PAX6

Chr 11AD

paired box 6

Also known as: AN, AN1, AN2, ASGD5, D11S812E, FVH1, MGDA, WAGR

This gene encodes paired box protein Pax-6, one of many human homologs of the Drosophila melanogaster gene prd. In addition to a conserved paired box domain, a hallmark feature of this gene family, the encoded protein also contains a homeobox domain. Both domains are known to bind DNA and function as regulators of gene transcription. Activity of this protein is key in the development of neural tissues, particularly the eye. This gene is regulated by multiple enhancers located up to hundreds of kilobases distant from this locus. Mutations in this gene or in the enhancer regions can cause ocular disorders such as aniridia and Peter's anomaly. Use of alternate promoters and alternative splicing results in multiple transcript variants encoding different isoforms. Interestingly, inclusion of a particular alternate coding exon has been shown to increase the length of the paired box domain and alter its DNA binding specificity. Consequently, isoforms that carry the shorter paired box domain regulate a different set of genes compared to the isoforms carrying the longer paired box domain. [provided by RefSeq, Mar 2019]

GeneReviewsOMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

?Coloboma of optic nerveMIM #120430
AD
?Morning glory disc anomalyMIM #120430
AD
AniridiaMIM #106210
AD
Anterior segment dysgenesis 5, multiple subtypesMIM #604229
AD
Cataract with late-onset corneal dystrophyMIM #106210
AD
Foveal hypoplasia 1MIM #136520
AD
KeratitisMIM #148190
AD
Microphthalmia/coloboma 12MIM #120200
AD
Optic nerve hypoplasiaMIM #165550
AD
UniProtAniridia 1
UniProtKeratitis hereditary
UniProtBilateral optic nerve hypoplasia
UniProtAniridia 2

Clinical highlights

Gene-disease validity (ClinGen)
PAX6-related ocular dysgenesis · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
258
Pubs (1 yr)
P/LP submissions
P/LP missense
0.17
LOEUF· LoF intol.
LOF
Mechanism· G2P
📖
GeneReview available — PAX6
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint?
0.17LOEUF
pLI 1.000
Z-score 4.74
OE 0.04 (0.010.17)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
2.82Z-score
OE missense 0.49 (0.420.57)
120 obs / 243.8 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.04 (0.010.17)
00.351.4
Missense OE?0.49 (0.420.57)
00.61.4
Synonymous OE?1.11
01.21.6
LoF obs/exp: 1 / 28.1Missense obs/exp: 120 / 243.8Syn Z: -0.85

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

PAX6 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.