TMEM160

Summary

TMEM160 (transmembrane protein 160, HGNC:26042) is a protein-coding gene on chromosome 19q13.32, encoding Transmembrane protein 160 (Q9NX00).

Located in mitochondrial inner membrane.

Source: NCBI Gene 54958 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 16 total
• MANE Select transcript: NM_017854

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26042
Approved symbol	TMEM160
Name	transmembrane protein 160
Location	19q13.32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20512
Ensembl gene	ENSG00000130748
Ensembl biotype	protein_coding
OMIM	620258
Entrez	54958

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000253047

RefSeq mRNA: 1 — MANE Select: NM_017854 NM_017854

CCDS: CCDS12695

Canonical transcript exons

ENST00000253047 — 3 exons

Exon	Start	End
ENSE00000895968	47045909	47046252
ENSE00000895970	47046593	47046685
ENSE00001213408	47048407	47048624

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 93.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.9067 / max 178.3257, expressed in 1816 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
181711	24.1575	1816
181710	2.5598	980
181709	0.1894	94

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
amygdala	UBERON:0001876	93.90	gold quality
Brodmann (1909) area 9	UBERON:0013540	93.88	gold quality
anterior cingulate cortex	UBERON:0009835	93.69	gold quality
cingulate cortex	UBERON:0003027	93.64	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	93.59	gold quality
prefrontal cortex	UBERON:0000451	93.54	gold quality
granulocyte	CL:0000094	92.90	gold quality
right frontal lobe	UBERON:0002810	92.88	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	92.51	gold quality
neocortex	UBERON:0001950	91.28	gold quality
frontal cortex	UBERON:0001870	91.15	gold quality
frontal lobe	UBERON:0016525	91.15	gold quality
monocyte	CL:0000576	91.02	gold quality
mononuclear cell	CL:0000842	90.81	gold quality
leukocyte	CL:0000738	90.76	gold quality
hindlimb stylopod muscle	UBERON:0004252	90.61	gold quality
apex of heart	UBERON:0002098	90.31	gold quality
cerebral cortex	UBERON:0000956	90.20	gold quality
caudate nucleus	UBERON:0001873	89.95	gold quality
putamen	UBERON:0001874	89.94	gold quality
telencephalon	UBERON:0001893	89.37	gold quality
nucleus accumbens	UBERON:0001882	89.34	gold quality
cortical plate	UBERON:0005343	88.53	gold quality
Ammon’s horn	UBERON:0001954	88.51	gold quality
forebrain	UBERON:0001890	88.16	gold quality
metanephros cortex	UBERON:0010533	87.86	gold quality
temporal lobe	UBERON:0001871	87.76	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	87.54	gold quality
brain	UBERON:0000955	87.36	gold quality
mucosa of transverse colon	UBERON:0004991	87.27	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-8205	yes	195.36
E-MTAB-7037	yes	48.61
E-ANND-3	yes	9.36
E-MTAB-7606	no	864.05

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• Knockdown of TMEM160 leads to an increase in reactive oxygen species generation and the induction of the mitochondrial unfolded protein response. (PMID:36217717)
• TMEM160 promotes tumor immune evasion and radiotherapy resistance via PD-L1 binding in colorectal cancer. (PMID:38454413)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem160	ENSDARG00000069649
mus_musculus	Tmem160	ENSMUSG00000019158
rattus_norvegicus	Tmem160	ENSRNOG00000080425

Protein

Protein identifiers

Transmembrane protein 160 — Q9NX00 (reviewed: Q9NX00)

All UniProt accessions (1): Q9NX00

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Mitochondrion inner membrane.

Similarity. Belongs to the TMEM160 family.

RefSeq proteins (1): NP_060324* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026801	TMEM160	Family

UniProt features (8 total): transmembrane region 2, region of interest 2, transit peptide 1, chain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NX00-F1	75.99	0.46

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): 48

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 95 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, AACWWCAANK_UNKNOWN, GOCC_MITOCHONDRIAL_ENVELOPE, GOCC_ORGANELLE_INNER_MEMBRANE, KIM_WT1_TARGETS_DN, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, GOCC_ORGANELLE_ENVELOPE, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17, GCNP_SHH_UP_EARLY.V1_DN, KRAS.DF.V1_UP, GSE5503_PLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, ASH1L_TARGET_GENES, BARX1_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1
organelle inner membrane	1
mitochondrial membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

900 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM160	ZNF608	Q9ULD9	691
TMEM160	MTIF3	Q9H2K0	650
TMEM160	NUDT3	O95989	621
TMEM160	DNAJC27	Q9NZQ0	621
TMEM160	QPCTL	Q9NXS2	605
TMEM160	POC5	Q8NA72	601
TMEM160	GNPDA2	Q8TDQ7	599
TMEM160	SEC16B	Q96JE7	599
TMEM160	V9GXZ4	V9GXZ4	599
TMEM160	TNNI3K	Q59H18	591
TMEM160	FAIM2	Q9BWQ8	587
TMEM160	ZC3H4	Q9UPT8	579
TMEM160	RPL27A	P46776	571
TMEM160	LINGO2	Q7L985	570
TMEM160	GPRC5B	Q9NZH0	570
TMEM160	MTCH2	Q9Y6C9	570

IntAct

137 interactions, top by confidence:

A	B	Type	Score
PRKCZ	PRKCI	psi-mi:“MI:0914”(association)	0.890
TSSK6	HSP90AA1	psi-mi:“MI:0914”(association)	0.740
KBTBD7	METTL15	psi-mi:“MI:0914”(association)	0.730
PHF19	EED	psi-mi:“MI:0914”(association)	0.730
GABARAPL2	IPO5	psi-mi:“MI:0914”(association)	0.690
ASPH	STXBP3	psi-mi:“MI:0914”(association)	0.640
VSIG1	TTI1	psi-mi:“MI:0914”(association)	0.640
CAMKV	AP3B1	psi-mi:“MI:0914”(association)	0.640
B3GAT3	GOLIM4	psi-mi:“MI:0914”(association)	0.640
GYPA	GOLGA7	psi-mi:“MI:0914”(association)	0.640
GPR156	PLD2	psi-mi:“MI:0914”(association)	0.640
GYPA	TCAF2	psi-mi:“MI:0914”(association)	0.640
VWCE	HSPA5	psi-mi:“MI:0914”(association)	0.640
GABARAPL1	IPO5	psi-mi:“MI:0914”(association)	0.590
EMP1	TMEM160	psi-mi:“MI:0915”(physical association)	0.560
SLC16A13	TMEM160	psi-mi:“MI:0915”(physical association)	0.560
C3AR1	TMEM120B	psi-mi:“MI:0914”(association)	0.530
VWCE	ZNF316	psi-mi:“MI:0914”(association)	0.530
VSIG1	TNPO2	psi-mi:“MI:0914”(association)	0.530
CD70	METTL15	psi-mi:“MI:0914”(association)	0.530
LGALS3	PODXL	psi-mi:“MI:0914”(association)	0.530

BioGRID (104): TMEM160 (Affinity Capture-MS), TMEM160 (Affinity Capture-MS), TMEM160 (Affinity Capture-MS), TMEM160 (Affinity Capture-MS), TMEM160 (Affinity Capture-MS), TMEM160 (Affinity Capture-MS), TMEM160 (Affinity Capture-MS), TMEM160 (Proximity Label-MS), TMEM160 (Affinity Capture-MS), TMEM160 (Affinity Capture-MS), TMEM160 (Proximity Label-MS), TMEM160 (Affinity Capture-MS), TMEM160 (Affinity Capture-MS), TMEM160 (Affinity Capture-MS), TMEM160 (Affinity Capture-MS)

ESM2 similar proteins: A2A6C4, A5D7M7, A7MBM2, A9JSM3, B2RXF0, B9EJI9, E9PY61, F1SAM7, O75949, Q08E36, Q17QQ5, Q29RK8, Q2MJR0, Q2T9K0, Q3U5Q7, Q49LS1, Q49LS4, Q49LS8, Q5EBM0, Q5GH56, Q5GH59, Q5GH64, Q5GH67, Q5GH72, Q5GH73, Q5GH76, Q5SNT2, Q5T442, Q66K66, Q68FE7, Q6P6N5, Q6PB70, Q6PRD1, Q80XF7, Q80ZU9, Q8BG75, Q8BQU6, Q8CIV2, Q8IUH8, Q8N144

Diamond homologs: B3DJK0, Q24JY6, Q9D938, Q9NX00

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 169 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
Macroautophagy	8	8.1×	4e-03

GO biological processes:

GO term	Partners	Fold	FDR
mitophagy	10	21.2×	2e-08
autophagosome maturation	7	16.4×	8e-05
macroautophagy	7	11.2×	9e-04
positive regulation of protein localization to plasma membrane	6	10.9×	4e-03
autophagosome assembly	7	10.5×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	15
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

398 predictions. Top by Δscore:

Variant	Effect	Δscore
19:47046586:CACT:C	donor_loss	1.0000
19:47046587:ACTC:A	donor_loss	1.0000
19:47046588:CTCA:C	donor_loss	1.0000
19:47046589:TCA:T	donor_loss	1.0000
19:47046590:CA:C	donor_loss	1.0000
19:47046591:A:AC	donor_gain	1.0000
19:47046592:C:CA	donor_loss	1.0000
19:47046592:C:CC	donor_gain	1.0000
19:47046683:AGG:A	acceptor_gain	1.0000
19:47046684:GG:G	acceptor_gain	1.0000
19:47046686:C:CC	acceptor_gain	1.0000
19:47048403:CGAC:C	donor_loss	1.0000
19:47048404:GACCT:G	donor_loss	1.0000
19:47048405:A:T	donor_loss	1.0000
19:47048406:CCTGT:C	donor_gain	1.0000
19:47046604:TCCCG:T	donor_gain	0.9900
19:47046681:GAAGG:G	acceptor_gain	0.9900
19:47046682:AAGG:A	acceptor_gain	0.9900
19:47046683:AGGC:A	acceptor_loss	0.9900
19:47046684:GGCT:G	acceptor_loss	0.9900
19:47046685:GCT:G	acceptor_loss	0.9900
19:47046686:CTG:C	acceptor_loss	0.9900
19:47046687:T:G	acceptor_loss	0.9900
19:47048403:CGACC:C	donor_gain	0.9800
19:47046592:CCAT:C	donor_gain	0.9700
19:47048405:A:AC	donor_gain	0.9700
19:47048406:C:CC	donor_gain	0.9700
19:47046252:CCTG:C	acceptor_loss	0.9600
19:47046253:CTG:C	acceptor_loss	0.9600
19:47046254:T:C	acceptor_loss	0.9600

AlphaMissense

1169 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:47046640:C:T	G85E	0.999
19:47046646:C:T	G83D	0.999
19:47046661:C:T	G78D	0.999
19:47046109:A:G	W149R	0.998
19:47046109:A:T	W149R	0.998
19:47046641:C:A	G85W	0.998
19:47046641:C:G	G85R	0.998
19:47046641:C:T	G85R	0.998
19:47046647:C:G	G83R	0.998
19:47046662:C:G	G78R	0.998
19:47046663:A:C	N77K	0.998
19:47046663:A:T	N77K	0.998
19:47046099:G:T	A152D	0.997
19:47046235:C:G	G107R	0.997
19:47046237:C:T	G106D	0.997
19:47046238:C:G	G106R	0.997
19:47046248:G:C	F102L	0.997
19:47046248:G:T	F102L	0.997
19:47046250:A:G	F102L	0.997
19:47046627:G:C	F89L	0.997
19:47046627:G:T	F89L	0.997
19:47046629:A:G	F89L	0.997
19:47046217:C:G	G113R	0.996
19:47046234:C:T	G107D	0.996
19:47046611:C:A	G95C	0.996
19:47046611:C:G	G95R	0.996
19:47046634:A:T	I87N	0.996
19:47046658:A:T	L79H	0.996
19:47046674:A:G	W74R	0.996
19:47046674:A:T	W74R	0.996

dbSNP variants (sampled 300 via entrez): RS1000184865 (19:47047148 T>G), RS1000700398 (19:47049447 C>A,T), RS1000767991 (19:47048475 G>A,T), RS1000980952 (19:47048125 C>G,T), RS1001112783 (19:47049726 C>A,T), RS1001238131 (19:47045752 T>C), RS1002153241 (19:47049206 G>A), RS1002350519 (19:47050224 T>C), RS1002820893 (19:47047002 G>A), RS1002829319 (19:47047309 C>T), RS1003416903 (19:47048988 CTTTCTTTCTTTCTT>C), RS1003772348 (19:47049153 G>A), RS1004226398 (19:47048863 T>A), RS1004311428 (19:47047740 G>C), RS1004433913 (19:47047457 A>G)

Disease associations

OMIM: gene MIM:620258 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST000830_18	Body mass index	2.000000e-12
GCST002461_17	Body mass index	9.000000e-07
GCST005830_92	Hand grip strength	4.000000e-13
GCST011126_33	Caffeine consumption from coffee or tea	1.000000e-11

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0006941	grip strength measurement
EFO:0006781	coffee consumption measurement
EFO:0010091	tea consumption measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	6
sodium arsenite	increases expression, decreases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
dicrotophos	decreases expression	1
quercitrin	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
di-n-butylphosphoric acid	affects expression	1
K 7174	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Cisplatin	increases expression, affects cotreatment	1
Ivermectin	decreases expression	1
Oxygen	decreases expression	1
Ozone	affects expression, increases abundance	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Thapsigargin	decreases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3JK	Abcam HEK293T TMEM160 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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