TRMT10C

Chr 3AR

tRNA methyltransferase 10C, mitochondrial RNase P subunit

Also known as: COXPD30, HNYA, MRPP1, RG9MTD1

NCBI Gene: 54931 ENSG00000174173 UniProt: Q7L0Y3 OMIM: 615423

The protein is a subunit of mitochondrial ribonuclease P that processes the 5' end of mitochondrial tRNAs and confers RNA-binding capacity essential for transcript processing, RNA modification, translation and mitochondrial respiration. Mutations cause combined oxidative phosphorylation deficiency 30 through an autosomal recessive inheritance pattern. The pathogenic mechanism involves loss of function, disrupting mitochondrial tRNA processing and subsequent oxidative phosphorylation.

OMIM ResearchSummary from RefSeq, OMIM, UniProt, Mechanism

This gene encodes the precursor of a subunit of the mitochondrial ribonuclease P, which is involved in 5' processing of mitochondrial tRNAs. The encoded protein may confer RNA-binding capacity to mitochondrial ribonuclease P and may be essential for transcript processing, RNA modification, translation and mitochondrial respiration. [provided by RefSeq, Nov 2012]

OMIM ResearchGenerating clinical summary…

DNmechanismARLOEUF 1.141 OMIM phenotype

Clinical Summary— TRMT10C

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Gene-Disease Validity (ClinGen)

mitochondrial disease · ARModerate

Moderate evidence — consider for supplementary testing

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Population Constraint (gnomAD)

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

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ClinVar Variants

1 unique Pathogenic / Likely Pathogenic· 76 VUS of 102 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.14LOEUF

pLI 0.000

Z-score 1.22

OE 0.63 (0.37–1.14)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.77Z-score

OE missense 0.85 (0.75–0.96)

174 obs / 205.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.63 (0.37–1.14)

0≤0.351.4

Missense OE?0.85 (0.75–0.96)

0≤0.61.4

Synonymous OE?0.94

0≤1.21.6

LoF obs/exp: 8 / 12.7Missense obs/exp: 174 / 205.0Syn Z: 0.39

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

strongTRMT10C-related mitochondrial RNA processing and multiple respiratory chain deficienciesOTHERAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

0.6551th %ile

GOF

0.5269th %ile

LOF

0.2484th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

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

ClinVar Variant Classifications

102 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

VUS76

Likely Benign19

Benign2

Conflicting2

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	1	0	0	1
Likely Pathogenic	0	0	0	0	0
VUS	0	73	3	0	76
Likely Benign	0	5	0	14	19
Benign	0	1	1	0	2
Conflicting	—				2
Total	0	80	4	14	100

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

View in ClinVar →

10 pathogenic / likely-pathogenic (of 15) ClinVar copy-number / structural variants overlap TRMT10C — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →