SIX3 – Holoprosencephaly

SIX3 encodes a homeodomain transcription factor that regulates early forebrain and eye development. Heterozygous variants in SIX3 underlie holoprosencephaly (HPE), a spectrum of forebrain cleavage defects (cyclopia to microforms) classified as HPE2 on chromosome 2p21. SIX3 is highly conserved and functions upstream of Sonic hedgehog (SHH) signaling in the ventral diencephalon (PMID:11039582).

Autosomal dominant inheritance with variable expressivity and reduced penetrance characterises SIX3-associated HPE. In a cohort of 800 HPE probands, SIX3 mutations were identified in 4.7% (n=38), and cascade testing revealed a total of 138 affected individuals across multiple families (PMID:19346217). A large pedigree study documented 15 mutation carriers with phenotypes ranging from alobar HPE to asymptomatic adults, illustrating intrafamilial variability (PMID:19353631).

The SIX3 variant spectrum comprises at least 46 distinct alleles: missense, nonsense, frameshift, and small indels clustered in the SIX and homeodomains. A recurrent missense, c.770G>C (p.Arg257Pro), disrupts a conserved residue and abrogates interaction with the nuclear receptor NOR1 (PMID:15523651).

Functional studies define haploinsufficiency as the primary mechanism: Six3+/- mice and knock-in of HPE-associated alleles fail to activate Shh in the rostral diencephalon ventral midline, recapitulating human HPE phenotypes (PMID:18694563). Zebrafish assays demonstrate that 89% of SIX3 mutations are loss-of-function, underscoring concordant experimental data (PMID:18791198).

Although rare microdeletions and novel regulatory variants in SIX3 exhibit incomplete penetrance, no large studies refute the dominant association of SIX3 with HPE. Inherited whole-gene deletions in two families showed reduced penetrance but confirmed disease linkage by molecular cascade testing (PMID:28670735).

Integration of genetic and experimental evidence firmly establishes SIX3 haploinsufficiency as a cause of autosomal dominant HPE with variable expressivity. Molecular diagnosis enables accurate recurrence risk assessment and guides prenatal counseling. Key take-home: SIX3 testing is clinically actionable for HPE, informing diagnosis, family planning, and interpretation of variable phenotypes.

References

• Journal of medical genetics • 2009 • Clinical spectrum of SIX3-associated mutations in holoprosencephaly: correlation between genotype, phenotype and function. PMID:19346217
• American journal of medical genetics. Part A • 2009 • A novel SIX3 mutation segregates with holoprosencephaly in a large family. PMID:19353631
• Human mutation • 2004 • Functional characterization of SIX3 homeodomain mutations in holoprosencephaly: interaction with the nuclear receptor NR4A3/NOR1. PMID:15523651
• Developmental cell • 2008 • Haploinsufficiency of Six3 fails to activate Sonic hedgehog expression in the ventral forebrain and causes holoprosencephaly. PMID:18694563
• Human molecular genetics • 2008 • Mutations in the human SIX3 gene in holoprosencephaly are loss of function. PMID:18791198
• Congenital anomalies • 2018 • SIX3 deletions and incomplete penetrance in families affected by holoprosencephaly. PMID:28670735

Evidence Based Scoring (AI generated)