PKNOX1

Chr 21

PBX/knotted 1 homeobox 1

Also known as: PREP1, pkonx1c

NCBI Gene: 5316ENSG00000160199UniProt: P55347

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in angiogenesis and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within camera-type eye development; hemopoiesis; and regulation of transcription by RNA polymerase II. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

GeneReviewsResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
0
Active trials
8
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.26
LOEUF· LoF intol.
LOF
Mechanism· predicted
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GeneReview available — PKNOX1
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.26LOEUF
pLI 0.994
Z-score 4.17
OE 0.08 (0.03–0.26)
Highly constrained

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

Missense Constraint?
1.47Z-score
OE missense 0.74 (0.66–0.83)
187 obs / 253.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.08 (0.03–0.26)
0≤0.351.4
Missense OE?0.74 (0.66–0.83)
0≤0.61.4
Synonymous OE?1.14
0≤1.21.6
LoF obs/exp: 2 / 24.0Missense obs/exp: 187 / 253.0Syn Z: -1.14

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PKNOX1 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients