RPL13

Chr 16AD

ribosomal protein L13

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

NCBI Gene: 6137ENSG00000167526UniProt: P26373

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]

Primary Disease Associations & Inheritance

Spondyloepimetaphyseal dysplasia, Isidor-Toutain typeMIM #618728
AD
122
ClinVar variants
50
Pathogenic / LP
0.95
pLI score· haploinsufficient
0
Active trials
Clinical Summary— RPL13
⚡
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.
📋
ClinVar Variants
50 Pathogenic / Likely Pathogenic· 66 VUS of 122 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
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?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.32Z-score
OE missense 1.08 (0.94–1.24)
141 obs / 130.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.00 (0.00–0.32)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.08 (0.94–1.24)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.24
0≤1.21.6
LoF obs/exp: 0 / 9.5Missense obs/exp: 141 / 130.7Syn Z: -1.36

ClinVar Variant Classifications

122 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic39
Likely Pathogenic11
VUS66
Likely Benign3
Benign2
Conflicting1
39
Pathogenic
11
Likely Pathogenic
66
VUS
3
Likely Benign
2
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
3
3
33
0
39
Likely Pathogenic
3
1
7
0
11
VUS
1
36
29
0
66
Likely Benign
0
2
1
0
3
Benign
0
0
0
2
2
Conflicting
—1
Total742702122

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

View in ClinVar →

Protein Context — Lollipop Plot

RPL13 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

RPL13-related spondyloepimetaphyseal dysplasia with severe short stature

limited
ADUndeterminedUncertain
Dev. Disorders
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Spondyloepimetaphyseal dysplasia, Isidor-Toutain type

MIM #618728

Molecular basis of disorder known

Autosomal dominant
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Evolution of clinical and radiological presentations of spondyloepimetaphyseal dysplasia, RPL13-related: Description of 11 further cases.
Díaz-González F et al.·Clin Genet
2023Review
Novel RPL13 Variants and Variable Clinical Expressivity in a Human Ribosomopathy With Spondyloepimetaphyseal Dysplasia.
Costantini A et al.·J Bone Miner Res
2021
Beyond the Known: Expanding the Clinical and Genetic Spectrum of Rare RPL13-Related Spondyloepimetaphyseal Dysplasia.
Gorodilova D et al.·Int J Mol Sci
2025
[Clinical and genetic analysis of a patient with short stature due to variant of RPL13 gene].
Wen H et al.·Zhonghua Yi Xue Yi Chuan Xue Za Zhi
2024Case report
RPL13 Variants Cause Spondyloepimetaphyseal Dysplasia with Severe Short Stature.
Le Caignec C et al.·Am J Hum Genet
2019
Genetic and allelic heterogeneity in 248 Indians with skeletal dysplasia.
Jacob P et al.·Eur J Hum Genet
2025
Model system identification of novel congenital heart disease gene candidates: focus on RPL13.
Schroeder AM et al.·Hum Mol Genet
2019Functional
Expanding the phenotypic spectrum of RPL13-related skeletal dysplasia.
Reinsch B et al.·Am J Med Genet A
2021Case report
Bioinformatics-based analysis of potential therapeutic target genes for polycystic ovary syndrome.
Liu Y et al.·Cell Mol Biol (Noisy-le-grand)
2024
Dysregulation of Immune Cell Subpopulations in Atypical Hemolytic Uremic Syndrome.
Chen IR et al.·Int J Mol Sci
2023
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools