RPS4Y2

Chr Y

ribosomal protein S4 Y-linked 2

Also known as: RPS4Y2P

NCBI Gene: 140032 ENSG00000280969 UniProt: Q8TD47 OMIM: 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.

OMIM ResearchSummary from RefSeq

The protein encoded by this gene is a ribosomal protein that is highly similar to RPS4Y1. This gene is located in the male-specific region of the Y chromosome. [provided by RefSeq, Aug 2012]

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 1.92

Clinical Summary— RPS4Y2

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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

2 total variants — no pathogenic classifications of 2 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?

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 OE?1.38 (0.61–1.92)

0≤0.351.4

Missense OE?1.42 (1.16–1.74)

0≤0.61.4

Synonymous OE?1.09

0≤1.21.6

LoF obs/exp: 4 / 2.9Missense obs/exp: 65 / 45.8Syn Z: -0.28

This gene — mechanism propensity

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

2 submitted variants in ClinVar

ClinVar

Classification Summary

Curated Variants Distribution

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

Classification	LoF	Missense + Inframe	Non-coding	Synonymous
Pathogenic	—	—	—	—
Likely Pathogenic	—	—	—	—
VUS	—	—	—	—
Likely Benign	—	—	—	—
Benign	—	—	—	—
Total	—

Counts from ClinVar esearch · Updated hourly

View in ClinVar →

71 pathogenic / likely-pathogenic (of 85) ClinVar copy-number / structural variants overlap RPS4Y2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →