TRMT10A

Chr 4AR

tRNA methyltransferase 10A

Also known as: HEL-S-88, MSSGM, MSSGM1, RG9MTD2, TRM10

NCBI Gene: 93587ENSG00000145331UniProt: Q8TBZ6

This gene encodes a protein that belongs to the tRNA (Guanine-1)-methyltransferase family. A similar gene in yeast modifies several different tRNA species. Mutations in this gene are associated with microcephaly, short stature, and impaired glucose metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]

Primary Disease Associations & Inheritance

Microcephaly, short stature, and impaired glucose metabolism 1MIM #616033
AR
0
Active trials
37
Pathogenic / LP
182
ClinVar variants
4
Pubs (1 yr)
0.4
Missense Z
1.18
LOEUF
Clinical Summary— TRMT10A
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
37 Pathogenic / Likely Pathogenic· 89 VUS of 182 total submissions
Some data sources returned errors (1)

pubtator: TimeoutError: The operation was aborted due to timeout

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.18LOEUF
pLI 0.000
Z-score 0.91
OE 0.79 (0.54–1.18)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.44Z-score
OE missense 0.91 (0.80–1.03)
166 obs / 182.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.79 (0.54–1.18)
0≤0.351.4
Missense OE0.91 (0.80–1.03)
0≤0.61.4
Synonymous OE0.80
0≤1.21.6
LoF obs/exp: 17 / 21.5Missense obs/exp: 166 / 182.6Syn Z: 1.24

ClinVar Variant Classifications

182 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic23
Likely Pathogenic14
VUS89
Likely Benign46
Benign3
Conflicting7
23
Pathogenic
14
Likely Pathogenic
89
VUS
46
Likely Benign
3
Benign
7
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
1
21
0
23
Likely Pathogenic
7
0
7
0
14
VUS
2
72
15
0
89
Likely Benign
0
2
19
25
46
Benign
0
0
3
0
3
Conflicting
—7
Total10756525182

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

View in ClinVar →

TRMT10A · protein map & ClinVar variants

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

Gene2Phenotype Curations

TRMT10A-related intellectual developmental disorder

definitive
ARLoss Of FunctionAbsent Gene Product
Dev. Disorders
G2P ↗

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients