TMEM169

Summary

TMEM169 (transmembrane protein 169, HGNC:25130) is a protein-coding gene on chromosome 2q35, encoding Transmembrane protein 169 (Q96HH4).

Predicted to be located in membrane.

Source: NCBI Gene 92691 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 57 total
• MANE Select transcript: NM_001142311

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25130
Approved symbol	TMEM169
Name	transmembrane protein 169
Location	2q35
Locus type	gene with protein product
Status	Approved
Aliases	FLJ34263
Ensembl gene	ENSG00000163449
Ensembl biotype	protein_coding
Entrez	92691

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 10 protein_coding

ENST00000295658, ENST00000406027, ENST00000433112, ENST00000437356, ENST00000454545, ENST00000455479, ENST00000899825, ENST00000899826, ENST00000913767, ENST00000967331

RefSeq mRNA: 4 — MANE Select: NM_001142311 NM_001142310, NM_001142311, NM_001142312, NM_138390

CCDS: CCDS2401

Canonical transcript exons

ENST00000437356 — 3 exons

Exon	Start	End
ENSE00001074713	216095838	216096234
ENSE00001074714	216081919	216081979
ENSE00001827256	216099920	216102783

Expression profiles

Bgee: expression breadth ubiquitous, 154 present calls, max score 85.38.

FANTOM5 (CAGE): breadth broad, TPM avg 2.6858 / max 139.8894, expressed in 653 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
25187	2.6139	650
25188	0.0719	41

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	85.38	gold quality
buccal mucosa cell	CL:0002336	82.21	gold quality
ganglionic eminence	UBERON:0004023	81.91	gold quality
embryo	UBERON:0000922	81.90	gold quality
secondary oocyte	CL:0000655	77.72	gold quality
prefrontal cortex	UBERON:0000451	74.49	gold quality
stromal cell of endometrium	CL:0002255	70.14	gold quality
Brodmann (1909) area 9	UBERON:0013540	70.11	gold quality
frontal cortex	UBERON:0001870	68.75	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	68.68	gold quality
neocortex	UBERON:0001950	68.62	gold quality
ventricular zone	UBERON:0003053	68.59	gold quality
cerebellar cortex	UBERON:0002129	68.17	gold quality
cerebellar hemisphere	UBERON:0002245	68.13	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	67.84	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	67.73	gold quality
right frontal lobe	UBERON:0002810	67.38	gold quality
anterior cingulate cortex	UBERON:0009835	67.25	gold quality
cerebellum	UBERON:0002037	66.99	gold quality
right hemisphere of cerebellum	UBERON:0014890	66.66	gold quality
primary visual cortex	UBERON:0002436	66.44	gold quality
cerebral cortex	UBERON:0000956	66.24	gold quality
spinal cord	UBERON:0002240	65.52	gold quality
hypothalamus	UBERON:0001898	64.95	gold quality
oocyte	CL:0000023	64.90	gold quality
islet of Langerhans	UBERON:0000006	64.54	gold quality
metanephros cortex	UBERON:0010533	64.36	gold quality
granulocyte	CL:0000094	64.02	gold quality
middle temporal gyrus	UBERON:0002771	63.73	silver quality
amygdala	UBERON:0001876	62.89	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

116 targeting TMEM169, 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-5692A	100.00	74.40	6850
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-548AT-5P	99.96	70.83	2666
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-96-5P	99.95	72.80	2140
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-3663-3P	99.84	70.39	798
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-6844	99.82	70.69	2423

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem169a	ENSDARG00000027131
danio_rerio	tmem169b	ENSDARG00000078762
mus_musculus	Tmem169	ENSMUSG00000026188
drosophila_melanogaster	CG4596	FBGN0037849

Protein

Protein identifiers

Transmembrane protein 169 — Q96HH4 (reviewed: Q96HH4)

All UniProt accessions (3): C9J1P0, C9JZB1, Q96HH4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (4): NP_001135782, NP_001135783, NP_001135784, NP_612399 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029386	TMEM169	Family

Pfam: PF15052

UniProt features (8 total): topological domain 3, transmembrane region 2, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96HH4-F1	54.97	0.02

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 83 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, GGGTGGRR_PAX4_03, TAATTA_CHX10_01, GEORGES_TARGETS_OF_MIR192_AND_MIR215, S8_01, GSE13547_CTRL_VS_ANTI_IGM_STIM_BCELL_2H_DN, ID2_TARGET_GENES, IRF5_TARGET_GENES, ZNF184_TARGET_GENES, ZNF618_TARGET_GENES, ZNF7_TARGET_GENES, MIR5696, MIR548AR_3P, MIR548F_3P, MIR548BC

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

388 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM169	RNF38	Q9H0F5	497
TMEM169	SLC10A4	Q96EP9	492
TMEM169	BSN	Q9UPA5	491
TMEM169	KSR2	Q6VAB6	433
TMEM169	LPAR2	Q9HBW0	415
TMEM169	SLC35D4	Q24JQ0	403
TMEM169	NKAIN1	Q4KMZ8	397
TMEM169	OPCML	Q14982	396
TMEM169	DNM3	Q9UQ16	392
TMEM169	TMEM74B	Q9NUR3	391
TMEM169	ZSCAN2	Q7Z7L9	383
TMEM169	CCDC81	Q6ZN84	371
TMEM169	TIGD6	Q17RP2	369
TMEM169	KLHL18	O94889	357
TMEM169	C9orf50	Q5SZB4	348
TMEM169	A0A087WTP8	A0A087WTP8	348

IntAct

3 interactions, top by confidence:

A	B	Type	Score
TMEM169	GPR89A	psi-mi:“MI:0914”(association)	0.350
TMEM169	PTGES3L-AARSD1	psi-mi:“MI:0914”(association)	0.350

BioGRID (73): TMEM169 (Reconstituted Complex), TMEM169 (Affinity Capture-RNA), MIS18BP1 (Affinity Capture-MS), EXOG (Affinity Capture-MS), ABCB1 (Affinity Capture-MS), ST7 (Affinity Capture-MS), GP1BB (Affinity Capture-MS), POM121 (Affinity Capture-MS), XRCC6BP1 (Affinity Capture-MS), LPHN3 (Affinity Capture-MS), PIGA (Affinity Capture-MS), EFNB1 (Affinity Capture-MS), FAM134C (Affinity Capture-MS), FZD3 (Affinity Capture-MS), LMBR1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GRQ0, A0A1B0GSZ0, A0A1B0GVT2, A0A590UK83, A0PK05, A2VDU1, A2VE22, A4QNL6, A5D7B5, A5D992, O43609, O75324, P0DKX4, P29414, P61807, P61808, Q0VFM5, Q15053, Q16655, Q17Q87, Q1L0X2, Q2KIK3, Q2TBG9, Q3MHM8, Q498C7, Q4V921, Q58CU5, Q5RBD8, Q5RF07, Q5RGQ8, Q64448, Q6UWT2, Q80ZU4, Q8BGN6, Q8BUM6, Q8C3K5, Q8C817, Q8K1D8, Q8N6S5, Q91VT8

Diamond homologs: Q2TBG9, Q8BG50, Q96HH4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	51
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

547 predictions. Top by Δscore:

Variant	Effect	Δscore
2:216096234:GGT:G	donor_loss	1.0000
2:216096235:G:C	donor_loss	1.0000
2:216096236:TAA:T	donor_loss	1.0000
2:216099914:CTGCA:C	acceptor_loss	1.0000
2:216099915:TGCAG:T	acceptor_loss	1.0000
2:216099916:GCAG:G	acceptor_loss	1.0000
2:216099917:CA:C	acceptor_loss	1.0000
2:216099918:AGAT:A	acceptor_loss	1.0000
2:216099919:GATAT:G	acceptor_gain	1.0000
2:216081956:GC:G	donor_gain	0.9900
2:216081971:C:T	donor_gain	0.9900
2:216096231:GATG:G	donor_gain	0.9900
2:216096235:G:GG	donor_gain	0.9900
2:216099918:A:AG	acceptor_gain	0.9900
2:216099919:G:GA	acceptor_gain	0.9900
2:216099919:GAT:G	acceptor_gain	0.9900
2:216099919:GATA:G	acceptor_gain	0.9900
2:216096233:TG:T	donor_gain	0.9800
2:216096234:GG:G	donor_gain	0.9800
2:216099911:A:AG	acceptor_gain	0.9800
2:216099912:C:G	acceptor_gain	0.9800
2:216099919:GA:G	acceptor_gain	0.9800
2:216081974:GT:G	donor_gain	0.9700
2:216081980:G:GG	donor_gain	0.9700
2:216096230:TGATG:T	donor_gain	0.9700
2:216096231:GATGG:G	donor_gain	0.9700
2:216081976:GTGG:G	donor_gain	0.9600
2:216092636:ATCTT:A	acceptor_gain	0.9500
2:216095832:TTTCA:T	acceptor_loss	0.9500
2:216095833:TTCA:T	acceptor_loss	0.9500

AlphaMissense

1939 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:216099971:T:A	I108N	0.998
2:216100207:T:A	W187R	0.998
2:216100207:T:C	W187R	0.998
2:216099953:T:A	V102D	0.997
2:216099959:T:C	L104S	0.997
2:216099964:G:T	G106W	0.997
2:216099965:G:A	G106E	0.997
2:216099971:T:G	I108S	0.997
2:216099971:T:C	I108T	0.996
2:216100394:A:T	E249V	0.996
2:216100013:T:A	V122D	0.995
2:216100135:T:A	W163R	0.995
2:216100135:T:C	W163R	0.995
2:216100196:G:A	G183D	0.995
2:216100399:G:C	G251R	0.995
2:216100441:T:C	C265R	0.995
2:216100466:T:C	L273S	0.995
2:216099964:G:A	G106R	0.994
2:216099964:G:C	G106R	0.994
2:216100007:T:C	I120T	0.994
2:216100369:T:A	W241R	0.994
2:216100369:T:C	W241R	0.994
2:216100417:T:C	C257R	0.994
2:216100419:C:G	C257W	0.994
2:216099977:G:C	R110P	0.993
2:216099980:G:A	G111E	0.993
2:216100007:T:G	I120S	0.993
2:216100147:T:C	C167R	0.993
2:216100443:T:G	C265W	0.993
2:216100448:C:A	P267H	0.993

dbSNP variants (sampled 300 via entrez): RS1000061409 (2:216102590 T>A), RS1000294906 (2:216089613 C>T), RS1000327145 (2:216089866 A>G), RS1000794897 (2:216095185 T>A), RS1000862439 (2:216096890 A>G), RS1001029367 (2:216100971 T>G), RS1001061700 (2:216101144 T>G), RS1001175796 (2:216094605 C>T), RS1001452118 (2:216081817 C>A,G,T), RS1001563708 (2:216081018 G>A), RS1001864019 (2:216081857 A>C), RS1001883399 (2:216082210 C>G,T), RS1002139312 (2:216100260 C>A), RS1002249278 (2:216093209 C>A,G), RS1002365109 (2:216086970 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

1 associations (top):

Study	Trait	p-value
GCST012335_12	Hodgkin’s lymphoma	2.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression	6
trichostatin A	increases expression, affects expression, decreases expression	2
sodium arsenite	affects expression, increases expression	2
entinostat	decreases expression, affects cotreatment	2
Panobinostat	affects cotreatment, decreases expression	2
Benzo(a)pyrene	decreases expression, decreases methylation, increases methylation	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Silicon Dioxide	decreases expression	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
resorcinol	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
beta-methylcholine	affects 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
jinfukang	increases expression	1
Temozolomide	increases expression	1
Leflunomide	increases expression	1
Caffeine	decreases phosphorylation	1
Diethylhexyl Phthalate	decreases expression	1
Folic Acid	decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment, decreases expression	1
Urethane	increases expression	1
Aflatoxin B1	decreases expression, decreases methylation	1

Clinical trials (associated diseases)

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