NMD3

Chr 3

NMD3 ribosome export adaptor

Also known as: CGI-07

NCBI Gene: 51068 ENSG00000169251 UniProt: Q96D46

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]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.82

LOEUF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

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

Background carrier burden — how many people carry a rare variant somewhere in NMD3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 99

638 rare PASS variants

Rare truncating (LoF)

1 in 1,800

127 rare PASS variants

Rare synonymous (reference)

1 in 150

234 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for NMD3. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 120	1 in 2,000
South Asian	~43k	1 in 87	1 in 1,800
Remaining (unassigned)	~30k	1 in 83	1 in 3,200
European (Finnish)	~27k	1 in 300	1 in 2,600
Admixed American	~22k	1 in 100	1 in 1,300
African / African American	~21k	1 in 90	1 in 760
East Asian	~20k	1 in 86	1 in 2,400
Ashkenazi Jewish	~13k	1 in 330	none seen
Middle Eastern	~2,884	1 in 89	≈ 1 in 2,500

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 7 of 15 coding exons well covered in gnomAD exomes; exons 5, 7, 8, 9, 12 and 3 more marginal. Genomes: 14 of 15 (exon 2 below).? see exons ↓