PLXDC2

Chr 10

plexin domain containing 2

Also known as: PLXDC2-OT, TEM7R

NCBI Gene: 84898ENSG00000120594UniProt: Q6UX71

PLXDC2 encodes a membrane-bound protein that may be involved in tumor angiogenesis. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.45), but no definitive human disease associations have been established for mutations in this gene. Clinical significance of PLXDC2 variants in pediatric neurological conditions remains to be determined.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
12
Pubs (1 yr)
10
P/LP submissions
0%
P/LP missense
0.45
LOEUF
—
Mechanism
Clinical Summary— PLXDC2
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.25) despite low pLI — interpret in context.
📋
ClinVar Variants
10 unique Pathogenic / Likely Pathogenic· 74 VUS of 108 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.45LOEUF
pLI 0.134
Z-score 3.92
OE 0.25 (0.15–0.45)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.77Z-score
OE missense 0.87 (0.79–0.97)
260 obs / 297.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.25 (0.15–0.45)
0≤0.351.4
Missense OE0.87 (0.79–0.97)
0≤0.61.4
Synonymous OE1.04
0≤1.21.6
LoF obs/exp: 8 / 31.8Missense obs/exp: 260 / 297.5Syn Z: -0.32

ClinVar Variant Classifications

108 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic9
Likely Pathogenic1
VUS74
Likely Benign6
Benign2
9
Pathogenic
1
Likely Pathogenic
74
VUS
6
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
9
0
9
Likely Pathogenic
0
0
1
0
1
VUS
0
61
13
0
74
Likely Benign
0
4
0
2
6
Benign
0
1
1
0
2
Total06624292

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

View in ClinVar →

Protein Context — Lollipop Plot

PLXDC2 · 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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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