NMD3

Chr 3

NMD3 ribosome export adaptor

Also known as: CGI-07

NCBI Gene: 51068 ENSG00000169251 UniProt: Q96D46 OMIM: 611021

Ribosomal 40S and 60S subunits associate in the nucleolus and are exported to the cytoplasm. The protein encoded by this gene is involved in the passage of the 60S subunit through the nuclear pore complex and into the cytoplasm. Several transcript variants exist for this gene, but the full-length natures of only two have been described to date. [provided by RefSeq, Feb 2016]

OMIM Research

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 0.82

Clinical Summary— NMD3

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

82 VUS of 104 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.82LOEUF

pLI 0.000

Z-score 2.34

OE 0.55 (0.37–0.82)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.19Z-score

OE missense 0.97 (0.87–1.07)

260 obs / 268.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.55 (0.37–0.82)

0≤0.351.4

Missense OE?0.97 (0.87–1.07)

0≤0.61.4

Synonymous OE?1.30

0≤1.21.6

LoF obs/exp: 17 / 31.1Missense obs/exp: 260 / 268.5Syn Z: -2.23

This gene — mechanism propensity

0.6647th %ile

GOF

0.4579th %ile

LOF

0.3648th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

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

ClinVar Variant Classifications

104 submitted variants in ClinVar

ClinVar

Classification Summary

VUS82

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	82	82
Likely Benign	0	0
Benign	0	0
Total	82	82

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

View in ClinVar →

20 pathogenic / likely-pathogenic (of 27) ClinVar copy-number / structural variants overlap NMD3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →