NDC1

Chr 1AR

NDC1 transmembrane nucleoporin

NDC1 encodes a component of the nuclear pore complex that is required for nuclear pore assembly and anchoring in the nuclear envelope membrane. Mutations cause a neurodevelopmental disorder with achalasia, polyneuropathy, and alacrima, inherited in an autosomal recessive pattern. This gene is highly constrained against loss-of-function variants, indicating its essential cellular role.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.241 OMIM phenotype
Clinical SummaryNDC1
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.
Some data sources returned errors (1)

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint
0.24LOEUF
pLI 0.999
Z-score 5.17
OE 0.10 (0.050.24)
Highly constrained

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

Missense Constraint
1.09Z-score
OE missense 0.83 (0.760.92)
290 obs / 347.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.10 (0.050.24)
00.351.4
Missense OE0.83 (0.760.92)
00.61.4
Synonymous OE1.10
01.21.6
LoF obs/exp: 4 / 38.7Missense obs/exp: 290 / 347.4Syn Z: -0.87
DN
0.3892th %ile
GOF
0.2895th %ile
LOF
0.74top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.24

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

NDC1 · 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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