Trait
Small head present at birth
Clinical name: Primary microcephaly
Head circumference below 2 standard deviations below the mean for age and gender at birth.
Summary
- Also called
- Congenital decreased head circumference, Congenital microcephaly, Congenital small skull, Decreased head circumference present at birth, Microcephaly present at birth, Small cranium present at birth
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
Read the genes linked to Small head present at birth, and the rest of your genome, with one test.
From $449Free shipping · Results in 6–8 weeks
Get my Genome Test101 genes linked to Small head present at birth
Changes in these genes cause rare conditions in which Small head present at birth 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 |
|---|---|---|
| ANKLE2ankyrin repeat and LEM domain containing 2 | Always | In 1 condition |
| ARHGEF2Rho/Rac guanine nucleotide exchange factor 2 | Always | In 1 condition |
| ASNSasparagine synthetase (glutamine-hydrolyzing) | Always | In 1 condition |
| ATXN7L3ataxin 7 like 3 | Always | In 1 condition |
| BUB1BUB1 mitotic checkpoint serine/threonine kinase | Always | In 1 condition |
| CDK5RAP2CDK5 regulatory subunit associated protein 2 | Always | In 1 condition |
| CDK6cyclin dependent kinase 6 | Always | In 1 condition |
| CENPEcentromere protein E | Always | In 1 condition |
| CEP135centrosomal protein 135 | Always | In 1 condition |
| CEP295centrosomal protein 295 | Always | In 1 condition |
| CEP63centrosomal protein 63 | Always | In 1 condition |
| CITcitron rho-interacting serine/threonine kinase | Always | In 1 condition |
| COASYCoenzyme A synthase | Always | In 1 condition |
| CRNKL1crooked neck pre-mRNA splicing factor 1 | Always | In 1 condition |
| CTNNB1catenin beta 1 | Always | In 2 conditions |
| DTYMKdeoxythymidylate kinase | Always | In 1 condition |
| EEFSECeukaryotic elongation factor, selenocysteine-tRNA specific | Always | In 1 condition |
| ELFN1extracellular leucine rich repeat and fibronectin type III domain containing 1 | Always | In 1 condition |
| FZR1fizzy and cell division cycle 20 related 1 | Always | In 1 condition |
| GINS3GINS complex subunit 3 | Always | In 1 condition |
| GTPBP1GTP binding protein 1 | Always | In 1 condition |
| GTPBP2GTP binding protein 2 | Always | In 1 condition |
| IARS1isoleucyl-tRNA synthetase 1 | Always | In 1 condition |
| IER3IP1immediate early response 3 interacting protein 1 | Always | In 1 condition |
| KAT6Alysine acetyltransferase 6A | Always | In 1 condition |
| KNL1kinetochore scaffold 1 | Always | In 1 condition |
| LAGE3L antigen family member 3 | Always | In 1 condition |
| LGI1leucine rich glioma inactivated 1 | Always | In 1 condition |
| LMNB2lamin B2 | Always | In 1 condition |
| MCPH1microcephalin 1 | Always | In 1 condition |
| NBNnibrin | Always | In 1 condition |
| NCAPD2non-SMC condensin I complex subunit D2 | Always | In 1 condition |
| NDE1nudE neurodevelopment protein 1 | Always | In 3 conditions |
| NOTCH3notch receptor 3 | Always | In 1 condition |
| NUP188nucleoporin 188 | Always | In 1 condition |
| NUP37nucleoporin 37 | Always | In 1 condition |
| PCDH12protocadherin 12 | Always | In 1 condition |
| PDCD6IPprogrammed cell death 6 interacting protein | Always | In 1 condition |
| PHGDHphosphoglycerate dehydrogenase | Always | In 3 conditions |
| PPFIBP1PPFIB scaffold protein 1 | Always | In 1 condition |
Show 61 more genes
| Gene | How often it is seen | Conditions |
|---|---|---|
| RBBP8RB binding protein 8, endonuclease | Always | In 2 conditions |
| SASS6SAS-6 centriolar assembly protein | Always | In 1 condition |
| SLC25A19solute carrier family 25 member 19 | Always | In 1 condition |
| SPOPspeckle type BTB/POZ protein | Always | In 1 condition |
| STILSTIL centriolar assembly protein | Always | In 1 condition |
| TOP2BDNA topoisomerase II beta | Always | In 1 condition |
| TP53RKTP53 regulating kinase | Always | In 1 condition |
| TPRKBTP53RK binding protein | Always | In 1 condition |
| TRAPPC14trafficking protein particle complex subunit 14 | Always | In 1 condition |
| TRMT10AtRNA methyltransferase 10A | Always | In 2 conditions |
| TUBBtubulin beta class I | Always | In 1 condition |
| WSB2WD repeat and SOCS box containing 2 | Always | In 1 condition |
| ZNF335zinc finger protein 335 | Always | In 1 condition |
| CLPBClpB family mitochondrial disaggregase | Very often (80–99%) | In 1 condition |
| KATNB1katanin regulatory subunit B1 | Very often (80–99%) | In 1 condition |
| PORCNporcupine O-acyltransferase | Very often (80–99%) | In 1 condition |
| PPP1R15Bprotein phosphatase 1 regulatory subunit 15B | Very often (80–99%) | In 1 condition |
| PSAT1phosphoserine aminotransferase 1 | Very often (80–99%) | In 1 condition |
| RELNreelin | Very often (80–99%) | In 1 condition |
| TELO2telomere maintenance 2 | Very often (80–99%) | In 1 condition |
| TXN2thioredoxin 2 | Very often (80–99%) | In 1 condition |
| AFF3ALF transcription elongation factor 3 | Often (30–79%) | In 1 condition |
| COG7component of oligomeric golgi complex 7 | Often (30–79%) | In 2 conditions |
| DNM1Ldynamin 1L | Often (30–79%) | In 1 condition |
| DYRK1Adual specificity tyrosine phosphorylation regulated kinase 1A | Often (30–79%) | In 1 condition |
| EIF5Aeukaryotic translation initiation factor 5A | Often (30–79%) | In 1 condition |
| EOMESeomesodermin | Often (30–79%) | In 1 condition |
| FBXO22F-box protein 22 | Often (30–79%) | In 1 condition |
| FIG4FIG4 phosphoinositide 5-phosphatase | Often (30–79%) | In 1 condition |
| FRMD4AFERM domain containing 4A | Often (30–79%) | In 2 conditions |
| GON4Lgon-4 like | Often (30–79%) | In 1 condition |
| GRIN2Aglutamate ionotropic receptor NMDA type subunit 2A | Often (30–79%) | In 2 conditions |
| GTF3C3general transcription factor IIIC subunit 3 | Often (30–79%) | In 1 condition |
| HIVEP2HIVEP zinc finger 2 | Often (30–79%) | In 1 condition |
| ITGAVintegrin subunit alpha V | Often (30–79%) | In 1 condition |
| KICS2KICSTOR subunit 2 | Often (30–79%) | In 1 condition |
| MAU2MAU2 sister chromatid cohesion factor | Often (30–79%) | In 1 condition |
| NSFN-ethylmaleimide sensitive factor, vesicle fusing ATPase | Often (30–79%) | In 1 condition |
| RNF2ring finger protein 2 | Often (30–79%) | In 1 condition |
| RNU4-2RNA, U4 small nuclear 2 | Often (30–79%) | In 1 condition |
| SLC1A4solute carrier family 1 member 4 | Often (30–79%) | In 1 condition |
| SLC25A12solute carrier family 25 member 12 | Often (30–79%) | In 1 condition |
| SMC3structural maintenance of chromosomes 3 | Often (30–79%) | In 1 condition |
| SNAPINSNAP associated protein | Often (30–79%) | In 1 condition |
| TBL1XR1TBL1X/Y related 1 | Often (30–79%) | In 1 condition |
| TRAPPC12trafficking protein particle complex subunit 12 | Often (30–79%) | In 1 condition |
| TRIOtrio Rho guanine nucleotide exchange factor | Often (30–79%) | In 1 condition |
| TSEN54tRNA splicing endonuclease subunit 54 | Often (30–79%) | In 1 condition |
| VAC14VAC14 component of PIKFYVE complex | Often (30–79%) | In 1 condition |
| VPS4Avacuolar protein sorting 4 homolog A | Often (30–79%) | In 1 condition |
| YRDCyrdC N6-threonylcarbamoyltransferase domain containing | Often (30–79%) | In 1 condition |
| AFG2AAAA ATPase AFG2A | Sometimes (5–29%) | In 1 condition |
| CDK4cyclin dependent kinase 4 | Sometimes (5–29%) | In 1 condition |
| IFIH1interferon induced with helicase C domain 1 | Sometimes (5–29%) | In 1 condition |
| INPP4Ainositol polyphosphate-4-phosphatase type I A | Sometimes (5–29%) | In 1 condition |
| MED16mediator complex subunit 16 | Sometimes (5–29%) | In 1 condition |
| TBCDtubulin folding cofactor D | Sometimes (5–29%) | In 1 condition |
| TUBB3tubulin beta 3 class III | Sometimes (5–29%) | In 1 condition |
| WDR83OSWD repeat domain 83 opposite strand | Sometimes (5–29%) | In 1 condition |
| ZEB2zinc finger E-box binding homeobox 2 | Sometimes (5–29%) | In 2 conditions |
| MECP2methyl-CpG binding protein 2 | Rarely (1–4%) | 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.
Broader traits
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.
One test. A lifetime of answers.
From $449Free shipping · Results in 6–8 weeks