IMP3

Chr 15

IMP U3 small nucleolar ribonucleoprotein 3

Also known as: BRMS2, C15orf12, MRPS4

NCBI Gene: 55272 ENSG00000177971 UniProt: Q8TCT8

This gene encodes the human homolog of the yeast Imp3 protein. The protein localizes to the nucleoli and interacts with the U3 snoRNP complex. The protein contains an S4 domain. [provided by RefSeq, Jul 2008]

Research

ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtImmunodeficiency 86

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.97

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?

1.97LOEUF

pLI 0.000

Z-score -1.99

OE 2.10 (1.01–1.97)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.77Z-score

OE missense 1.21 (1.05–1.40)

130 obs / 107.6 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?2.10 (1.01–1.97)

0≤0.351.4

Missense OE?1.21 (1.05–1.40)

0≤0.61.4

Synonymous OE?1.34

0≤1.21.6

LoF obs/exp: 8 / 3.8Missense obs/exp: 130 / 107.6Syn Z: -1.91

Background carrier burden — how many people carry a rare variant somewhere in IMP3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 430

311 rare PASS variants

Rare truncating (LoF)

1 in 3,000

44 rare PASS variants

Rare synonymous (reference)

1 in 340

180 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for IMP3. 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 370	1 in 2,600
South Asian	~43k	1 in 210	1 in 3,600
Remaining (unassigned)	~30k	1 in 510	1 in 3,800
European (Finnish)	~27k	1 in 870	≈ 1 in 8,600
Admixed American	~22k	1 in 190	≈ 1 in 7,100
African / African American	~21k	1 in 110	1 in 2,700
East Asian	~20k	1 in 180	1 in 1,500
Ashkenazi Jewish	~13k	1 in 770	none seen
Middle Eastern	~2,884	1 in 480	≈ 1 in 960

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): All 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓