RPS4Y2

Chr Y

ribosomal protein S4 Y-linked 2

Also known as: RPS4Y2P

NCBI Gene: 140032ENSG00000280969UniProt: Q8TD47OMIM: 400030

This gene encodes a ribosomal protein that is highly similar to RPS4Y1 and is located in the male-specific region of the Y chromosome, functioning as a component of the ribosomal machinery for protein synthesis. The gene shows low constraint against loss-of-function variants (pLI 0.0007, LOEUF 1.92), and no well-established disease associations have been reported for RPS4Y2 mutations. Given its Y chromosome location, any potential phenotypes would follow a patrilineal inheritance pattern affecting only males.

OMIMResearchSummary from RefSeq
DNmechanismLOEUF 1.92
Clinical Summary— RPS4Y2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
71 unique Pathogenic / Likely Pathogenic· 7 VUS of 87 total submissions
Explore recent and relevant literature in Research Assistant →
Some data sources returned errors (1)

opentargets: TimeoutError: The operation was aborted due to timeout

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.92LOEUF
pLI 0.001
Z-score -0.60
OE 1.38 (0.61–1.92)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-1.01Z-score
OE missense 1.42 (1.16–1.74)
65 obs / 45.8 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.38 (0.61–1.92)
0≤0.351.4
Missense OE1.42 (1.16–1.74)
0≤0.61.4
Synonymous OE1.09
0≤1.21.6
LoF obs/exp: 4 / 2.9Missense obs/exp: 65 / 45.8Syn Z: -0.28
DN
0.6552th %ile
GOF
0.2895th %ile
LOF
0.4528th %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

87 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic69
Likely Pathogenic2
VUS7
Likely Benign7
69
Pathogenic
2
Likely Pathogenic
7
VUS
7
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
————69
Likely Pathogenic
————2
VUS
————7
Likely Benign
————7
Benign
————0
Total—85

Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

RPS4Y2 · 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

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients