TMEM170B

Summary

TMEM170B (transmembrane protein 170B, HGNC:34244) is a protein-coding gene on chromosome 6p24.2, encoding Transmembrane protein 170B (Q5T4T1). Negatively regulates the canonical Wnt signaling in breast cancer cells.

Involved in negative regulation of canonical Wnt signaling pathway. Located in plasma membrane.

Source: NCBI Gene 100113407 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 15 total
• MANE Select transcript: NM_001100829

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34244
Approved symbol	TMEM170B
Name	transmembrane protein 170B
Location	6p24.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000205269
Ensembl biotype	protein_coding
Entrez	100113407

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000379426, ENST00000903357

RefSeq mRNA: 1 — MANE Select: NM_001100829 NM_001100829

CCDS: CCDS43425

Canonical transcript exons

ENST00000379426 — 3 exons

Exon	Start	End
ENSE00001480952	11575431	11583524
ENSE00001480957	11565666	11565836
ENSE00001480960	11537749	11538374

Expression profiles

Bgee: expression breadth ubiquitous, 228 present calls, max score 95.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.5473 / max 1264.3588, expressed in 1235 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
65809	6.8980	1065
65808	2.2502	919
65810	0.3992	117

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 23	UBERON:0013554	95.73	gold quality
monocyte	CL:0000576	93.45	gold quality
endothelial cell	CL:0000115	92.99	gold quality
leukocyte	CL:0000738	92.68	gold quality
Brodmann (1909) area 46	UBERON:0006483	90.99	gold quality
postcentral gyrus	UBERON:0002581	90.43	gold quality
superior frontal gyrus	UBERON:0002661	90.03	gold quality
entorhinal cortex	UBERON:0002728	89.80	gold quality
primary visual cortex	UBERON:0002436	89.62	gold quality
parietal lobe	UBERON:0001872	89.25	gold quality
cerebellar vermis	UBERON:0004720	88.97	gold quality
cortical plate	UBERON:0005343	88.89	gold quality
occipital lobe	UBERON:0002021	88.62	gold quality
bone marrow	UBERON:0002371	87.13	gold quality
ventricular zone	UBERON:0003053	86.78	gold quality
trabecular bone tissue	UBERON:0002483	86.45	gold quality
middle temporal gyrus	UBERON:0002771	85.23	gold quality
pons	UBERON:0000988	84.36	gold quality
ganglionic eminence	UBERON:0004023	84.36	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	83.78	gold quality
lateral nuclear group of thalamus	UBERON:0002736	83.17	gold quality
cerebral cortex	UBERON:0000956	83.11	gold quality
frontal cortex	UBERON:0001870	83.09	gold quality
prefrontal cortex	UBERON:0000451	82.93	gold quality
temporal lobe	UBERON:0001871	82.92	gold quality
biceps brachii	UBERON:0001507	82.89	gold quality
neocortex	UBERON:0001950	82.84	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	82.52	gold quality
pigmented layer of retina	UBERON:0001782	82.09	gold quality
vastus lateralis	UBERON:0001379	81.82	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.88
E-MTAB-6142	no	28.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

390 targeting TMEM170B, 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-5011-5P	100.00	83.46	5820
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698

Literature-anchored findings (GeneRIF, showing 2)

• these results highlight TMEM170B as a novel tumor suppressor target in association with the beta-catenin pathway. (PMID:29367600)
• CAFs-derived exosomes promote the development of cervical cancer by regulating miR-18a-5p-TMEM170B signaling axis. (PMID:38147699)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem170b	ENSDARG00000071205
mus_musculus	Tmem170b	ENSMUSG00000087370
rattus_norvegicus	Tmem170b	ENSRNOG00000031495
drosophila_melanogaster	CG12341	FBGN0033550
caenorhabditis_elegans	F43G9.13	WBGENE00009673

Paralogs (1): TMEM170A (ENSG00000166822)

Protein

Protein identifiers

Transmembrane protein 170B — Q5T4T1 (reviewed: Q5T4T1)

All UniProt accessions (1): Q5T4T1

UniProt curated annotations — full annotation on UniProt →

Function. Negatively regulates the canonical Wnt signaling in breast cancer cells. Exerts an inhibitory effect on breast cancer growth by inhibiting CTNNB1 stabilization and nucleus translocation, which reduces the activity of Wnt targets.

Subunit / interactions. Interacts with CTNNB1.

Subcellular location. Cell membrane.

Tissue specificity. Expressed in normal breast tissues. Down-regulated in breast cancer cells (at protein level).

Similarity. Belongs to the TMEM170 family.

RefSeq proteins (1): NP_001094299* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019334	TMEM170A/B/YPR153W-like	Family

Pfam: PF10190

UniProt features (9 total): topological domain 4, transmembrane region 3, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T4T1-F1	88.58	0.64

Functional residue map

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

Glycosylation sites (1): 12

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 213 (showing top): chr6p24, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_CANONICAL_WNT_SIGNALING_PATHWAY, GOBP_NEGATIVE_REGULATION_OF_WNT_SIGNALING_PATHWAY, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, GEORGES_TARGETS_OF_MIR192_AND_MIR215, DURAND_STROMA_NS_UP, GSE13522_WT_VS_IFNG_KO_SKING_T_CRUZI_Y_STRAIN_INF_DN, GOBP_NEGATIVE_REGULATION_OF_CANONICAL_WNT_SIGNALING_PATHWAY, GSE10240_IL22_VS_IL17_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP, NAB2_TARGET_GENES, ZNF596_TARGET_GENES, MIR153_5P, MIR607, MIR616_5P

GO Biological Process (2): Wnt signaling pathway (GO:0016055), negative regulation of canonical Wnt signaling pathway (GO:0090090)

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

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell surface receptor signaling pathway	1
negative regulation of Wnt signaling pathway	1
canonical Wnt signaling pathway	1
regulation of canonical Wnt signaling pathway	1
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

174 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM170B	ASCL5	Q7RTU5	483
TMEM170B	TRAM2	Q15035	472
TMEM170B	LRRC32	Q14392	390
TMEM170B	TMEM236	Q5W0B7	381
TMEM170B	TMEM168	Q9H0V1	361
TMEM170B	TMEM117	Q9H0C3	349
TMEM170B	CFDP1	Q9UEE9	336
TMEM170B	MCPH1	Q8NEM0	333
TMEM170B	VSTM4	Q8IW00	331
TMEM170B	SYCP2L	Q5T4T6	321
TMEM170B	CLVS1	Q8IUQ0	320
TMEM170B	LYRM4	Q9HD34	301
TMEM170B	RANBP6	O60518	296
TMEM170B	SHISA7	A6NL88	276
TMEM170B	TMEM64	Q6YI46	274

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A8I3S9V6, A0M8U1, A6NH52, E1BWM5, O35089, P13666, P86050, Q00765, Q0VCK9, Q0X0A5, Q1RLU8, Q29S14, Q2PG42, Q3KNM2, Q3ZC24, Q5BJU5, Q5M7T4, Q5R9I4, Q5R9K4, Q5RE33, Q5T4T1, Q5ZJ41, Q5ZJD7, Q6DD32, Q6GM44, Q6NYF1, Q6P360, Q6PI25, Q7TQ48, Q86TD4, Q8C407, Q8L5Y9, Q8MK44, Q8R1Z9, Q91ZQ0, Q940S0, Q96GC9, Q99K70, Q99KU0, Q9BSR8

Diamond homologs: A3KPL7, P86050, Q5T4T1, Q5ZM31, Q6DF87, Q7TQ79, Q8WVE7, Q9D342

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

961 predictions. Top by Δscore:

Variant	Effect	Δscore
6:11538373:GG:G	donor_gain	1.0000
6:11538374:GG:G	donor_gain	1.0000
6:11565660:TTTCA:T	acceptor_loss	1.0000
6:11565661:TTCA:T	acceptor_loss	1.0000
6:11565662:TCAGA:T	acceptor_loss	1.0000
6:11565663:CA:C	acceptor_loss	1.0000
6:11565664:A:AG	acceptor_gain	1.0000
6:11565665:G:GG	acceptor_gain	1.0000
6:11565665:GA:G	acceptor_gain	1.0000
6:11565665:GAGA:G	acceptor_gain	1.0000
6:11565665:GAGAT:G	acceptor_gain	1.0000
6:11565834:CCA:C	donor_gain	1.0000
6:11565835:CA:C	donor_gain	1.0000
6:11565837:G:GG	donor_gain	1.0000
6:11565837:GTAAG:G	donor_loss	1.0000
6:11565838:TA:T	donor_loss	1.0000
6:11565839:AA:A	donor_loss	1.0000
6:11538373:GGGTA:G	donor_loss	0.9900
6:11538374:GGTA:G	donor_loss	0.9900
6:11538375:G:GG	donor_gain	0.9900
6:11538375:GT:G	donor_loss	0.9900
6:11538376:T:A	donor_loss	0.9900
6:11565832:TACCA:T	donor_gain	0.9900
6:11565833:ACCA:A	donor_gain	0.9900
6:11538364:G:GT	donor_gain	0.9800
6:11562036:A:G	acceptor_gain	0.9700
6:11565835:CAGT:C	donor_gain	0.9700
6:11565836:AGTA:A	donor_gain	0.9700
6:11565838:T:TG	donor_gain	0.9700
6:11565718:T:TA	acceptor_gain	0.9600

AlphaMissense

850 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:11565689:T:A	W41R	0.999
6:11565689:T:C	W41R	0.999
6:11575499:G:C	G113R	0.999
6:11575499:G:T	G113C	0.999
6:11575505:G:A	G115R	0.999
6:11575505:G:C	G115R	0.999
6:11565671:T:A	W35R	0.998
6:11565671:T:C	W35R	0.998
6:11565794:A:C	S76R	0.998
6:11565796:C:A	S76R	0.998
6:11565796:C:G	S76R	0.998
6:11565801:G:A	G78E	0.998
6:11575443:C:A	A94E	0.998
6:11575500:G:A	G113D	0.998
6:11565687:T:C	L40P	0.997
6:11565714:T:A	V49D	0.997
6:11565719:G:C	G51R	0.997
6:11565800:G:A	G78R	0.997
6:11565800:G:C	G78R	0.997
6:11565821:G:A	G85R	0.997
6:11565821:G:C	G85R	0.997
6:11565836:A:C	S90R	0.997
6:11575432:T:A	S90R	0.997
6:11575432:T:G	S90R	0.997
6:11575506:G:A	G115E	0.997
6:11575557:T:A	L132H	0.997
6:11565687:T:A	L40H	0.996
6:11565696:T:C	L43P	0.996
6:11565728:G:A	G54R	0.996
6:11565728:G:C	G54R	0.996

dbSNP variants (sampled 300 via entrez): RS1000002795 (6:11563091 C>T), RS1000026837 (6:11567106 G>A), RS1000051631 (6:11562831 C>G,T), RS1000057842 (6:11567348 A>G), RS1000282397 (6:11561455 G>C), RS1000330295 (6:11574113 G>A,C,T), RS1000340642 (6:11554977 C>A), RS1000363364 (6:11549978 C>T), RS1000417245 (6:11549739 A>C,G), RS1000496552 (6:11568110 G>A), RS1000568879 (6:11561029 C>T), RS1000632098 (6:11556378 C>G), RS1000664604 (6:11556630 T>C,G), RS1000770833 (6:11537688 G>A,C), RS1001057177 (6:11561530 T>C)

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

6 associations (top):

Study	Trait	p-value
GCST003390_10	Thrombosis	4.000000e-07
GCST003518_55	Daytime sleep phenotypes	1.000000e-06
GCST005150_40	Colorectal cancer	5.000000e-07
GCST006976_17	Macular thickness	3.000000e-25
GCST007576_121	Chronotype	8.000000e-10
GCST90002395_425	Mean platelet volume	4.000000e-15

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0003907	deep vein thrombosis
EFO:0007828	daytime rest measurement
EFO:0008328	chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	4
trichostatin A	decreases expression, increases expression, affects cotreatment	3
Benzo(a)pyrene	decreases expression, decreases methylation	3
entinostat	decreases expression, affects cotreatment	2
Panobinostat	affects cotreatment, decreases expression	2
Dexamethasone	increases expression, affects cotreatment	2
Estradiol	affects cotreatment, decreases expression, increases expression	2
Cyclosporine	decreases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	increases expression	1
afuresertib	increases expression	1
bisphenol A	increases expression	1
2-methyl-4-isothiazolin-3-one	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	increases expression	1
Sunitinib	increases expression	1
Leflunomide	decreases expression	1
Azathioprine	decreases expression	1
Cadmium	increases abundance, increases expression	1
Cisplatin	increases expression	1
Demecolcine	decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Quercetin	decreases expression	1
Tretinoin	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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