RPL13

Chr 16AD

ribosomal protein L13

Also known as: BBC1, D16S444E, D16S44E, L13, SEMDIST, eL13

NCBI Gene: 6137 ENSG00000167526 UniProt: P26373 OMIM: 113703

This protein is a component of the large 60S ribosomal subunit that catalyzes peptide bond formation during protein synthesis and plays a role in bone development. Mutations cause spondyloepimetaphyseal dysplasia, Isidor-Toutain type, inherited in an autosomal dominant pattern. The gene is highly constrained against loss-of-function variants (pLI 0.95, LOEUF 0.32), suggesting intolerance to protein loss.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

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 60S subunit. The protein belongs to the L13E family of ribosomal proteins. It is located in the cytoplasm. This gene is expressed at significantly higher levels in benign breast lesions than in breast carcinomas. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2011]

OMIM ResearchGenerating clinical summary…

LOFmechanismADLOEUF 0.321 OMIM phenotype

Clinical Summary— RPL13

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.95). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

10 unique Pathogenic / Likely Pathogenic· 37 VUS of 66 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.32LOEUF

pLI 0.951

Z-score 2.85

OE 0.00 (0.00–0.32)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

-0.32Z-score

OE missense 1.08 (0.94–1.24)

141 obs / 130.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.32)

0≤0.351.4

Missense OE?1.08 (0.94–1.24)

0≤0.61.4

Synonymous OE?1.24

0≤1.21.6

LoF obs/exp: 0 / 9.5Missense obs/exp: 141 / 130.7Syn Z: -1.36

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

limitedRPL13-related spondyloepimetaphyseal dysplasia with severe short statureOTHERAD

This gene — mechanism propensity

0.3694th %ile

GOF

0.1899th %ile

LOF

0.75top 10%

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

LOFprediction above median · 60% of P/LP variants are LoF · LOEUF 0.32

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

66 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic6

Likely Pathogenic4

VUS37

Likely Benign3

Benign2

Conflicting2

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	3	3	0	0	6
Likely Pathogenic	3	1	0	0	4
VUS	1	35	1	0	37
Likely Benign	0	2	1	0	3
Benign	0	0	0	2	2
Conflicting	—				2
Total	7	41	2	2	54

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

41 pathogenic / likely-pathogenic (of 73) ClinVar copy-number / structural variants overlap RPL13 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →