raremaprare-disease reference indexOrphadata 2026-06-23 · HPO 2026-09-01
ORPHA:2162

Holoprosencephaly

Synonyms: HPE

Type
Malformation syndrome
Group
Disorder
Inheritance
Autosomal recessive, Multigenic/multifactorial, Not applicable, Oligogenic, X-linked dominant
Age of onset
Antenatal, Neonatal
Status
active

A rare complex brain malformation characterized by incomplete cleavage of the prosencephalon, and affecting both the forebrain and face and resulting in neurological manifestations and facial anomalies of variable severity.

1

Names in Orphadata languages

12 of 12 languages
LangNameSynonyms
enHoloprosencephalyHPE
frHoloprosencéphalie= en
deHoloprosenzephalie= en
esHoloprosencefalia= en
itOloprosencefalia= en
nlHoloprosencefalie= en
ptHoloprosencefalia
plHoloprosencefalia= en
csHoloprosencefalie= en
ukГолопрозенцефалія= en
zh前脑无裂畸形= en
trHoloprozensefali= en

Definition in:

2

Cross-references

qualifier = Orphanet mapping relation
SourceCodeQualifierICD relationValidation
OMIM142945BTNTvalidated
OMIM142946BTNTvalidated
OMIM147250BTNTvalidated
OMIM157170BTNTvalidated
OMIM236100Evalidated
OMIM605934BTNTvalidated
OMIM609408BTNTvalidated
OMIM609637BTNTvalidated
OMIM610828BTNTvalidated
OMIM610829BTNTvalidated
OMIM612530NTBTvalidated
OMIM614226BTNTvalidated
OMIM619895BTNTvalidated
ICD-10Q04.2Especificvalidated
ICD-11LA05.2Especificvalidated
MONDO0016296Evalidated
MeSHD016142Evalidated
UMLSC0079541Evalidated
GARD6665Evalidated
MedDRA10056304Evalidated

E exact · NTBT this ORPHAcode is narrower than the target · BTNT broader than the target · ND not decided.

3

Classification

Preferential parent (Orphanet linearisation):

Parents in the classifications (5):

Children (5):

4

Genes

0 direct · 81 via subtypes

Orphanet records no gene directly on this code.

Recorded by Orphanet on subtypes of this disorder:

GeneSubtypeAssociationStatusHGNCEnsemblOMIMLocusNameSource of validation
FGFR1ORPHA:93924Lobar holoprosencephalyCandidate gene tested inNot yet assessedHGNC:3688ENSG000000777821363508p11.23fibroblast growth factor receptor 127363716[PMID]
SMC1AORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) (loss of function) inAssessedHGNC:11111ENSG00000072501300040Xp11.22structural maintenance of chromosomes 1A31334757[PMID]
STAG2ORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) (loss of function) inAssessedHGNC:11355ENSG00000101972300826Xq25STAG2 cohesin complex component31334757[PMID]
STAG2ORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) (loss of function) inAssessedHGNC:11355ENSG00000101972300826Xq25STAG2 cohesin complex component31334757[PMID]
CDONORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:17104ENSG0000006430960870711q24.2cell adhesion associated, oncogene regulated
CDONORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:17104ENSG0000006430960870711q24.2cell adhesion associated, oncogene regulated
CDONORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:17104ENSG0000006430960870711q24.2cell adhesion associated, oncogene regulated
CDONORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:17104ENSG0000006430960870711q24.2cell adhesion associated, oncogene regulated
CDONORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:17104ENSG0000006430960870711q24.2cell adhesion associated, oncogene regulated
CRIPTOORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:11701ENSG000002411861873953p21.31cripto, EGF-CFC family member
CRIPTOORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:11701ENSG000002411861873953p21.31cripto, EGF-CFC family member
CRIPTOORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:11701ENSG000002411861873953p21.31cripto, EGF-CFC family member
CRIPTOORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:11701ENSG000002411861873953p21.31cripto, EGF-CFC family member
CRIPTOORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:11701ENSG000002411861873953p21.31cripto, EGF-CFC family member
DISP1ORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:19711ENSG000001543096075021q41dispatched RND transporter family member 1
DISP1ORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:19711ENSG000001543096075021q41dispatched RND transporter family member 1
DISP1ORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:19711ENSG000001543096075021q41dispatched RND transporter family member 1
DISP1ORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:19711ENSG000001543096075021q41dispatched RND transporter family member 1
DISP1ORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:19711ENSG000001543096075021q41dispatched RND transporter family member 1
DLL1ORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:2908ENSG000001987196065826q27delta like canonical Notch ligand 1
DLL1ORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:2908ENSG000001987196065826q27delta like canonical Notch ligand 1
DLL1ORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:2908ENSG000001987196065826q27delta like canonical Notch ligand 1
DLL1ORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:2908ENSG000001987196065826q27delta like canonical Notch ligand 1
DLL1ORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:2908ENSG000001987196065826q27delta like canonical Notch ligand 1
FGF8ORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:3686ENSG0000010783160048310q24.32fibroblast growth factor 8
FGF8ORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:3686ENSG0000010783160048310q24.32fibroblast growth factor 8
FGF8ORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:3686ENSG0000010783160048310q24.32fibroblast growth factor 8
FGF8ORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:3686ENSG0000010783160048310q24.32fibroblast growth factor 8
FGF8ORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:3686ENSG0000010783160048310q24.32fibroblast growth factor 8
FGFR1ORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:3688ENSG000000777821363508p11.23fibroblast growth factor receptor 127363716[PMID]
FOXH1ORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:3814ENSG000001609736036218q24.3forkhead box H1
FOXH1ORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:3814ENSG000001609736036218q24.3forkhead box H1
FOXH1ORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:3814ENSG000001609736036218q24.3forkhead box H1
FOXH1ORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:3814ENSG000001609736036218q24.3forkhead box H1
FOXH1ORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:3814ENSG000001609736036218q24.3forkhead box H1
GAS1ORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:4165ENSG000001804471391859q21.33growth arrest specific 1
GAS1ORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:4165ENSG000001804471391859q21.33growth arrest specific 1
GAS1ORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:4165ENSG000001804471391859q21.33growth arrest specific 1
GAS1ORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:4165ENSG000001804471391859q21.33growth arrest specific 1
GAS1ORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:4165ENSG000001804471391859q21.33growth arrest specific 1
GLI2ORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:4318ENSG000000740471652302q14.2GLI family zinc finger 2
GLI2ORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:4318ENSG000000740471652302q14.2GLI family zinc finger 2
GLI2ORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:4318ENSG000000740471652302q14.2GLI family zinc finger 2
GLI2ORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:4318ENSG000000740471652302q14.2GLI family zinc finger 2
GLI2ORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:4318ENSG000000740471652302q14.2GLI family zinc finger 2
NODALORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:7865ENSG0000015657460126510q22.1nodal growth differentiation factor
NODALORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:7865ENSG0000015657460126510q22.1nodal growth differentiation factor
NODALORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:7865ENSG0000015657460126510q22.1nodal growth differentiation factor
NODALORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:7865ENSG0000015657460126510q22.1nodal growth differentiation factor
NODALORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:7865ENSG0000015657460126510q22.1nodal growth differentiation factor
PLCH1ORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:29185ENSG000001148056128353q25.31phospholipase C eta 133820834[PMID]
PTCH1ORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:9585ENSG000001859206013099q22.32patched 1
PTCH1ORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:9585ENSG000001859206013099q22.32patched 1
PTCH1ORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:9585ENSG000001859206013099q22.32patched 1
PTCH1ORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:9585ENSG000001859206013099q22.32patched 1
PTCH1ORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:9585ENSG000001859206013099q22.32patched 1
SHHORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10848ENSG000001646906007257q36.3sonic hedgehog signaling molecule
SHHORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10848ENSG000001646906007257q36.3sonic hedgehog signaling molecule
SHHORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10848ENSG000001646906007257q36.3sonic hedgehog signaling molecule
SHHORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10848ENSG000001646906007257q36.3sonic hedgehog signaling molecule
SHHORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10848ENSG000001646906007257q36.3sonic hedgehog signaling molecule
SIX3ORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10889ENSG000001380836037142p21SIX homeobox 3
SIX3ORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10889ENSG000001380836037142p21SIX homeobox 3
SIX3ORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10889ENSG000001380836037142p21SIX homeobox 3
SIX3ORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10889ENSG000001380836037142p21SIX homeobox 3
SIX3ORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10889ENSG000001380836037142p21SIX homeobox 3
STILORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10879ENSG000001234731815901p33STIL centriolar assembly protein29785796[PMID]
STILORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10879ENSG000001234731815901p33STIL centriolar assembly protein29785796[PMID]
STILORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10879ENSG000001234731815901p33STIL centriolar assembly protein29785796[PMID]
STILORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10879ENSG000001234731815901p33STIL centriolar assembly protein29785796[PMID]
STILORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:10879ENSG000001234731815901p33STIL centriolar assembly protein29785796[PMID]
TGIF1ORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:11776ENSG0000017742660263018p11.31TGFB induced factor homeobox 1
TGIF1ORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:11776ENSG0000017742660263018p11.31TGFB induced factor homeobox 1
TGIF1ORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:11776ENSG0000017742660263018p11.31TGFB induced factor homeobox 1
TGIF1ORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:11776ENSG0000017742660263018p11.31TGFB induced factor homeobox 1
TGIF1ORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:11776ENSG0000017742660263018p11.31TGFB induced factor homeobox 1
ZIC2ORPHA:93924Lobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:12873ENSG0000004335560307313q32.3Zic family zinc finger 2
ZIC2ORPHA:93925Alobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:12873ENSG0000004335560307313q32.3Zic family zinc finger 2
ZIC2ORPHA:93926Midline interhemispheric variant of holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:12873ENSG0000004335560307313q32.3Zic family zinc finger 2
ZIC2ORPHA:220386Semilobar holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:12873ENSG0000004335560307313q32.3Zic family zinc finger 2
ZIC2ORPHA:280195Septopreoptic holoprosencephalyDisease-causing germline mutation(s) inAssessedHGNC:12873ENSG0000004335560307313q32.3Zic family zinc finger 2
5

Prevalence and incidence

8 records
TypeClassValueAreaQualificationValidationSource
Prevalence at birth1-5 / 10 00013.4 / 100 000EuropeValue and classValidated20104599[PMID]_[EXPERT]_EUROCAT European surveillance of congenital anomalies[OTHER]
Prevalence at birth1-9 / 100 0005.5 / 100 000United StatesValue and classNot yet validated9409876[PMID]_ORPHANET
Prevalence at birth1-5 / 10 00021.6 / 100 000Latin AmericaValue and classValidated17987642[PMID]
Prevalence at birth1-5 / 10 00015 / 100 000United KingdomValue and classNot yet validated11349198[PMID]_17286306[PMID]_8818944[PMID]_ORPHANET
Prevalence at birth6-9 / 10 00060.6 / 100 000Taiwan, Province of ChinaValue and classValidated15844779[PMID]
Prevalence at birth>1 / 1000502 / 100 000JapanValue and classValidated15329827[PMID]
Point prevalenceUnknown—WorldwideClass onlyNot yet validatedORPHANET
Prevalence at birth1-5 / 10 00010.9 / 100 000Specific populationValue and classValidated10703035[PMID]

Value is Orphadata's ValMoy: the mean estimate per 100 000 for prevalence and incidence, the number of cases or families for case reports.

6

HPO phenotypes

93 annotations · validated 2016-06-01
HPOTerm (as annotated by Orphanet)Diagnostic
Very frequent (99-80%)
HP:0001999Abnormal facial shape
HP:0012639Abnormal nervous system morphology
HP:0100336Bilateral cleft lip
HP:0001360Holoprosencephaly
HP:0000161Median cleft lip
HP:0009099Median cleft palate
HP:0006315Single median maxillary incisor
Frequent (79-30%)
HP:0000528Anophthalmia
HP:0000458Anosmia
HP:0007370Aplasia/Hypoplasia of the corpus callosum
HP:0000453Choanal atresia
HP:0100543Cognitive impairment
HP:0009914Cyclopia
HP:0000457Depressed nasal ridge
HP:0000819Diabetes mellitus
HP:0001332Dystonia
HP:0002020Gastroesophageal reflux
HP:0001263Global developmental delay
HP:0001943Hypoglycemia
HP:0004409Hyposmia
HP:0000601Hypotelorism
HP:0001252Hypotonia
HP:0000612Iris coloboma
HP:0000252Microcephaly
HP:0000568Microphthalmia
HP:0001324Muscle weakness
HP:0001250Seizure
HP:0001257Spasticity
HP:0009804Tooth agenesis
Occasional (29-5%)
HP:0001679Abnormal aortic morphology
HP:0003312Abnormal form of the vertebral bodies
HP:0000377Abnormal pinna morphology
HP:0001641Abnormal pulmonary valve morphology
HP:0000929Abnormal skull morphology
HP:0002269Abnormality of neuronal migration
HP:0009738Abnormality of the antihelix
HP:0001743Abnormality of the spleen
HP:0000079Abnormality of the urinary system
HP:0100596Absent nares
HP:0000830Anterior hypopituitarism
HP:0000463Anteverted nares
HP:0009924Aplasia/Hypoplasia involving the nose
HP:0007360Aplasia/Hypoplasia of the cerebellum
HP:0006703Aplasia/Hypoplasia of the lungs
HP:0011675Arrhythmia
HP:0000581Blepharophimosis
HP:0001156Brachydactyly
HP:0009794Branchial anomaly
HP:0000289Broad philtrum
HP:0002072Chorea
HP:0000567Chorioretinal coloboma
HP:0000776Congenital diaphragmatic hernia
HP:0002019Constipation
HP:0000028Cryptorchidism
HP:0001305Dandy-Walker malformation
HP:0002002Deep philtrum
HP:0000490Deeply set eye
HP:0000437Depressed nasal tip
HP:0000873Diabetes insipidus
HP:0002084Encephalocele
HP:0000286Epicanthus
HP:0001531Failure to thrive in infancy
HP:0008872Feeding difficulties in infancy
HP:0005469Flat occiput
HP:0002007Frontal bossing
HP:0001161Hand polydactyly
HP:0002553Highly arched eyebrow
HP:0000238Hydrocephalus
HP:0000316Hypertelorism
HP:0002902Hyponatremia
HP:0008736Hypoplasia of penis
HP:0010669Hypoplasia of the zygomatic bone
HP:0011100Intestinal atresia
HP:0001382Joint hypermobility
HP:0000256Macrocephaly
HP:0000400Macrotia
HP:0001539Omphalocele
HP:0000648Optic atrophy
HP:0000871Panhypopituitarism
HP:0000093Proteinuria
HP:0000508Ptosis
HP:0002093Respiratory insufficiency
HP:0000488Retinopathy
HP:0002650Scoliosis
HP:0000470Short neck
HP:0010302Spinal cord tumor
HP:0010301Spinal dysraphism
HP:0000664Synophrys
HP:0001883Talipes
HP:0001636Tetralogy of Fallot
HP:0000574Thick eyebrow
HP:0000582Upslanted palpebral fissure
HP:0001629Ventricular septal defect

Run the differential on the 7 obligate / very frequent terms

7

Sources for this card