Central cleft upper lip is seen. Most people with this trait have none of those conditions, and a gene on this list says nothing about anyone's own genome.

Gene	How often it is seen	Conditions
INTUinturned planar cell polarity protein	Always	In 1 condition
TGIF1TGFB induced factor homeobox 1	Always	In 5 conditions
DDX59DEAD-box helicase 59	Very often (80–99%)	In 2 conditions
OFD1OFD1 centriole and centriolar satellite protein	Very often (80–99%)	In 2 conditions
RIPK4receptor interacting serine/threonine kinase 4	Very often (80–99%)	In 1 condition
TCTN3tectonic family member 3	Very often (80–99%)	In 1 condition
CDONcell adhesion associated, oncogene regulated	Often (30–79%)	In 4 conditions
CILK1ciliogenesis associated kinase 1	Often (30–79%)	In 1 condition
CRIPTOcripto, EGF-CFC family member	Often (30–79%)	In 4 conditions
DISP1dispatched RND transporter family member 1	Often (30–79%)	In 4 conditions
DLL1delta like canonical Notch ligand 1	Often (30–79%)	In 4 conditions
DYNC2LI1dynein cytoplasmic 2 light intermediate chain 1	Often (30–79%)	In 1 condition
FGF8fibroblast growth factor 8	Often (30–79%)	In 4 conditions
FGFR1fibroblast growth factor receptor 1	Often (30–79%)	In 3 conditions
FOXH1forkhead box H1	Often (30–79%)	In 4 conditions
GAS1growth arrest specific 1	Often (30–79%)	In 4 conditions
GJA1gap junction protein alpha 1	Often (30–79%)	In 1 condition
GLI2GLI family zinc finger 2	Often (30–79%)	In 4 conditions
KDM6Alysine demethylase 6A	Often (30–79%)	In 1 condition
KMT2Dlysine methyltransferase 2D	Often (30–79%)	In 1 condition
NEK1NIMA related kinase 1	Often (30–79%)	In 3 conditions
NODALnodal growth differentiation factor	Often (30–79%)	In 4 conditions
NUAK2NUAK family kinase 2	Often (30–79%)	In 1 condition
PIGNphosphatidylinositol glycan anchor biosynthesis class N	Often (30–79%)	In 1 condition
PLCH1phospholipase C eta 1	Often (30–79%)	In 2 conditions
PTCH1patched 1	Often (30–79%)	In 5 conditions
SHHsonic hedgehog signaling molecule	Often (30–79%)	In 4 conditions
SIX3SIX homeobox 3	Often (30–79%)	In 5 conditions
SMC1Astructural maintenance of chromosomes 1A	Often (30–79%)	In 1 condition
STAG2STAG2 cohesin complex component	Often (30–79%)	In 3 conditions
STILSTIL centriolar assembly protein	Often (30–79%)	In 4 conditions
ZIC2Zic family zinc finger 2	Often (30–79%)	In 4 conditions
ZSWIM6zinc finger SWIM-type containing 6	Often (30–79%)	In 1 condition
EPG5ectopic P-granules 5 autophagy tethering factor	Sometimes (5–29%)	In 1 condition
ZRSR2zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2	Sometimes (5–29%)	In 1 condition
ALX3ALX homeobox 3	Not recorded	In 1 condition
HYLS1HYLS1 centriolar and ciliogenesis associated	Not recorded	In 1 condition
SMOsmoothened, frizzled class receptor	Not recorded	In 1 condition
TBC1D32TBC1 domain family member 32	Not recorded	In 1 condition

How often is among people with one of the gene's conditions, the most often across them, as the Human Phenotype Ontology records it. These pages describe traits and the research behind them; they are not a diagnosis, and a doctor or genetic counsellor is the person to ask about symptoms.

Narrower traits

Median pseudocleft lip3 genes

Broader traits

Cleft upper lip

Where this comes from

The Human Phenotype Ontology, release 2026-09-01: the trait, its names, its definition and the genes linked to it. Find out more at hpo.jax.org.
Data release 2026.10.16-c6eea6bf.

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