PLXND1

Chr 3AR

plexin D1

Also known as: CHTD9, PLEXD1

NCBI Gene: 23129ENSG00000004399UniProt: Q9Y4D7OMIM: 604282

PLXND1 encodes a cell surface receptor for semaphorins that regulates cell migration, synapse formation, and cardiovascular development. Mutations cause autosomal recessive congenital heart defects with multiple cardiac malformations. This gene is highly constrained against loss-of-function variants, indicating it is essential for normal development.

OMIMResearchSummary from RefSeq, OMIM, UniProt
ARLOEUF 0.161 OMIM phenotype
Clinical Summary— PLXND1
⚡
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.
📋
ClinVar Variants
10 unique Pathogenic / Likely Pathogenic· 287 VUS of 400 total submissions
Explore recent and relevant literature in Research Assistant →

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 OE0.08 (0.05–0.16)
0≤0.351.4
Missense OE0.72 (0.68–0.76)
0≤0.61.4
Synonymous OE0.99
0≤1.21.6
LoF obs/exp: 7 / 83.9Missense obs/exp: 821 / 1138.8Syn Z: 0.12

ClinVar Variant Classifications

400 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic9
Likely Pathogenic1
VUS287
Likely Benign29
Benign26
9
Pathogenic
1
Likely Pathogenic
287
VUS
29
Likely Benign
26
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
4
4
0
9
Likely Pathogenic
1
0
0
0
1
VUS
3
283
1
0
287
Likely Benign
0
7
2
20
29
Benign
0
7
6
13
26
Total53011333352

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in 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.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

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