TMA16

Summary

TMA16 (translation machinery associated 16 homolog, HGNC:25638) is a protein-coding gene on chromosome 4q32.2, encoding Translation machinery-associated protein 16 (Q96EY4). Involved in the biogenesis of the 60S ribosomal subunit in the nucleus. It is a common-essential gene (DepMap: required in 93.3% of cancer cell lines).

Enables preribosome binding activity. Involved in ribosomal large subunit biogenesis. Located in nucleolus and nucleoplasm.

Source: NCBI Gene 55319 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 39 total
• Cancer dependency (DepMap): dependent in 93.3% of screened cell lines (common-essential)
• MANE Select transcript: NM_018352

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25638
Approved symbol	TMA16
Name	translation machinery associated 16 homolog
Location	4q32.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ11184
Ensembl gene	ENSG00000198498
Ensembl biotype	protein_coding
Entrez	55319

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 10 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000358572, ENST00000503148, ENST00000506214, ENST00000508268, ENST00000508652, ENST00000509657, ENST00000511562, ENST00000513134, ENST00000513272, ENST00000860148, ENST00000911659, ENST00000911660, ENST00000911661, ENST00000911662

RefSeq mRNA: 1 — MANE Select: NM_018352 NM_018352

CCDS: CCDS43278

Canonical transcript exons

ENST00000358572 — 7 exons

Exon	Start	End
ENSE00001412060	163519334	163520539
ENSE00001431769	163494690	163494804
ENSE00003516562	163512822	163512859
ENSE00003520368	163517434	163517476
ENSE00003586361	163515313	163515461
ENSE00003623015	163507033	163507145
ENSE00003627204	163514074	163514158

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 91.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.3667 / max 253.7529, expressed in 1811 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
50403	23.2382	1807
50402	1.5209	1022
50405	1.4341	790
50401	1.1092	695
50404	0.9620	615
50406	0.0927	31
50407	0.0095	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	91.29	gold quality
ventricular zone	UBERON:0003053	90.09	gold quality
monocyte	CL:0000576	89.43	gold quality
left testis	UBERON:0004533	89.35	gold quality
mononuclear cell	CL:0000842	89.07	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.80	gold quality
leukocyte	CL:0000738	88.72	gold quality
right testis	UBERON:0004534	88.45	gold quality
ganglionic eminence	UBERON:0004023	88.33	gold quality
testis	UBERON:0000473	87.52	gold quality
adrenal tissue	UBERON:0018303	87.42	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.32	gold quality
body of pancreas	UBERON:0001150	87.22	gold quality
tibial artery	UBERON:0007610	87.19	gold quality
popliteal artery	UBERON:0002250	87.18	gold quality
stromal cell of endometrium	CL:0002255	86.78	gold quality
islet of Langerhans	UBERON:0000006	86.12	gold quality
aorta	UBERON:0000947	86.02	gold quality
pancreas	UBERON:0001264	85.41	gold quality
descending thoracic aorta	UBERON:0002345	85.31	gold quality
left coronary artery	UBERON:0001626	85.25	gold quality
body of uterus	UBERON:0009853	85.21	gold quality
thoracic aorta	UBERON:0001515	84.98	gold quality
rectum	UBERON:0001052	84.97	gold quality
ascending aorta	UBERON:0001496	84.93	gold quality
omental fat pad	UBERON:0010414	84.73	gold quality
ectocervix	UBERON:0012249	84.72	gold quality
left ovary	UBERON:0002119	84.69	gold quality
peritoneum	UBERON:0002358	84.69	gold quality
esophagus mucosa	UBERON:0002469	84.11	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting TMA16, 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-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-369-3P	99.85	70.52	2264
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-4755-5P	99.71	70.34	2716

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 93.3% of screened cell lines, common-essential.

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	tma16	ENSDARG00000008068
mus_musculus	Tma16	ENSMUSG00000025591
rattus_norvegicus	Tma16	ENSRNOG00000089425
drosophila_melanogaster	CG15027	FBGN0030611

Protein

Protein identifiers

Translation machinery-associated protein 16 — Q96EY4 (reviewed: Q96EY4)

All UniProt accessions (5): Q96EY4, D6RA57, D6RC31, D6RE67, H0Y9X1

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the biogenesis of the 60S ribosomal subunit in the nucleus.

Subunit / interactions. Associates with pre-60S ribosomal particles.

Subcellular location. Nucleus.

Similarity. Belongs to the TMA16 family.

RefSeq proteins (1): NP_060822* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021346	Tma16	Family
IPR038356	Tma16_sf	Homologous_superfamily

Pfam: PF11176

UniProt features (8 total): sequence variant 3, chain 1, region of interest 1, compositionally biased region 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

9 structures.

PDB	Method	Resolution (Å)
8FLB	ELECTRON MICROSCOPY	2.55
8FLA	ELECTRON MICROSCOPY	2.63
8FLC	ELECTRON MICROSCOPY	2.76
8IDT	ELECTRON MICROSCOPY	2.8
8IDY	ELECTRON MICROSCOPY	3
8INF	ELECTRON MICROSCOPY	3
6LU8	ELECTRON MICROSCOPY	3.13
8INE	ELECTRON MICROSCOPY	3.2
6LSS	ELECTRON MICROSCOPY	3.23

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96EY4-F1	83.34	0.62

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): 9

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 162 (showing top): GOBP_RIBOSOME_BIOGENESIS, chr4q32, SHEPARD_CRASH_AND_BURN_MUTANT_UP, FOSTER_TOLERANT_MACROPHAGE_UP, FONTAINE_PAPILLARY_THYROID_CARCINOMA_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, MASSARWEH_RESPONSE_TO_ESTRADIOL, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS, NUYTTEN_EZH2_TARGETS_DN, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN, GOCC_NUCLEOLUS, GOMF_RIBONUCLEOPROTEIN_COMPLEX_BINDING, YAUCH_HEDGEHOG_SIGNALING_PARACRINE_UP, DUTERTRE_ESTRADIOL_RESPONSE_6HR_UP

GO Biological Process (2): ribosomal large subunit biogenesis (GO:0042273), ribosome biogenesis (GO:0042254)

GO Molecular Function (3): protein-macromolecule adaptor activity (GO:0030674), preribosome binding (GO:1990275), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ribonucleoprotein complex biogenesis	2
nuclear lumen	2
ribosome biogenesis	1
protein binding	1
molecular adaptor activity	1
ribonucleoprotein complex binding	1
binding	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1138 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMA16	PHYHIPL	Q96FC7	586
TMA16	TMEM192	Q8IY95	530
TMA16	PHACTR3	Q96KR7	529
TMA16	LSG1	Q9H089	527
TMA16	RRP15	Q9Y3B9	525
TMA16	ARRDC2	Q8TBH0	491
TMA16	C1orf53	Q5VUE5	475
TMA16	CHLSN	Q9BRJ6	466
TMA16	SYTL2	Q9HCH5	442
TMA16	SURF6	O75683	436
TMA16	NSA2	O95478	436
TMA16	NMD3	Q96D46	402
TMA16	SGK3	Q96BR1	395
TMA16	PAK1IP1	Q9NWT1	394
TMA16	NOL9	Q5SY16	389

IntAct

54 interactions, top by confidence:

A	B	Type	Score
TMA16	KLHL2	psi-mi:“MI:0915”(physical association)	0.780
KLHL2	TMA16	psi-mi:“MI:0915”(physical association)	0.780
TMA16	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-7	TMA16	psi-mi:“MI:0915”(physical association)	0.560
TMA16	TSPYL2	psi-mi:“MI:0915”(physical association)	0.560
AP2M1	TMA16	psi-mi:“MI:0915”(physical association)	0.560
CASTOR1	TMA16	psi-mi:“MI:0915”(physical association)	0.560
HTT	TMA16	psi-mi:“MI:0915”(physical association)	0.560
TMA16	TNPO2	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
MAP1LC3B	NIPSNAP2	psi-mi:“MI:0914”(association)	0.520
RPL10	RPS6	psi-mi:“MI:0914”(association)	0.350
CBX4	SDC2	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
CAND1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
TMA16	SEC24D	psi-mi:“MI:0914”(association)	0.350
PATJ	LIN7A	psi-mi:“MI:0914”(association)	0.350
G3BP1	HAT1	psi-mi:“MI:0914”(association)	0.350
SP100	SART1	psi-mi:“MI:0914”(association)	0.350
TP53BP1	BCKDK	psi-mi:“MI:0914”(association)	0.350
N	POLRMT	psi-mi:“MI:0914”(association)	0.350

BioGRID (113): TMA16 (Two-hybrid), KRTAP10-7 (Two-hybrid), TMA16 (Affinity Capture-MS), TMA16 (Affinity Capture-MS), TMA16 (Affinity Capture-MS), PHF3 (Affinity Capture-MS), TNPO2 (Affinity Capture-MS), RBM12 (Affinity Capture-MS), SLC9A3R2 (Affinity Capture-MS), PYGB (Affinity Capture-MS), PPID (Affinity Capture-MS), CENPF (Affinity Capture-MS), KLHL20 (Affinity Capture-MS), TNPO1 (Affinity Capture-MS), SUPT4H1 (Affinity Capture-MS)

ESM2 similar proteins: A0PJP4, A2VDP1, A4FV29, A4II71, E9PSK7, F1RCP1, O00472, O60271, Q0IHE5, Q15545, Q1LZE0, Q28DG8, Q2HJG8, Q2TBQ7, Q3U1T3, Q498D5, Q4R5A5, Q4V8V1, Q58A65, Q5DTM8, Q5EA95, Q5M7T3, Q5PSV4, Q5R6Y9, Q5R7L9, Q5RHQ8, Q5VTR2, Q5ZKF4, Q5ZLL9, Q5ZLS3, Q62739, Q68CZ1, Q6AZT4, Q6DC03, Q6R1L1, Q7ZXA8, Q8BXG3, Q8CG73, Q8IZC4, Q8K0Q5

Diamond homologs: A4II15, A7MCB7, Q3T071, Q4V7N4, Q96EY4, Q9CR02, Q9VXY4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 55 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
mRNA Splicing	6	15.7×	1e-04
SARS-CoV-2-host interactions	5	14.2×	1e-03
Processing of Capped Intron-Containing Pre-mRNA	7	13.7×	5e-05
SARS-CoV-2 Infection	7	13.4×	5e-05
SARS-CoV Infections	10	13.2×	9e-07
mRNA Polyadenylation	5	10.5×	3e-03
mRNA Splicing - Major Pathway	8	10.4×	5e-05
Viral Infection Pathways	10	7.3×	5e-05

GO biological processes:

GO term	Partners	Fold	FDR
mRNA splicing, via spliceosome	6	11.0×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	22
Likely benign	2
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1231 predictions. Top by Δscore:

Variant	Effect	Δscore
4:163507023:T:G	acceptor_gain	1.0000
4:163507025:C:G	acceptor_gain	1.0000
4:163507026:A:AG	acceptor_gain	1.0000
4:163507027:T:G	acceptor_gain	1.0000
4:163507031:A:AG	acceptor_gain	1.0000
4:163507032:G:GG	acceptor_gain	1.0000
4:163507032:GCCC:G	acceptor_gain	1.0000
4:163507032:GCCCA:G	acceptor_gain	1.0000
4:163507141:GAAAA:G	donor_gain	1.0000
4:163507142:AAAA:A	donor_gain	1.0000
4:163507143:AAA:A	donor_gain	1.0000
4:163507143:AAAGT:A	donor_loss	1.0000
4:163507144:AA:A	donor_gain	1.0000
4:163507144:AAG:A	donor_loss	1.0000
4:163507145:AG:A	donor_loss	1.0000
4:163507146:G:A	donor_loss	1.0000
4:163507146:G:GG	donor_gain	1.0000
4:163507147:TAAG:T	donor_loss	1.0000
4:163512819:A:G	acceptor_gain	1.0000
4:163515449:GGA:G	donor_gain	1.0000
4:163494793:G:GT	donor_gain	0.9900
4:163494849:G:GT	donor_gain	0.9900
4:163507022:A:AG	acceptor_gain	0.9900
4:163507024:A:AG	acceptor_gain	0.9900
4:163507028:TTTA:T	acceptor_loss	0.9900
4:163507029:TTA:T	acceptor_loss	0.9900
4:163507030:TAGCC:T	acceptor_loss	0.9900
4:163507032:G:A	acceptor_loss	0.9900
4:163507032:GC:G	acceptor_gain	0.9900
4:163507032:GCC:G	acceptor_gain	0.9900

AlphaMissense

1356 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:163507083:T:A	H18Q	0.996
4:163507083:T:G	H18Q	0.996
4:163519338:T:A	W146R	0.996
4:163519338:T:C	W146R	0.996
4:163507081:C:G	H18D	0.995
4:163507095:A:C	R22S	0.995
4:163507095:A:T	R22S	0.995
4:163507094:G:C	R22T	0.994
4:163514088:T:A	W57R	0.994
4:163514088:T:C	W57R	0.994
4:163507090:A:C	S21R	0.993
4:163507092:T:A	S21R	0.993
4:163507092:T:G	S21R	0.993
4:163517440:C:A	P132Q	0.993
4:163514083:T:C	L55P	0.992
4:163514092:T:C	F58S	0.991
4:163515326:T:C	F85L	0.991
4:163515328:C:A	F85L	0.991
4:163515328:C:G	F85L	0.991
4:163519340:G:C	W146C	0.991
4:163519340:G:T	W146C	0.991
4:163507081:C:A	H18N	0.990
4:163507082:A:G	H18R	0.990
4:163507094:G:T	R22I	0.989
4:163507091:G:A	S21N	0.988
4:163515324:G:C	R84P	0.988
4:163517440:C:G	P132R	0.988
4:163519360:T:C	L153S	0.985
4:163507093:A:G	R22G	0.984
4:163507099:G:C	A24P	0.984

dbSNP variants (sampled 300 via entrez): RS1000058593 (4:163500952 A>G), RS10000612 (4:163503818 A>G), RS1000143133 (4:163519133 T>C), RS1000178692 (4:163513827 A>G), RS1000249388 (4:163513529 A>G), RS10002969 (4:163517053 G>A,C), RS1000345619 (4:163499279 G>T), RS1000359717 (4:163500210 C>G,T), RS1000548074 (4:163494110 G>C), RS1000658194 (4:163499594 G>A,T), RS1001002705 (4:163518806 C>T), RS1001181822 (4:163512024 T>C), RS1001212593 (4:163494367 A>G), RS1001250436 (4:163511725 T>C), RS1001281163 (4:163492905 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004746_28	Small cell lung carcinoma	5.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	decreases expression, increases abundance	2
Benzo(a)pyrene	decreases expression, increases methylation	2
Tetrachlorodibenzodioxin	decreases expression	2
Cyclosporine	increases expression	2
Aflatoxin B1	affects expression, decreases expression	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
urushiol	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
glycidyl methacrylate	increases expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, increases reaction	1
sodium arsenite	decreases expression	1
2-palmitoylglycerol	increases expression	1
nutlin 3	affects cotreatment, increases secretion	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Air Pollutants, Occupational	decreases expression	1
Dactinomycin	increases secretion, affects cotreatment	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Estradiol	increases expression	1
Ivermectin	increases expression	1
Nickel	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1
Smoke	decreases expression, increases abundance	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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