PLXND1

Chr 3AR

plexin D1

Also known as: CHTD9, PLEXD1

NCBI Gene: 23129ENSG00000004399UniProt: Q9Y4D7OMIM: 604282

Enables protein domain specific binding activity. Predicted to be involved in several processes, including positive regulation of axonogenesis; semaphorin-plexin signaling pathway; and synapse assembly. Predicted to act upstream of or within circulatory system development; dichotomous subdivision of terminal units involved in salivary gland branching; and kidney development. Located in lamellipodium. [provided by Alliance of Genome Resources, Jul 2025]

OMIMResearchGenerating clinical summary…
ARLOEUF 0.161 OMIM phenotype
Clinical Summary— PLXND1
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Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?
0.16LOEUF
pLI 1.000
Z-score 7.78
OE 0.08 (0.05–0.16)
Highly constrained

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

Missense Constraint?
3.35Z-score
OE missense 0.72 (0.68–0.76)
821 obs / 1138.8 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?
LoF OE?0.08 (0.05–0.16)
0≤0.351.4
Missense OE?0.72 (0.68–0.76)
0≤0.61.4
Synonymous OE?0.99
0≤1.21.6
LoF obs/exp: 7 / 83.9Missense obs/exp: 821 / 1138.8Syn Z: 0.12

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PLXND1 · 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.

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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