MRPL9

Chr 1

mitochondrial ribosomal protein L9

Also known as: L9mt, bL9m

NCBI Gene: 65005 ENSG00000143436 UniProt: Q9BYD2

This is a nuclear gene encoding a protein component of the 39S subunit of the mitochondrial ribosome. Alternative splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 8. [provided by RefSeq, Jul 2014]

Research

ResearchGenerating clinical summary…

DNmechanismLOEUF 1.05

Clinical Summary— MRPL9

⚡

Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

📋

ClinVar Variants

54 VUS of 90 total submissions

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.05LOEUF

pLI 0.000

Z-score 1.43

OE 0.58 (0.34–1.05)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.26Z-score

OE missense 0.94 (0.82–1.08)

141 obs / 150.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.58 (0.34–1.05)

0≤0.351.4

Missense OE?0.94 (0.82–1.08)

0≤0.61.4

Synonymous OE?1.12

0≤1.21.6

LoF obs/exp: 8 / 13.7Missense obs/exp: 141 / 150.1Syn Z: -0.75

This gene — mechanism propensity

0.6552th %ile

GOF

0.4974th %ile

LOF

0.3357th %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

90 submitted variants in ClinVar

ClinVar

Classification Summary

VUS54

Likely Benign4

Benign2

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	54	0	0	54
Likely Benign	1	2	1	4
Benign	0	2	0	2
Total	55	4	1	60

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

View in ClinVar →

12 pathogenic / likely-pathogenic (of 14) ClinVar copy-number / structural variants overlap MRPL9 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →