NDE1

Chr 16AR

nudE neurodevelopment protein 1

Also known as: HOM-TES-87, LIS4, MHAC, NDE, NUDE, NUDE1

The protein localizes to the centrosome and regulates dynein function as part of a multiprotein complex essential for microtubule organization, mitosis, and neuronal migration. Autosomal recessive mutations cause lissencephaly 4, characterized by lissencephaly, severe brain atrophy, microcephaly, and severe cognitive disability, as well as microhydranencephaly. The pathogenic mechanism involves disruption of normal neuronal migration during brain development.

OMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
LOFmechanismARLOEUF 0.692 OMIM phenotypes
Clinical SummaryNDE1
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Gene-Disease Validity (ClinGen)
microcephaly with lissencephaly and/or hydranencephaly · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
0.69LOEUF
pLI 0.007
Z-score 2.56
OE 0.37 (0.210.69)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
-1.13Z-score
OE missense 1.22 (1.101.36)
246 obs / 200.8 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.37 (0.210.69)
00.351.4
Missense OE1.22 (1.101.36)
00.61.4
Synonymous OE1.19
01.21.6
LoF obs/exp: 7 / 19.1Missense obs/exp: 246 / 200.8Syn Z: -1.35
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveNDE1-related lissencephalyLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.80top 10%
GOF
0.5759th %ile
LOF
0.3551th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

NDE1 · 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

No active trials found for this gene.

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Clinical Literature
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