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Holoprosencephaly

Rare and Inherited Diseases · NLM MeSH · updated 2026-10-29 · version 1

Citations verified against PubMedNot yet clinician-reviewed10 referencesApproximately 5 min read

Anterior midline brain, cranial, and facial malformations resulting from the failure of the embryonic prosencephalon to undergo segmentation and cleavage.

Table of Contents

1. Definition2. Research landscape3. Reading the evidence4. Open-access studies5. Key reviews6. References7. About this article

Definition and research guide

This page combines a MeSH definition, publication statistics and selected research abstracts. It is a starting point for reading the literature, not a medical textbook or a systematic evidence review.

Content available: 4 complete abstracts (1,006 words), 10 references. Full article text is not stored or reproduced here; follow the PMID, DOI or PMC links to read the original sources and their access terms.

Definition

Anterior midline brain, cranial, and facial malformations resulting from the failure of the embryonic prosencephalon to undergo segmentation and cleavage. Alobar prosencephaly is the most severe form and features anophthalmia; cyclopia; severe intellectual disability; cleft lip; cleft palate; seizures; and microcephaly. Semilobar holoprosencepaly is characterized by hypotelorism, microphthalmia, coloboma, nasal malformations, and variable degrees of intellectual disability. Lobar holoprosencephaly is associated with mild (or absent) facial malformations and intellectual abilities that range from mild intellectual disability to normal. Holoprosencephaly is associated with chromosome abnormalities.

Definition: NLM Medical Subject Headings (MeSH) scope note (Public domain (U.S. National Library of Medicine); attribution requested). View the MeSH record.

Also known as: Holoprosencephalies; Arhinencephaly; Arhinencephalies; Alobar Holoprosencephaly; Alobar Holoprosencephalies; Holoprosencephalies, Alobar; Holoprosencephaly, Alobar; Holoprosencephaly, Familial Alobar.

Where it fits in the MeSH classification

Broader topics
Craniofacial Abnormalities; Agenesis of Corpus Callosum; Abnormalities, Multiple; Chromosome Disorders

Related concepts

  • Intellectual Disability
  • Cleft Lip
  • Cleft Palate
  • Seizures
  • Chromosome Abnormalities

Research landscape

PubMed indexes 1,321 records tagged with the MeSH heading “Holoprosencephaly” (counts retrieved 2026-10-29). 138 of them (10.4%) were published from 2020 onward, and the busiest period so far is 2000-2009 with 432 records.

Reviews account for 236 records (17.9%) and meta-analyses for 1. Randomized controlled trials number 1 (0.1%) as a share of all records on the topic. Randomized trials make up only a small share of this literature, so much of what is known comes from laboratory, observational or descriptive work.

PubMed records by publication periodthrough 1999: 352 records; 2000-2009: 432 records; 2010-2019: 399 records; 2020 onward: 138 records352through 19994322000-20093992010-20191382020 onward
Records in PubMed indexed with this heading, by publication period. Real counts from NCBI E-utilities; the final period covers only part of the current year. Volume reflects how much has been published, not how strong the evidence is.
Show the data
PeriodRecords
through 1999352
2000-2009432
2010-2019399
2020 onward138
Share of records by publication typeReviews: 17.9 percent; Meta-analyses: 0.1 percent; Randomized controlled trials: 0.1 percentReviews17.9% (236)Meta-analyses0.1% (1)Randomized controlled trials0.1% (1)
Share of all PubMed records on this heading that carry each publication type. Types overlap with other records, so the shares do not sum to 100%.
Publication-type chart data
Publication types among 1,321 PubMed records
TypeRecordsShare
Reviews23617.9%
Meta-analyses10.1%
Randomized controlled trials10.1%

Method: PubMed query "Holoprosencephaly"[MeSH Terms] with publication-type and date filters, retrieved 2026-10-29.

Reading the evidence in rare and inherited diseases

Rare conditions are difficult to study: few patients means small studies, case reports and registries are common, and randomized trials are the exception. Small samples limit precision and can exaggerate effects, and cases reported in the literature may be the most severe or unusual. Evidence from many small studies is best read together. Check how patients were identified, how many were included and how long they were followed.

Evidence from open-access studies

These open-access studies come from PubMed’s best-match results for this heading (papers whose main topic it is), ranked here by citation count, with one recent addition. Each abstract is reproduced in full under its recorded open licence so that you can read the authors’ own words. They illustrate the literature; they are not a systematic summary of it. Citation counts measure attention, not reliability or clinical benefit.

Study comparison — selected abstracts, not a systematic review
Study / authorsYearSource label / designEurope PMC citationsLicence / source
Holoprosencephaly
Dubourg C, Bendavid C, Pasquier L, Henry C, Odent S, David V
2007Review article
Design not recorded in structured metadata
251cc by
PMID 17274816 · DOI · PMC1802747
The teratogenic effects of prenatal ethanol exposure are exacerbated by Sonic Hedgehog or GLI2 haploinsufficiency in the mouse
Kietzman HW, Everson JL, Sulik KK, Lipinski RJ
2014Research article
Design not recorded in structured metadata
104cc by
PMID 24586787 · DOI · PMC3929747
Loss of Tgif function causes holoprosencephaly by disrupting the SHH signaling pathway
Taniguchi K, Anderson AE, Sutherland AE, Wotton D
2012Research article
Design not recorded in structured metadata
69cc by
PMID 22383895 · DOI · PMC3285584
Ophthalmologic Findings in an Induced Model of Holoprosencephaly in Zebrafish
Bulk J, Kyrychenko V, Heermann S
2025Research article
Design not recorded in structured metadata
1cc by
PMID 41207878 · DOI · PMC12597868

Holoprosencephaly [1]

Review article Dubourg C, Bendavid C, Pasquier L, Henry C, Odent S, David V · · 2007 · cited 251 times (Europe PMC)

Abstract reading summary — source excerpts
Opening excerpt
Holoprosencephaly (HPE) is a complex brain malformation resulting from incomplete cleavage of the prosencephalon, occurring between the 18th and the 28th day of gestation and affecting both the forebrain and the face.
Closing excerpt
Mildly affected children may exhibit few symptoms and may live a normal life.
Interpretation limits
Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (324 words)

Holoprosencephaly (HPE) is a complex brain malformation resulting from incomplete cleavage of the prosencephalon, occurring between the 18th and the 28th day of gestation and affecting both the forebrain and the face. It is estimated to occur in 1/16,000 live births and 1/250 conceptuses. Three ranges of increasing severity are described: lobar, semi-lobar and alobar HPE. Another milder subtype of HPE called middle interhemispheric variant (MIHF) or syntelencephaly is also reported. In most of the cases, facial anomalies are observed in HPE, like cyclopia, proboscis, median or bilateral cleft lip/palate in severe forms, ocular hypotelorism or solitary median maxillary central incisor in minor forms. These latter midline defects can occur without the cerebral malformations and then are called microforms. Children with HPE have many medical problems: developmental delay and feeding difficulties, epilepsy, instability of temperature, heart rate and respiration. Endocrine disorders like diabetes insipidus, adrenal hypoplasia, hypogonadism, thyroid hypoplasia and growth hormone deficiency are frequent. To date, seven genes have been positively implicated in HPE: Sonic hedgehog (SHH), ZIC2, SIX3, TGIF, PTCH, GLI2 and TDGF1. A molecular diagnosis can be performed by gene sequencing and allele quantification for the four main genes SHH, ZIC2, SIX3 and TGIF. Major rearrangements of the subtelomeres can also be identified by multiplex ligation-dependent probe amplification (MLPA). Nevertheless, in about 70% of cases, the molecular basis of the disease remains unknown, suggesting the existence of several other candidate genes or environmental factors. Consequently, a "multiple-hit hypothesis" of genetic and/or environmental factors (like maternal diabetes) has been proposed to account for the extreme clinical variability. In a practical approach, prenatal diagnosis is based on ultrasound and magnetic resonance imaging (MRI) rather than on molecular diagnosis. Treatment is symptomatic and supportive, and requires a multidisciplinary management. Child outcome depends on the HPE severity and the medical and neurological complications associated. Severely affected children have a very poor prognosis. Mildly affected children may exhibit few symptoms and may live a normal life.

Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 17274816 · DOI · PMC1802747

The teratogenic effects of prenatal ethanol exposure are exacerbated by Sonic Hedgehog or GLI2 haploinsufficiency in the mouse [2]

Research article Kietzman HW, Everson JL, Sulik KK, Lipinski RJ · · 2014 · cited 104 times (Europe PMC)

Abstract reading summary — source excerpts
Opening excerpt
Disruption of the Hedgehog signaling pathway has been implicated as an important molecular mechanism in the pathogenesis of fetal alcohol syndrome.
Closing excerpt
By demonstrating an interaction between specific genetic and environmental risk factors, this study provides important insights into the multifactorial etiology and complex pathogenesis of fetal alcohol syndrome and holoprosencephaly.
Interpretation limits
Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (262 words)

Disruption of the Hedgehog signaling pathway has been implicated as an important molecular mechanism in the pathogenesis of fetal alcohol syndrome. In severe cases, the abnormalities of the face and brain that result from prenatal ethanol exposure fall within the spectrum of holoprosencephaly. Single allele mutations in the Hh pathway genes Sonic Hedgehog (SHH) and GLI2 cause holoprosencephaly with extremely variable phenotypic penetrance in humans. Here, we tested whether mutations in these genes alter the frequency or severity of ethanol-induced dysmorphology in a mouse model. Timed pregnancies were established by mating Shh(+/-) or Gli2(+/-) male mice backcrossed to C57BL/6J strain, with wildtype females. On gestational day 7, dams were treated with two i.p. doses of 2.9 g/kg ethanol (or vehicle alone), administered four hrs apart. Fetuses were then genotyped and imaged, and the severity of facial dysmorphology was assessed. Following ethanol exposure, mean dysmorphology scores were increased by 3.2- and 6.6-fold in Shh(+/-) and Gli2(+/-) groups, respectively, relative to their wildtype littermates. Importantly, a cohort of heterozygous fetuses exhibited phenotypes not typically produced in this model but associated with severe holoprosencephaly, including exencephaly, median cleft lip, otocephaly, and proboscis. As expected, a correlation between the severity of facial dysmorphology and medial forebrain deficiency was observed in affected animals. While Shh(+/-) and Gli2(+/-) mice have been described as phenotypically normal, these results illustrate a functional haploinsufficiency of both genes in combination with ethanol exposure. By demonstrating an interaction between specific genetic and environmental risk factors, this study provides important insights into the multifactorial etiology and complex pathogenesis of fetal alcohol syndrome and holoprosencephaly.

Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 24586787 · DOI · PMC3929747

Loss of Tgif function causes holoprosencephaly by disrupting the SHH signaling pathway [3]

Research article Taniguchi K, Anderson AE, Sutherland AE, Wotton D · · 2012 · cited 69 times (Europe PMC)

Abstract reading summary — source excerpts
Opening excerpt
Holoprosencephaly (HPE) is a severe human genetic disease affecting craniofacial development, with an incidence of up to 1/250 human conceptions and 1.
Closing excerpt
These data show for the first time that Tgif1 mutation in mouse contributes to HPE pathogenesis and provide evidence that this is due to disruption of the Shh pathway.
Interpretation limits
Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (297 words)

Holoprosencephaly (HPE) is a severe human genetic disease affecting craniofacial development, with an incidence of up to 1/250 human conceptions and 1.3 per 10,000 live births. Mutations in the Sonic Hedgehog (SHH) gene result in HPE in humans and mice, and the Shh pathway is targeted by other mutations that cause HPE. However, at least 12 loci are associated with HPE in humans, suggesting that defects in other pathways contribute to this disease. Although the TGIF1 (TG-interacting factor) gene maps to the HPE4 locus, and heterozygous loss of function TGIF1 mutations are associated with HPE, mouse models have not yet explained how loss of Tgif1 causes HPE. Using a conditional Tgif1 allele, we show that mouse embryos lacking both Tgif1 and the related Tgif2 have HPE-like phenotypes reminiscent of Shh null embryos. Eye and nasal field separation is defective, and forebrain patterning is disrupted in embryos lacking both Tgifs. Early anterior patterning is relatively normal, but expression of Shh is reduced in the forebrain, and Gli3 expression is up-regulated throughout the neural tube. Gli3 acts primarily as an antagonist of Shh function, and the introduction of a heterozygous Gli3 mutation into embryos lacking both Tgif genes partially rescues Shh signaling, nasal field separation, and HPE. Tgif1 and Tgif2 are transcriptional repressors that limit Transforming Growth Factor β/Nodal signaling, and we show that reducing Nodal signaling in embryos lacking both Tgifs reduces the severity of HPE and partially restores the output of Shh signaling. Together, these results support a model in which Tgif function limits Nodal signaling to maintain the appropriate output of the Shh pathway in the forebrain. These data show for the first time that Tgif1 mutation in mouse contributes to HPE pathogenesis and provide evidence that this is due to disruption of the Shh pathway.

Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 22383895 · DOI · PMC3285584

Ophthalmologic Findings in an Induced Model of Holoprosencephaly in Zebrafish [4]

Research article Bulk J, Kyrychenko V, Heermann S · · 2025 · cited 1 times (Europe PMC)

Abstract reading summary — source excerpts
Opening excerpt
Holoprosencephaly (HPE) is the most frequent developmental disorder of the forebrain.
Closing excerpt
We found a spectrum of ocular phenotypes: ocular hypotelorism, cases of synophthalmia, and cyclopia.
Interpretation limits
Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (123 words)

Holoprosencephaly (HPE) is the most frequent developmental disorder of the forebrain. In this condition, the separation of the early precursor domains is hampered. A spectrum of clinical manifestations can be observed, for example, severe forms like alobar HPE and less severe forms like lobar HPE. Ophthalmologic findings that accompany HPE also occur as a spectrum that ranges from ocular hypotelorism and synophthalmia to cyclopia and anophthalmia. In this brief analysis, we made use of a recently established zebrafish model of HPE. This model is based on experimental BMP ligand induction that resulted in anophthalmia. We attenuated the induction protocol to investigate whether the ophthalmologic phenotype can also be attenuated. We found a spectrum of ocular phenotypes: ocular hypotelorism, cases of synophthalmia, and cyclopia.

Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 41207878 · DOI · PMC12597868

Key reviews and meta-analyses

The most cited review-type papers among PubMed’s best-match results for this heading, listed with bibliographic details only. Follow the links for the full text and access terms.

  • Research article Multiple hits during early embryonic development: digenic diseases and holoprosencephaly [5]
    Ming JE, Muenke M · Am J Hum Genet · 2002 · cited 223 times (Europe PMC)
  • Research article Genetics of ventral forebrain development and holoprosencephaly [6]
    Muenke M, Beachy PA · Curr Opin Genet Dev · 2000 · cited 197 times (Europe PMC)
  • Research article The molecular genetics of holoprosencephaly [7]
    Roessler E, Muenke M · Am J Med Genet C Semin Med Genet · 2010 · cited 172 times (Europe PMC)
  • Research article Holoprosencephaly: clinical, anatomic, and molecular dimensions [8]
    Cohen MM · Birth Defects Res A Clin Mol Teratol · 2006 · cited 145 times (Europe PMC)
  • Research article Mutations in holoprosencephaly [9]
    Wallis D, Muenke M · Hum Mutat · 2000 · cited 131 times (Europe PMC)
  • Research article Teratogenesis of holoprosencephaly [10]
    Cohen MM, Shiota K · Am J Med Genet · 2002 · cited 124 times (Europe PMC)

References

  1. Dubourg C, Bendavid C, Pasquier L, Henry C, Odent S, David V. Holoprosencephaly. . 2007. PMID 17274816 · DOI · PMC1802747
  2. Kietzman HW, Everson JL, Sulik KK, Lipinski RJ. The teratogenic effects of prenatal ethanol exposure are exacerbated by Sonic Hedgehog or GLI2 haploinsufficiency in the mouse. . 2014. PMID 24586787 · DOI · PMC3929747
  3. Taniguchi K, Anderson AE, Sutherland AE, Wotton D. Loss of Tgif function causes holoprosencephaly by disrupting the SHH signaling pathway. . 2012. PMID 22383895 · DOI · PMC3285584
  4. Bulk J, Kyrychenko V, Heermann S. Ophthalmologic Findings in an Induced Model of Holoprosencephaly in Zebrafish. . 2025. PMID 41207878 · DOI · PMC12597868
  5. Ming JE, Muenke M. Multiple hits during early embryonic development: digenic diseases and holoprosencephaly. Am J Hum Genet. 2002. PMID 12395298 · DOI · PMC385082
  6. Muenke M, Beachy PA. Genetics of ventral forebrain development and holoprosencephaly. Curr Opin Genet Dev. 2000. PMID 10826992 · DOI
  7. Roessler E, Muenke M. The molecular genetics of holoprosencephaly. Am J Med Genet C Semin Med Genet. 2010. PMID 20104595 · DOI · PMC2815021
  8. Cohen MM. Holoprosencephaly: clinical, anatomic, and molecular dimensions. Birth Defects Res A Clin Mol Teratol. 2006. PMID 17001700 · DOI
  9. Wallis D, Muenke M. Mutations in holoprosencephaly. Hum Mutat. 2000. PMID 10923031 · DOI
  10. Cohen MM, Shiota K. Teratogenesis of holoprosencephaly. Am J Med Genet. 2002. PMID 11932986 · DOI

About this article

Sources
NLM Medical Subject Headings (definition, synonyms); NCBI PubMed (counts, identifiers); Europe PMC (open-access abstracts and citation counts).
Verification
Every reference was resolved against PubMed on 2026-10-31; title, year and DOI matched.
Review state
automated source verified; no human expert review has been recorded yet.
Version
1, last updated 2026-10-29.

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At a glance

1,321
PubMed records on this heading
10%
published since 2020
236
review articles
1
randomized trials
10
verified references below

Counts come from PubMed on 2026-10-29; they show how much has been written, not how strong the evidence is.

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