TRMT10A

Summary

TRMT10A (tRNA methyltransferase 10A, HGNC:28403) is a protein-coding gene on chromosome 4q23, encoding tRNA methyltransferase 10 homolog A (Q8TBZ6). S-adenosyl-L-methionine-dependent guanine N(1)-methyltransferase that catalyzes the formation of N(1)-methylguanine at position 9 (m1G9) in tRNAs.

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.

Source: NCBI Gene 93587 — RefSeq curated summary.

At a glance

• Gene–disease (curated): microcephaly, short stature, and impaired glucose metabolism 1 (Definitive, GenCC) — +1 more curated relationship
• GWAS associations: 2
• Clinical variants (ClinVar): 167 total — 9 pathogenic, 10 likely-pathogenic
• Phenotypes (HPO): 77
• Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
• MANE Select transcript: NM_001134665

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28403
Approved symbol	TRMT10A
Name	tRNA methyltransferase 10A
Location	4q23
Locus type	gene with protein product
Status	Approved
Aliases	MGC27034, TRM10
Ensembl gene	ENSG00000145331
Ensembl biotype	protein_coding
OMIM	616013
Entrez	93587

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 retained_intron

ENST00000273962, ENST00000394876, ENST00000394877, ENST00000455368, ENST00000507394, ENST00000514547, ENST00000515831, ENST00000891637, ENST00000891638, ENST00000963791

RefSeq mRNA: 6 — MANE Select: NM_001134665 NM_001134665, NM_001134666, NM_001375880, NM_001375881, NM_001375882, NM_152292

CCDS: CCDS3650

Canonical transcript exons

ENST00000394876 — 8 exons

Exon	Start	End
ENSE00000969996	99557345	99557416
ENSE00000969998	99553785	99553934
ENSE00000969999	99550885	99550990
ENSE00001194207	99558049	99558211
ENSE00001519879	99546711	99549356
ENSE00001519888	99563913	99564039
ENSE00003557077	99556146	99556220
ENSE00003658746	99559154	99559361

Expression profiles

Bgee: expression breadth ubiquitous, 201 present calls, max score 85.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.9524 / max 66.8083, expressed in 1668 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
53284	2.6218	1205
53285	1.7594	1101
53286	0.9646	641
53283	0.4953	237
53282	0.1113	34

Top tissues by expression

246 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.91	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.55	gold quality
calcaneal tendon	UBERON:0003701	81.69	gold quality
adrenal tissue	UBERON:0018303	79.98	gold quality
islet of Langerhans	UBERON:0000006	79.58	gold quality
right uterine tube	UBERON:0001302	79.23	gold quality
body of pancreas	UBERON:0001150	77.18	gold quality
right lobe of liver	UBERON:0001114	77.16	gold quality
bronchial epithelial cell	CL:0002328	77.04	gold quality
pancreas	UBERON:0001264	76.82	gold quality
ileal mucosa	UBERON:0000331	76.49	gold quality
bronchus	UBERON:0002185	75.40	gold quality
monocyte	CL:0000576	75.36	gold quality
leukocyte	CL:0000738	75.13	gold quality
right adrenal gland cortex	UBERON:0035827	75.04	gold quality
right adrenal gland	UBERON:0001233	75.02	gold quality
rectum	UBERON:0001052	74.62	gold quality
testis	UBERON:0000473	74.56	gold quality
left testis	UBERON:0004533	74.18	gold quality
right testis	UBERON:0004534	74.03	gold quality
left adrenal gland	UBERON:0001234	74.00	gold quality
gastrocnemius	UBERON:0001388	74.00	gold quality
muscle of leg	UBERON:0001383	73.97	gold quality
stromal cell of endometrium	CL:0002255	73.94	gold quality
ventricular zone	UBERON:0003053	73.58	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	73.33	gold quality
body of stomach	UBERON:0001161	73.18	gold quality
smooth muscle tissue	UBERON:0001135	73.12	gold quality
left adrenal gland cortex	UBERON:0035825	72.87	gold quality
embryo	UBERON:0000922	72.81	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

108 targeting TRMT10A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-6508-5P	99.92	70.67	2465

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 9)

• This is the first study describing the impact of TRMT10A deficiency in mammals, highlighting a role in the pathogenesis of microcephaly and early onset diabetes. (PMID:24204302)
• TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly. (PMID:25053765)
• Homozygous deletion of TRMT10A is associated with a syndrome of failure to thrive, delayed puberty, intellectual disability and diabetes mellitus. (PMID:26297882)
• A homozygous G to T transition in exon 2 of gene TRMT10A at nucleotide position 79 of the coding sequence was identified in a family with young-adult onset diabetes with intellectual disability, microcephaly and epilepsy. (PMID:26526202)
• tRNA guanosine 9 hypomethylation leads to tRNAGln fragmentation and that 5’-tRNAGln fragments mediate TRMT10A deficiency-induced beta-cell death. This study unmasks tRNA hypomethylation and fragmentation as a hitherto unknown mechanism of pancreatic beta-cell demise relevant to monogenic and polygenic forms of diabetes. (PMID:30247717)
• demonstrate that human TRMT10A (hTRMT10A) and human TRMT10B (hTRMT10B) are not biochemically redundant (PMID:31292261)
• transcripts with increased m(6)A upon TRMT10A ablation contain an overrepresentation of m(1)G9-containing tRNAs codons read by tRNA(Gln(TTG)), tRNA(Arg(CCG)), and tRNA(Thr(CGT)) These findings collectively reveal the presence of coordinated mRNA and tRNA methylations and demonstrate a mechanism for regulating gene expression through the interactions between mRNA and tRNA modifying enzymes. (PMID:32213595)
• Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B. (PMID:32392304)
• TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice. (PMID:38950903)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	trmt10a	ENSDARG00000036678
mus_musculus	Trmt10a	ENSMUSG00000004127
rattus_norvegicus	Trmt10a	ENSRNOG00000011025
drosophila_melanogaster	CG14618	FBGN0031189
caenorhabditis_elegans		WBGENE00009131

Paralogs (2): TRMT10B (ENSG00000165275), TRMT10C (ENSG00000174173)

Protein

Protein identifiers

tRNA methyltransferase 10 homolog A — Q8TBZ6 (reviewed: Q8TBZ6)

Alternative names: RNA (guanine-9-)-methyltransferase domain-containing protein 2, tRNA (guanine(9)-N(1))-methyltransferase TRMT10A

All UniProt accessions (4): D6R954, Q8TBZ6, V9HVY8, X6REK4

UniProt curated annotations — full annotation on UniProt →

Function. S-adenosyl-L-methionine-dependent guanine N(1)-methyltransferase that catalyzes the formation of N(1)-methylguanine at position 9 (m1G9) in tRNAs. Probably not able to catalyze formation of N(1)-methyladenine at position 9 (m1A9) in tRNAs.

Subunit / interactions. Interacts with tRNA.

Subcellular location. Nucleus. Nucleolus.

Tissue specificity. Expressed in embryonic and fetal brain. It is expressed throughout the dorsal telencephalon at 8 and 11 weeks of gestation, with highest expression in ventricular zone and marginal zone. Detected in cerebellar cortex and nuclei, but not in dorsal telencephalon, at later stages.

Disease relevance. Microcephaly, short stature, and impaired glucose metabolism 1 (MSSGM1) [MIM:616033] An autosomal recessive disease characterized by microcephaly, intellectual disability, short stature, and disturbed glucose metabolism. Additional clinical features include delayed puberty, hypoglycemia-related seizures, hyperinsulinemic hypoglycemia, and early-onset diabetes. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the class IV-like SAM-binding methyltransferase superfamily. TRM10 family.

RefSeq proteins (6): NP_001128137, NP_001128138, NP_001362809, NP_001362810, NP_001362811, NP_689505 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007356	tRNA_m1G_MeTrfase_euk	Family
IPR016653	TRM10/TRM10A	Family
IPR028564	MT_TRM10-typ	Domain
IPR038459	MT_TRM10-typ_sf	Homologous_superfamily

Enzyme classification (BRENDA):

• EC 2.1.1.221 — tRNA (guanine9-N1)-methyltransferase (BRENDA: 4 organisms, 53 substrates, 0 inhibitors, 11 Km, 9 kcat entries)

Substrate kinetics (BRENDA)

5 substrates with measured Km, best-characterized 5. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
GUANINE9 IN TRNAGLY	0.0032–0.0053	2
GUANINE9 IN TRNAGLYGCC	0.0002–0.0024	2
GUANINE9 IN TRNAVALUAC	0.0002–0.0019	2
GUANINE9 IN TRNAARG	—	0
GUANINE9 IN TRNAPHE	—	0

Catalyzed reactions (Rhea), 1 shown:

• guanosine(9) in tRNA + S-adenosyl-L-methionine = N(1)-methylguanosine(9) in tRNA + S-adenosyl-L-homocysteine + H(+) (RHEA:43156)

UniProt features (32 total): helix 9, sequence variant 6, strand 5, compositionally biased region 4, region of interest 2, chain 1, domain 1, sequence conflict 1, turn 1, coiled-coil region 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
4FMW	X-RAY DIFFRACTION	2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TBZ6-F1	76.77	0.48

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 336

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6782315	tRNA modification in the nucleus and cytosol

MSigDB gene sets: 293 (showing top): FXR_IR1_Q6, RORA1_01, GOBP_TRNA_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, TGACCTY_ERR1_Q2, MEF2_02, CAGCTG_AP4_Q5, GOBP_RNA_METHYLATION, AACWWCAANK_UNKNOWN, GOBP_RNA_MODIFICATION, WANG_LMO4_TARGETS_DN, WTGAAAT_UNKNOWN, GOBP_TRNA_METHYLATION, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, GARY_CD5_TARGETS_DN

GO Biological Process (3): tRNA N1-guanine methylation (GO:0002939), tRNA methylation (GO:0030488), methylation (GO:0032259)

GO Molecular Function (6): tRNA binding (GO:0000049), RNA binding (GO:0003723), tRNA (guanosine(9)-N1)-methyltransferase activity (GO:0052905), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740)

GO Cellular Component (6): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytosol (GO:0005829), actin cytoskeleton (GO:0015629), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
tRNA processing	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear lumen	2
cellular anatomical structure	2
tRNA methylation	1
RNA methylation	1
tRNA modification	1
metabolic process	1
RNA binding	1
nucleic acid binding	1
tRNA (guanine) methyltransferase activity	1
binding	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1
cytoplasm	1
cytoskeleton	1
extracellular vesicle	1

Protein interactions and networks

STRING

1170 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRMT10A	TRMT5	Q32P41	791
TRMT10A	WDR4	P57081	742
TRMT10A	METTL1	Q9UBP6	709
TRMT10A	FTSJ1	Q9UET6	708
TRMT10A	TRMT1	Q9NXH9	690
TRMT10A	NSUN2	Q08J23	683
TRMT10A	TRMT6	Q9UJA5	661
TRMT10A	TYW2	Q53H54	649
TRMT10A	PUS1	Q9Y606	637
TRMT10A	PUS3	Q9BZE2	635
TRMT10A	TRMT61A	Q96FX7	631
TRMT10A	PRORP	O15091	618
TRMT10A	TRIT1	Q9H3H1	615
TRMT10A	TARBP1	Q13395	611
TRMT10A	ADAT3	Q96EY9	609

IntAct

13 interactions, top by confidence:

A	B	Type	Score
TRMT10A	TRIM7	psi-mi:“MI:0915”(physical association)	0.560
TRMT10A		psi-mi:“MI:0213”(methylation reaction)	0.440
	TRMT10A	psi-mi:“MI:0213”(methylation reaction)	0.440
ZBTB33	SF3B1	psi-mi:“MI:0914”(association)	0.350
Myh9	GOSR1	psi-mi:“MI:0914”(association)	0.350
Rfx5	MRPL27	psi-mi:“MI:0914”(association)	0.350
MAD2L1	MAD1L1	psi-mi:“MI:0914”(association)	0.350
rep	VWA8	psi-mi:“MI:0914”(association)	0.350
SYT2	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
TRMT10A	TRIM7	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (28): TRMT10A (Affinity Capture-MS), TRMT10A (Affinity Capture-MS), TRMT10A (Affinity Capture-MS), TRMT10A (Affinity Capture-MS), TRMT10A (Affinity Capture-RNA), TRIM7 (Two-hybrid), TRMT10A (Affinity Capture-MS), TRMT10A (Co-fractionation), TRMT10A (Co-fractionation), TRMT10A (Co-fractionation), TRMT10A (Co-fractionation), TRMT10A (Co-fractionation), UPF2 (Co-fractionation), TRMT10A (Affinity Capture-MS), TRMT10A (Affinity Capture-MS)

ESM2 similar proteins: A0JMA8, A4IHS0, B5DF07, D3ZRC4, D6WMX4, E7EXT2, F7AEX0, F7BJB9, O15091, O93530, Q09287, Q14149, Q1L987, Q24558, Q28C44, Q2KI45, Q2TBE0, Q32NQ8, Q3MHI8, Q3UFY8, Q4KLI2, Q4R366, Q5RDI0, Q5U245, Q5U2R4, Q5VZ89, Q5XTS1, Q66JD1, Q66JJ4, Q6DDV1, Q6GLI9, Q7JUX9, Q7L0Y3, Q7Z401, Q86VD1, Q8C1Z8, Q8JZY4, Q8K1N1, Q8N6Q8, Q8TBZ6

Diamond homologs: A4IHS0, O14214, Q08BM0, Q08DP1, Q2KI45, Q3MHI8, Q3UFY8, Q4I8X0, Q4KLI2, Q4WXA1, Q59Q39, Q5B8X0, Q5U2R4, Q6C1W9, Q6PF06, Q7JUX9, Q7L0Y3, Q8C1Z8, Q8TBZ6, Q9VR56, P0CS10, P0CS11, Q12400, Q5RJK3, Q66JJ4, Q6BWG3, Q6CUM6, Q6FQB2, Q75A17, Q9D075

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

167 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	9
Likely pathogenic	10
Uncertain significance	81
Likely benign	45
Benign	3

Top pathogenic / likely-pathogenic (19)

Variant ID	HGVS	Classification
1332859	NM_001134665.3(TRMT10A):c.23dup (p.Phe9fs)	Pathogenic
1454256	NM_001134665.3(TRMT10A):c.193C>T (p.Arg65Ter)	Pathogenic
156230	NM_001134665.3(TRMT10A):c.616G>A (p.Gly206Arg)	Pathogenic
2024480	NM_001134665.3(TRMT10A):c.483G>A (p.Trp161Ter)	Pathogenic
2444063	NM_001134665.3(TRMT10A):c.346A>T (p.Lys116Ter)	Pathogenic
3377077	NM_001134665.3(TRMT10A):c.151C>T (p.Gln51Ter)	Pathogenic
3640410	NM_001134665.3(TRMT10A):c.387C>A (p.Tyr129Ter)	Pathogenic
4804695	NM_001134665.3(TRMT10A):c.492G>A (p.Trp164Ter)	Pathogenic
593751	NM_001134665.3(TRMT10A):c.79G>T (p.Glu27Ter)	Pathogenic
1348928	NM_001134665.3(TRMT10A):c.495+2T>C	Likely pathogenic
1709365	NM_001134665.3(TRMT10A):c.41del (p.Asn14fs)	Likely pathogenic
2063355	NM_001134665.3(TRMT10A):c.185+1_185+13del	Likely pathogenic
2837642	NM_001134665.3(TRMT10A):c.348+1G>T	Likely pathogenic
4077707	NM_001134665.3(TRMT10A):c.405_406del (p.Leu136fs)	Likely pathogenic
4531959	NM_001134665.3(TRMT10A):c.496-1G>A	Likely pathogenic
4531960	NM_001134665.3(TRMT10A):c.420+1G>A	Likely pathogenic
4845348	NM_001134665.3(TRMT10A):c.148_152del (p.Lys50fs)	Likely pathogenic
4849284	NM_001134665.3(TRMT10A):c.206del (p.Arg69fs)	Likely pathogenic
974899	NM_001134665.3(TRMT10A):c.697_698delinsTA (p.Pro233Ter)	Likely pathogenic

SpliceAI

1256 predictions. Top by Δscore:

Variant	Effect	Δscore
4:99553779:TAGTA:T	donor_loss	1.0000
4:99553781:GTAC:G	donor_loss	1.0000
4:99553782:TAC:T	donor_loss	1.0000
4:99553783:A:AC	donor_gain	1.0000
4:99553783:A:AT	donor_loss	1.0000
4:99553784:C:CC	donor_gain	1.0000
4:99553930:ATATC:A	acceptor_gain	1.0000
4:99553931:TATC:T	acceptor_gain	1.0000
4:99553932:ATC:A	acceptor_gain	1.0000
4:99553933:TC:T	acceptor_gain	1.0000
4:99553934:CC:C	acceptor_gain	1.0000
4:99553935:C:CC	acceptor_gain	1.0000
4:99553935:C:G	acceptor_loss	1.0000
4:99553935:C:T	acceptor_gain	1.0000
4:99553936:T:C	acceptor_gain	1.0000
4:99553936:T:G	acceptor_loss	1.0000
4:99553936:T:TC	acceptor_gain	1.0000
4:99553937:T:C	acceptor_gain	1.0000
4:99553937:T:TC	acceptor_gain	1.0000
4:99553943:C:CT	acceptor_gain	1.0000
4:99553944:A:T	acceptor_gain	1.0000
4:99553946:C:CT	acceptor_gain	1.0000
4:99553947:A:T	acceptor_gain	1.0000
4:99556141:ATTAC:A	donor_loss	1.0000
4:99556142:TTA:T	donor_loss	1.0000
4:99556143:TA:T	donor_loss	1.0000
4:99556144:A:AT	donor_loss	1.0000
4:99556221:C:CC	acceptor_gain	1.0000
4:99556233:T:C	acceptor_gain	1.0000
4:99556233:T:TC	acceptor_gain	1.0000

AlphaMissense

2262 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:99550899:A:G	L246S	0.999
4:99557385:C:G	R127P	0.999
4:99549318:A:G	W264R	0.998
4:99549318:A:T	W264R	0.998
4:99553800:A:C	D210E	0.998
4:99553800:A:T	D210E	0.998
4:99553810:C:T	G207E	0.998
4:99553813:C:T	G206E	0.998
4:99553823:A:C	Y203D	0.998
4:99553873:A:G	L186P	0.998
4:99557367:C:G	R133P	0.998
4:99557383:A:G	C128R	0.998
4:99557403:A:G	L121P	0.998
4:99549316:C:A	W264C	0.997
4:99549316:C:G	W264C	0.997
4:99550941:A:G	L232P	0.997
4:99553804:A:T	V209E	0.997
4:99549280:T:A	K276N	0.996
4:99549280:T:G	K276N	0.996
4:99550893:A:T	V248D	0.996
4:99553799:G:C	H211D	0.996
4:99553801:T:A	D210V	0.996
4:99553801:T:G	D210A	0.996
4:99553819:A:T	V204E	0.996
4:99553870:G:T	T187K	0.996
4:99553873:A:T	L186H	0.996
4:99556151:A:G	W164R	0.996
4:99556151:A:T	W164R	0.996
4:99557381:A:C	C128W	0.996
4:99557393:C:A	Q124H	0.996

dbSNP variants (sampled 300 via entrez): RS1000094006 (4:99562471 T>C,G), RS1000329177 (4:99559843 A>C,G), RS1000423057 (4:99551909 GA>G,GAA,GAAAAA), RS1000524859 (4:99558069 C>A,G), RS1000566369 (4:99557623 T>C), RS1000595179 (4:99565806 TGAA>T), RS1000676283 (4:99550265 C>G,T), RS10007569 (4:99557367 C>A,T), RS10007794 (4:99557583 C>A), RS1000791994 (4:99549986 A>G), RS10008896 (4:99552547 G>A), RS10008928 (4:99552755 C>A,G,T), RS1001028127 (4:99563926 T>C), RS1001159930 (4:99553371 G>A), RS10017816 (4:99561130 C>A,G)

Disease associations

OMIM: gene MIM:616013 | disease phenotypes: MIM:616033

GenCC curated gene-disease

Disease	Classification	Inheritance
microcephaly, short stature, and impaired glucose metabolism 1	Definitive	Autosomal recessive
primary microcephaly-mild intellectual disability-young-onset diabetes syndrome	Supportive	Autosomal recessive

Mondo (3): microcephaly, short stature, and impaired glucose metabolism 1 (MONDO:0000208), congenital nervous system disorder (MONDO:0002320), primary microcephaly-mild intellectual disability-young-onset diabetes syndrome (MONDO:0018320)

Orphanet (1): Primary microcephaly-mild intellectual disability-young-onset diabetes syndrome (Orphanet:391408)

HPO phenotypes

77 total (30 of 77 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000160	Narrow mouth
HP:0000219	Thin upper lip vermilion
HP:0000252	Microcephaly
HP:0000274	Small face
HP:0000275	Narrow face
HP:0000286	Epicanthus
HP:0000293	Full cheeks
HP:0000294	Low anterior hairline
HP:0000311	Round face
HP:0000322	Short philtrum
HP:0000341	Narrow forehead
HP:0000343	Long philtrum
HP:0000347	Micrognathia
HP:0000400	Macrotia
HP:0000407	Sensorineural hearing impairment
HP:0000445	Wide nose
HP:0000463	Anteverted nares
HP:0000470	Short neck
HP:0000494	Downslanted palpebral fissures
HP:0000592	Blue sclerae
HP:0000601	Hypotelorism
HP:0000664	Synophrys
HP:0000677	Oligodontia
HP:0000685	Hypoplasia of teeth
HP:0000767	Pectus excavatum
HP:0000786	Primary amenorrhea
HP:0000819	Diabetes mellitus
HP:0000821	Hypothyroidism
HP:0000823	Delayed puberty

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST002112_3	Celiac disease	5.000000e-06
GCST006921_3	Regular attendance at a pub or social club	4.000000e-25

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009592	social interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

40 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
Air Pollutants	increases abundance, increases methylation, decreases expression	2
Benzo(a)pyrene	decreases expression, increases methylation	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
dicrotophos	decreases expression	1
propionaldehyde	decreases expression	1
beta-lapachone	decreases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
butyraldehyde	decreases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
methacrylaldehyde	affects cotreatment, increases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
monomethylarsonous acid	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Acrolein	affects cotreatment, increases expression	1
Arsenic	increases abundance, increases expression, affects cotreatment	1
Cisplatin	affects cotreatment, decreases expression	1
Coumestrol	decreases expression	1
Doxorubicin	increases expression	1
Drugs, Chinese Herbal	increases expression	1
Gallic Acid	decreases expression	1
Hydrogen Peroxide	affects cotreatment, increases expression	1
Manganese	increases expression, affects cotreatment, increases abundance	1
Naphthoquinones	increases expression	1
Nitrogen Dioxide	increases abundance, increases methylation	1
Ozone	affects cotreatment, increases expression	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TU70	HAP1 TRMT10A (-) 1	Cancer cell line	Male
CVCL_TU71	HAP1 TRMT10A (-) 2	Cancer cell line	Male
CVCL_TU72	HAP1 TRMT10A (-) 3	Cancer cell line	Male
CVCL_TU73	HAP1 TRMT10A (-) 4	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.