RPS4Y1

Chr Y

ribosomal protein S4 Y-linked 1

Also known as: RPS4Y, S4

NCBI Gene: 6192 ENSG00000129824 UniProt: P22090 OMIM: 470000

This gene encodes ribosomal protein S4, a component of the 40S ribosomal subunit that catalyzes protein synthesis in the cytoplasm. Located on the Y chromosome, RPS4Y1 has a functionally equivalent X-linked counterpart (RPS4X), and haploinsufficiency of ribosomal protein S4 genes has been suggested to contribute to Turner syndrome, though this remains controversial. The gene shows moderate constraint against loss-of-function variants (pLI 0.63, LOEUF 0.94).

OMIM ResearchSummary from RefSeq

Cytoplasmic ribosomes, 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 ribosomal protein S4, a component of the 40S subunit. Ribosomal protein S4 is the only ribosomal protein known to be encoded by more than one gene, namely this gene and ribosomal protein S4, X-linked (RPS4X). The 2 isoforms encoded by these genes are not identical, but are functionally equivalent. Ribosomal protein S4 belongs to the S4E family of ribosomal proteins. It has been suggested that haploinsufficiency of the ribosomal protein S4 genes plays a role in Turner syndrome; however, this hypothesis is controversial. 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]

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.94

Clinical Summary— RPS4Y1

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.63) — some intolerance to loss-of-function variants.

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ClinVar Variants

36 total variants — no pathogenic classifications of 36 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.94LOEUF

pLI 0.627

Z-score 1.64

OE 0.00 (0.00–0.94)

Moderately constrained

Typical tolerance to LoF variation

Missense Constraint?

1.12Z-score

OE missense 0.54 (0.40–0.76)

26 obs / 47.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.94)

0≤0.351.4

Missense OE?0.54 (0.40–0.76)

0≤0.61.4

Synonymous OE?1.28

0≤1.21.6

LoF obs/exp: 0 / 3.1Missense obs/exp: 26 / 47.8Syn Z: -0.86

This gene — mechanism propensity

0.4884th %ile

GOF

0.2597th %ile

LOF

0.65top 25%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

36 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 →

61 pathogenic / likely-pathogenic (of 68) ClinVar copy-number / structural variants overlap RPS4Y1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →