RPL10

Chr XXLR

ribosomal protein L10

Also known as: AUTSX5, DXS648, DXS648E, L10, MRXS35, NOV, QM, uL16

NCBI Gene: 6134 ENSG00000147403 UniProt: P27635 OMIM: 312173

This gene encodes a ribosomal protein that is a component of the 60S ribosome subunit and plays a role in forming actively translating ribosomes. Mutations cause X-linked intellectual developmental disorder with syndromic features and have been associated with autism spectrum disorders, inherited in an X-linked recessive pattern. The gene shows high constraint against loss-of-function variants, suggesting mutations predominantly cause disease through haploinsufficiency or loss-of-function mechanisms.

OMIM ResearchSummary from RefSeq, OMIM, UniProt, Mechanism

This gene encodes a ribosomal protein that is a component of the 60S ribosome subunit. The related protein in chicken can bind to c-Jun and can repress c-Jun-mediated transcriptional activation. Some studies have detected an association between variation in this gene and autism spectrum disorders, though others do not detect this relationship. There are multiple pseudogenes of this gene dispersed throughout the genome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

OMIM ResearchGenerating clinical summary…

LOFmechanismXLRLOEUF 0.392 OMIM phenotypes

Clinical Summary— RPL10

🧬

Gene-Disease Validity (ClinGen)

X-linked syndromic intellectual disability · XLDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡

Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.91). One damaged copy is likely sufficient to cause disease.

📋

ClinVar Variants

9 unique Pathogenic / Likely Pathogenic· 42 VUS of 139 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?

0.39LOEUF

pLI 0.909

Z-score 2.58

OE 0.00 (0.00–0.39)

Highly constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

2.61Z-score

OE missense 0.22 (0.16–0.32)

20 obs / 89.6 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.39)

0≤0.351.4

Missense OE?0.22 (0.16–0.32)

0≤0.61.4

Synonymous OE?1.25

0≤1.21.6

LoF obs/exp: 0 / 7.7Missense obs/exp: 20 / 89.6Syn Z: -1.08

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

definitiveRPL10-related syndromic intellectual developmental disorderOTHERXLR

This gene — mechanism propensity

0.4587th %ile

GOF

0.1999th %ile

LOF

0.70top 10%

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

LOFprediction above median · LOEUF 0.39

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

139 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4

Likely Pathogenic5

VUS42

Likely Benign13

Benign6

Conflicting1

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	0	4	0	0	4
Likely Pathogenic	0	5	0	0	5
VUS	3	30	9	0	42
Likely Benign	0	2	5	6	13
Benign	0	4	2	0	6
Conflicting	—				1
Total	3	45	16	6	71

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

View in ClinVar →

138 pathogenic / likely-pathogenic (of 161) ClinVar copy-number / structural variants overlap RPL10 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →