RPS25

Chr 11

ribosomal protein S25

Also known as: S25, eS25

NCBI Gene: 6230 ENSG00000118181 UniProt: P62851

Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S25E family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

Research

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.46

LOEUF

LOF

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

Moderate LoF intolerance

LoF Constraint?

0.46LOEUF

pLI 0.863

Z-score 2.37

OE 0.00 (0.00–0.46)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.83Z-score

OE missense 0.36 (0.26–0.51)

23 obs / 64.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.46)

0≤0.351.4

Missense OE?0.36 (0.26–0.51)

0≤0.61.4

Synonymous OE?1.30

0≤1.21.6

LoF obs/exp: 0 / 6.5Missense obs/exp: 23 / 64.2Syn Z: -1.16

Background carrier burden — how many people carry a rare variant somewhere in RPS25?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 2,300

74 rare PASS variants

Rare truncating (LoF)

1 in 180,000

4 rare PASS variants

Rare synonymous (reference)

1 in 930

68 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for RPS25. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 8 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 2,100	≈ 1 in 280,000
South Asian	~43k	1 in 2,500	none seen
Remaining (unassigned)	~30k	1 in 3,800	none seen
European (Finnish)	~27k	1 in 5,300	none seen
Admixed American	~22k	1 in 3,200	≈ 1 in 11,000
African / African American	~21k	1 in 2,600	none seen
East Asian	~20k	1 in 770	none seen
Middle Eastern	~2,884	≈ 1 in 1,200	none seen

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): 3 of 4 coding exons well covered in gnomAD exomes; exon 4 marginal. Genomes: all 4.? see exons ↓