TMEM239

Summary

TMEM239 (transmembrane protein 239, HGNC:40044) is a protein-coding gene on chromosome 20p13, encoding Transmembrane protein 239 (Q8WW34).

Predicted to be located in membrane.

Source: NCBI Gene 100288797 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 29 total
• MANE Select transcript: NM_001167670

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40044
Approved symbol	TMEM239
Name	transmembrane protein 239
Location	20p13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000198326
Ensembl biotype	protein_coding
Entrez	100288797

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000361033, ENST00000380585

RefSeq mRNA: 2 — MANE Select: NM_001167670 NM_001167670, NM_001318207

CCDS: CCDS54444, CCDS82595

Canonical transcript exons

ENST00000380585 — 2 exons

Exon	Start	End
ENSE00001485547	2816544	2818062
ENSE00001485548	2816364	2816415

Expression profiles

Bgee: expression breadth broad, 29 present calls, max score 89.89.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0711 / max 66.7606, expressed in 3 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
183186	0.0556	3
183185	0.0089	3
208974	0.0066	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	89.89	gold quality
left testis	UBERON:0004533	89.88	gold quality
testis	UBERON:0000473	85.51	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	71.66	gold quality
adult organism	UBERON:0007023	66.42	gold quality
sperm	CL:0000019	56.87	gold quality
cartilage tissue	UBERON:0002418	54.50	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	53.09	gold quality
lateral nuclear group of thalamus	UBERON:0002736	52.70	gold quality
decidua	UBERON:0002450	51.43	silver quality
trabecular bone tissue	UBERON:0002483	50.47	gold quality
lower lobe of lung	UBERON:0008949	49.97	silver quality
substantia nigra pars reticulata	UBERON:0001966	49.96	gold quality
Brodmann (1909) area 46	UBERON:0006483	48.40	gold quality
skin of hip	UBERON:0001554	46.32	silver quality
biceps brachii	UBERON:0001507	46.19	gold quality
sural nerve	UBERON:0015488	45.70	gold quality
saphenous vein	UBERON:0007318	45.61	gold quality
bone marrow	UBERON:0002371	45.26	gold quality
lateral globus pallidus	UBERON:0002476	45.07	gold quality
deltoid	UBERON:0001476	43.60	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
placenta	UBERON:0001987	43.35	gold quality
vastus lateralis	UBERON:0001379	43.26	gold quality
quadriceps femoris	UBERON:0001377	43.17	gold quality
amniotic fluid	UBERON:0000173	42.87	gold quality
layer of synovial tissue	UBERON:0007616	42.64	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
heart right ventricle	UBERON:0002080	42.39	gold quality
bone marrow cell	CL:0002092	42.21	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	32.83
E-ANND-3	no	1.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting TMEM239, 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-6748-5P	100.00	65.81	1057
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-5693	99.24	66.67	1106
HSA-MIR-6815-3P	99.13	68.98	1530
HSA-MIR-4795-5P	99.11	66.90	876
HSA-MIR-421	98.90	67.04	1883
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-3922-5P	98.77	66.53	1059
HSA-MIR-7113-3P	98.75	65.71	1120
HSA-MIR-4709-5P	98.51	67.25	1335
HSA-MIR-5089-5P	98.45	66.06	1388
HSA-MIR-3670	97.88	64.39	763
HSA-MIR-2467-5P	97.36	67.71	991
HSA-MIR-194-3P	97.36	65.96	1027
HSA-MIR-6895-5P	97.05	64.96	522
HSA-MIR-6759-3P	96.94	68.31	823
HSA-MIR-3189-3P	96.80	66.34	896
HSA-MIR-597-3P	96.46	68.03	1035
HSA-MIR-2909	96.36	67.30	562
HSA-MIR-1266-3P	96.23	66.36	778
HSA-MIR-3174	94.63	63.64	577
HSA-MIR-1296-5P	93.94	67.71	305
HSA-MIR-4787-3P	89.45	70.48	40

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tmem239	ENSMUSG00000049692
rattus_norvegicus	Tmem239	ENSRNOG00000047004

Protein

Protein identifiers

Transmembrane protein 239 — Q8WW34 (reviewed: Q8WW34)

All UniProt accessions (1): Q8WW34

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8WW34-1	1	yes
Q8WW34-2	2

RefSeq proteins (2): NP_001161142, NP_001305136 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031694	TMEM239	Family

Pfam: PF15841

UniProt features (4 total): transmembrane region 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WW34-F1	73.01	0.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 36 (showing top): ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, MIR616_5P, MIR371B_5P, MIR373_5P, GSE10239_NAIVE_VS_MEMORY_CD8_TCELL_DN, MIR4719, MIR7106_5P, MIR6780A_5P, MIR1273H_5P, MIR6815_3P, MIR6779_5P, MIR30B_3P, MIR3689A_3P_MIR3689B_3P_MIR3689C, MIR1913, MIR6837_5P

GO Biological Process (0):

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

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

96 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM239	BPIFC	Q8NFQ6	591
TMEM239	AIRIM	Q9NX04	580
TMEM239	MORN2	Q502X0	506
TMEM239	AKIRIN1	Q9H9L7	485
TMEM239	ADCK1	Q86TW2	474
TMEM239	MRPS31	Q92665	433
TMEM239	ZDBF2	Q9HCK1	398
TMEM239	STYK1	Q6J9G0	392
TMEM239	TSPAN13	O95857	371
TMEM239	STMN3	Q9NZ72	360
TMEM239	DMTN	Q08495	355
TMEM239	FHIP2B	Q86V87	340
TMEM239	ST6GAL1	P15907	337
TMEM239	FBXL2	Q9UKC9	325
TMEM239	BUB3	O43684	312

IntAct

38 interactions, top by confidence:

A	B	Type	Score
TMEM239	SDCBP	psi-mi:“MI:0915”(physical association)	0.560
TMEM239	ATF7	psi-mi:“MI:0915”(physical association)	0.560
USP5	TMEM239	psi-mi:“MI:0915”(physical association)	0.560
FGD2	TMEM239	psi-mi:“MI:0915”(physical association)	0.560
MYG1	TMEM239	psi-mi:“MI:0915”(physical association)	0.560
TMEM239	COQ8A	psi-mi:“MI:0915”(physical association)	0.560
CXCL16	TMEM239	psi-mi:“MI:0915”(physical association)	0.560
TMEM239	LENG1	psi-mi:“MI:0915”(physical association)	0.560
TMEM239	NTAQ1	psi-mi:“MI:0915”(physical association)	0.560
TMEM239	SENP2	psi-mi:“MI:0915”(physical association)	0.560
POLI	TMEM239	psi-mi:“MI:0915”(physical association)	0.560
ATF7	TMEM239	psi-mi:“MI:0915”(physical association)	0.560
TMEM239	USP5	psi-mi:“MI:0915”(physical association)	0.560
TMEM239	FGD2	psi-mi:“MI:0915”(physical association)	0.560
COQ8A	TMEM239	psi-mi:“MI:0915”(physical association)	0.560
TMEM239	CXCL16	psi-mi:“MI:0915”(physical association)	0.560
NTAQ1	TMEM239	psi-mi:“MI:0915”(physical association)	0.560
SENP2	TMEM239	psi-mi:“MI:0915”(physical association)	0.560
TMEM239	MYG1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (77): TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid), TMEM239 (Two-hybrid)

ESM2 similar proteins: A0A096P2H6, A0A0D9S1R4, A0A2Y9GDB5, A0JNN2, A8MXV6, D2H5P6, E1BLZ4, E1C7U0, P0DKW1, P0DKW2, P0DKW3, P0DKW4, P0DKY3, P0DML4, P0DML5, P0DML6, P0DMN8, P0DOC4, P0DP53, P0DTG9, P0DTH0, P0DTH1, P0DTH2, P0DTH3, P0DTH4, P0DUP6, P24001, P55056, P55797, Q2TBQ4, Q32KP7, Q3SYR5, Q5EAA5, Q5JX69, Q5R7E2, Q5U2R2, Q68DK2, Q6MG51, Q6P0A1, Q6UJB9

Diamond homologs: Q8WW34, Q9DA47

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	29
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

292 predictions. Top by Δscore:

Variant	Effect	Δscore
20:2816413:GAG:G	donor_gain	1.0000
20:2816385:G:GT	donor_gain	0.9900
20:2816414:AGGTA:A	donor_loss	0.9900
20:2816416:G:GG	donor_gain	0.9800
20:2816412:AGAG:A	donor_gain	0.9200
20:2816413:GAGG:G	donor_gain	0.9200
20:2816538:CCCCA:C	acceptor_loss	0.9100
20:2816540:CCA:C	acceptor_loss	0.9100
20:2816541:CA:C	acceptor_loss	0.9100
20:2816806:T:A	acceptor_gain	0.9000
20:2816411:CAGAG:C	donor_gain	0.8900
20:2816414:AG:A	donor_gain	0.8800
20:2816415:GG:G	donor_gain	0.8800
20:2816804:ACT:A	acceptor_gain	0.8700
20:2816542:A:AG	acceptor_gain	0.8400
20:2816543:G:GG	acceptor_gain	0.8400
20:2816543:GGT:G	acceptor_gain	0.8000
20:2816418:AA:A	donor_loss	0.7900
20:2816916:C:CA	acceptor_gain	0.7200
20:2816999:G:GT	donor_gain	0.7000
20:2816804:ACTG:A	acceptor_gain	0.6900
20:2816503:CAAGG:C	acceptor_gain	0.6600
20:2816504:AAGG:A	acceptor_gain	0.6600
20:2816804:A:AG	acceptor_gain	0.6600
20:2816503:CAAG:C	acceptor_loss	0.6400
20:2816505:A:AT	acceptor_loss	0.6400
20:2816505:A:G	acceptor_gain	0.6400
20:2816506:GGTC:G	acceptor_loss	0.6400
20:2816490:T:TA	acceptor_loss	0.6300
20:2816807:G:A	acceptor_gain	0.6300

AlphaMissense

963 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:2816951:A:C	S176R	0.986
20:2816953:C:A	S176R	0.986
20:2816953:C:G	S176R	0.986
20:2816891:A:C	S156R	0.985
20:2816893:T:A	S156R	0.985
20:2816893:T:G	S156R	0.985
20:2816798:T:C	F125L	0.956
20:2816800:C:A	F125L	0.956
20:2816800:C:G	F125L	0.956
20:2816786:T:C	C121R	0.950
20:2816807:G:C	G128R	0.930
20:2816901:C:G	P159R	0.925
20:2816924:T:C	F167L	0.919
20:2816926:C:A	F167L	0.919
20:2816926:C:G	F167L	0.919
20:2816751:A:T	E109V	0.907
20:2816852:T:A	W143R	0.904
20:2816852:T:C	W143R	0.904
20:2816817:T:C	L131P	0.896
20:2816901:C:A	P159H	0.893
20:2816799:T:C	F125S	0.891
20:2816912:T:C	F163L	0.891
20:2816914:C:A	F163L	0.891
20:2816914:C:G	F163L	0.891
20:2816808:G:A	G128D	0.890
20:2816796:T:A	L124H	0.887
20:2816943:C:A	T173K	0.885
20:2816752:G:C	E109D	0.871
20:2816752:G:T	E109D	0.871
20:2816895:C:A	A157D	0.871

dbSNP variants (sampled 300 via entrez): RS1000129781 (20:2820214 G>A,C), RS1001669108 (20:2816656 G>A), RS1003213980 (20:2819405 A>C), RS1003233463 (20:2813958 A>C,G), RS1003677307 (20:2819072 C>T), RS1004826457 (20:2816131 G>A), RS1004940719 (20:2816330 G>A,C), RS1005492682 (20:2818699 C>T), RS1005602385 (20:2819119 T>C), RS1005824594 (20:2817235 A>G), RS1005940692 (20:2817489 C>A,G), RS1006607948 (20:2820548 C>T), RS1006714837 (20:2814591 C>A), RS1007120285 (20:2817485 G>A,C), RS1007238752 (20:2814900 G>A)

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

3 associations (top):

Study	Trait	p-value
GCST001760_7	White matter integrity	7.000000e-06
GCST006626_34	Pulse pressure	5.000000e-11
GCST008747_138	Estimated glomerular filtration rate	2.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004641	white matter integrity
EFO:0005763	pulse pressure measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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