Rare diseases · Sign or symptom
Primary microcephaly
HP:0011451
What it means
Head circumference below 2 standard deviations below the mean for age and gender at birth.
Rare diseases that can present with this33
Very common80–99%
7- 3-methylglutaconic aciduria-neonatal cataract-neurologic involvement-congenital neutropenia syndrome
- Combined oxidative phosphorylation defect type 29
- Focal dermal hypoplasia
- Lissencephaly syndrome, Norman-Roberts type
- Phosphoserine aminotransferase deficiency, infantile/juvenile form
- Primary microcephaly-mild intellectual disability-young-onset diabetes syndrome
- TELO2-related intellectual disability-neurodevelopmental disorder
Common30–79%
15- 3-phosphoglycerate dehydrogenase deficiency, infantile/juvenile form
- Autosomal recessive cutis laxa type 2A
- Blepharophimosis-intellectual disability syndrome, Verloes type
- COG7-CDG
- DYRK1A-related intellectual disability syndrome
- Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
- Intellectual disability-eye abnormalities-microcephaly-peripheral spasticity syndrome
- Microcephaly-glomerulonephritis-marfanoid habitus syndrome
- Microcephaly-polymicrogyria-corpus callosum agenesis syndrome
- Micrognathia-recurrent infections-behavioral abnormalities-mild intellectual disability syndrome
- Pierpont syndrome
- Pontocerebellar hypoplasia type 4
- Severe intellectual disability-corpus callosum agenesis-facial dysmorphism-cerebellar ataxia syndrome
- Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome
- Yunis-Varon syndrome
Sometimes5–29%
10- Cockayne syndrome
- Cortical dysgenesis with pontocerebellar hypoplasia due to TUBB3 mutation
- Early-onset epileptic encephalopathy and intellectual disability due to GRIN2A mutation
- Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome
- Hydranencephaly
- Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome
- Mowat-Wilson syndrome due to a ZEB2 point mutation
- Mowat-Wilson syndrome due to monosomy 2q22
and 2 more in this range
The range is how often this sign appears among people diagnosed with each disease — it is not a probability of having any of them. Many of these signs also occur in common, non-rare conditions. A sign on this page is a conversation to have with a clinician, not a conclusion.
Part of the broader category
Also called: Congenital decreased head circumference · Congenital microcephaly · Congenital small head · Congenital small head circumference · Congenital small skull · Decreased head circumference present at birth · Head circumference small for gestational age · Microcephaly present at birth
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Start free with EleplanThis page uses the Human Phenotype Ontology (2026-06-23) — Human Phenotype Ontology Consortium, hpo.jax.org. Disease associations from Orphanet (INSERM), CC BY 4.0. Content is educational and is not medical advice.