TMEM86B

Summary

TMEM86B (transmembrane protein 86B, HGNC:28448) is a protein-coding gene on chromosome 19q13.42, encoding Lysoplasmalogenase TMEM86B (Q8N661). Catalyzes the hydrolysis of the vinyl ether bond of choline or ethanolamine lysoplasmalogens, forming fatty aldehyde and glycerophosphocholine or glycerophosphoethanolamine, respectively and is specific for the sn-2-deacylated (lyso) form of plasmalogen.

Enables D-lysine 5,6-aminomutase activity; alkenylglycerophosphocholine hydrolase activity; and identical protein binding activity. Involved in ether lipid metabolic process. Located in cytoplasm and membrane.

Source: NCBI Gene 255043 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_173804

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28448
Approved symbol	TMEM86B
Name	transmembrane protein 86B
Location	19q13.42
Locus type	gene with protein product
Status	Approved
Aliases	MGC30208
Ensembl gene	ENSG00000180089
Ensembl biotype	protein_coding
OMIM	617806
Entrez	255043

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 retained_intron

ENST00000327042, ENST00000585416, ENST00000589190, ENST00000897954

RefSeq mRNA: 2 — MANE Select: NM_173804 NM_001372013, NM_173804

CCDS: CCDS12920

Canonical transcript exons

ENST00000327042 — 3 exons

Exon	Start	End
ENSE00001249893	55228191	55228437
ENSE00001249912	55228691	55228763
ENSE00002872744	55226638	55227563

Expression profiles

Bgee: expression breadth ubiquitous, 130 present calls, max score 92.13.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.7107 / max 105.0549, expressed in 69 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182752	0.5653	66
182754	0.0873	17
182753	0.0581	19

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	92.13	gold quality
blood	UBERON:0000178	88.54	gold quality
liver	UBERON:0002107	87.61	gold quality
gall bladder	UBERON:0002110	84.94	gold quality
granulocyte	CL:0000094	84.62	gold quality
body of stomach	UBERON:0001161	83.89	gold quality
fundus of stomach	UBERON:0001160	82.71	gold quality
lower esophagus mucosa	UBERON:0035834	82.55	gold quality
duodenum	UBERON:0002114	82.40	gold quality
spleen	UBERON:0002106	82.04	gold quality
right hemisphere of cerebellum	UBERON:0014890	81.72	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.55	gold quality
cerebellar hemisphere	UBERON:0002245	81.12	gold quality
cerebellar cortex	UBERON:0002129	80.94	gold quality
cerebellum	UBERON:0002037	80.89	gold quality
putamen	UBERON:0001874	80.88	gold quality
right frontal lobe	UBERON:0002810	80.75	gold quality
adenohypophysis	UBERON:0002196	80.51	gold quality
pituitary gland	UBERON:0000007	80.21	gold quality
stomach	UBERON:0000945	80.13	gold quality
right uterine tube	UBERON:0001302	79.14	gold quality
caudate nucleus	UBERON:0001873	78.72	gold quality
primary visual cortex	UBERON:0002436	78.56	gold quality
anterior cingulate cortex	UBERON:0009835	78.26	gold quality
amygdala	UBERON:0001876	78.06	gold quality
temporal lobe	UBERON:0001871	78.04	gold quality
small intestine Peyer’s patch	UBERON:0003454	77.88	gold quality
nucleus accumbens	UBERON:0001882	77.80	gold quality
small intestine	UBERON:0002108	77.61	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	77.60	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting TMEM86B, 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-4492	99.87	68.25	3611
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-128-1-5P	99.33	60.46	332
HSA-MIR-128-2-5P	99.33	60.83	311
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-6071	99.16	67.77	1780
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-6841-3P	98.08	66.54	604
HSA-MIR-3157-5P	97.41	67.61	998
HSA-MIR-2861	95.24	65.47	1056
HSA-MIR-639	88.87	61.76	78

Literature-anchored findings (GeneRIF, showing 1)

• Transient transfection of human embryonic kidney (HEK) 293T cells showed that TMEM86b cDNA yielded lysoplasmalogenase activity, and Western blot analyses confirmed the synthesis of TMEM86b protein (PMID:21515882)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem86b	ENSDARG00000038296
mus_musculus	Tmem86b	ENSMUSG00000045282
rattus_norvegicus	Tmem86b	ENSRNOG00000087324
drosophila_melanogaster	CG7582	FBGN0039681

Paralogs (1): TMEM86A (ENSG00000151117)

Protein

Protein identifiers

Lysoplasmalogenase TMEM86B — Q8N661 (reviewed: Q8N661)

Alternative names: Transmembrane protein 86B

All UniProt accessions (1): Q8N661

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the hydrolysis of the vinyl ether bond of choline or ethanolamine lysoplasmalogens, forming fatty aldehyde and glycerophosphocholine or glycerophosphoethanolamine, respectively and is specific for the sn-2-deacylated (lyso) form of plasmalogen.

Subunit / interactions. Homodimer.

Subcellular location. Endoplasmic reticulum membrane. Cytoplasm.

Activity regulation. Competitively inhibited by lysophosphatidic acid.

Similarity. Belongs to the TMEM86 family.

RefSeq proteins (2): NP_001358942, NP_776165* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR012506	TMEM86B-like	Family

Pfam: PF07947

Catalyzed reactions (Rhea), 2 shown:

• a 1-O-(1Z-alkenyl)-sn-glycero-3-phosphoethanolamine + H2O = a 2,3-saturated aldehyde + sn-glycero-3-phosphoethanolamine (RHEA:16905)
• a 1-O-(1Z-alkenyl)-sn-glycero-3-phosphocholine + H2O = a 2,3-saturated aldehyde + sn-glycerol 3-phosphocholine (RHEA:22544)

UniProt features (20 total): topological domain 9, transmembrane region 8, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N661-F1	89.76	0.81

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-1482788	Acyl chain remodelling of PC

MSigDB gene sets: 69 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_ACYL_CHAIN_REMODELING, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ORGANELLE_SUBCOMPARTMENT, GOMF_INTRAMOLECULAR_TRANSFERASE_ACTIVITY, GOMF_ISOMERASE_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ETHER_BONDS, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A

GO Biological Process (3): phosphatidylcholine acyl-chain remodeling (GO:0036151), ether lipid metabolic process (GO:0046485), lipid metabolic process (GO:0006629)

GO Molecular Function (6): ether hydrolase activity (GO:0016803), identical protein binding (GO:0042802), alkenylglycerophosphocholine hydrolase activity (GO:0047408), D-lysine 5,6-aminomutase activity (GO:0047826), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (4): cytoplasm (GO:0005737), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), endoplasmic reticulum (GO:0005783)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Glycerophospholipid biosynthesis	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
phosphatidylcholine metabolic process	1
lipid metabolic process	1
primary metabolic process	1
hydrolase activity, acting on ether bonds	1
protein binding	1
ether hydrolase activity	1
intramolecular aminotransferase activity	1
binding	1
catalytic activity	1
intracellular anatomical structure	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

492 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM86B	AGMO	Q6ZNB7	577
TMEM86B	ATP10D	Q9P241	541
TMEM86B	ISOC2	Q96AB3	537
TMEM86B	MS4A5	Q9H3V2	452
TMEM86B	CDH23	Q9H251	438
TMEM86B	RGPD1	P0C839	420
TMEM86B	SELENOI	Q9C0D9	417
TMEM86B	SIRPB1	O00241	411
TMEM86B	ALDH3A2	P51648	377
TMEM86B	RIGI	O95786	371
TMEM86B	LPCAT4	Q643R3	370
TMEM86B	AGPS	O00116	366
TMEM86B	ENPP6	Q6UWR7	365
TMEM86B	I3L0A0	I3L0A0	365
TMEM86B	KLHL17	Q6TDP4	355

IntAct

328 interactions, top by confidence:

A	B	Type	Score
TMEM86B	BCL2L13	psi-mi:“MI:0915”(physical association)	0.720
TMEM86B	TMX2	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	CD79A	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	HIBADH	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B		psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	GJA8	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	TMEM52B	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	MUC1	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	EVI2B	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	GJA4	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	HSD17B13	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	NEMP1	psi-mi:“MI:0915”(physical association)	0.560
VAMP2	TMEM86B	psi-mi:“MI:0915”(physical association)	0.560
RHOT2	TMEM86B	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	CLRN1	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	MSMO1	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	GOLM1	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	LAPTM4B	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (109): TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid), TMEM86B (Two-hybrid)

ESM2 similar proteins: A0A8C2M425, A1L1J9, B0BNF0, B0BNG2, B6CZ46, B6CZ56, C1BKZ7, F1RMN2, O88269, O95255, P86243, Q03518, Q28433, Q32L10, Q32LM8, Q3MHQ7, Q3T0W0, Q497J1, Q499P8, Q49LS7, Q4VV71, Q5KR61, Q5R8F6, Q5REM8, Q5T3U5, Q61672, Q6AZ83, Q6NVG1, Q6UW68, Q767L9, Q7TPN3, Q86VD9, Q8AVI9, Q8C0T0, Q8C3X8, Q8K0H7, Q8N2M4, Q8N661, Q8R1J1, Q8R4P9

Diamond homologs: B0BNF0, F1RMN2, Q3MHQ7, Q3T0W0, Q497J1, Q8N2M4, Q8N661, Q9D8N3, Q5ZU17

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 102 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.

GO biological processes:

GO term	Partners	Fold	FDR
vesicle fusion	6	40.1×	4e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

614 predictions. Top by Δscore:

Variant	Effect	Δscore
19:55227561:TGCC:T	acceptor_loss	1.0000
19:55227562:GCC:G	acceptor_loss	1.0000
19:55227563:CCTG:C	acceptor_loss	1.0000
19:55227561:TGC:T	acceptor_gain	0.9900
19:55227564:C:CC	acceptor_gain	0.9900
19:55227565:T:A	acceptor_loss	0.9900
19:55227559:CATGC:C	acceptor_gain	0.9800
19:55227562:GC:G	acceptor_gain	0.9800
19:55227563:CC:C	acceptor_gain	0.9800
19:55227569:G:T	acceptor_gain	0.9800
19:55228332:TG:T	donor_gain	0.9800
19:55227560:ATGC:A	acceptor_gain	0.9700
19:55228253:C:CA	donor_gain	0.9700
19:55228392:A:T	acceptor_gain	0.9700
19:55227451:GC:G	donor_gain	0.9600
19:55227568:C:CT	acceptor_gain	0.9600
19:55228185:ACTCA:A	donor_loss	0.9600
19:55228186:CTCAC:C	donor_loss	0.9600
19:55228187:T:TA	donor_loss	0.9600
19:55228188:CACC:C	donor_loss	0.9600
19:55228373:C:CT	acceptor_gain	0.9600
19:55228373:C:T	acceptor_gain	0.9600
19:55228394:C:CT	acceptor_gain	0.9600
19:55228389:C:CT	acceptor_gain	0.9500
19:55228395:A:T	acceptor_gain	0.9500
19:55228685:TCTCA:T	donor_loss	0.9500
19:55228686:CTCAC:C	donor_loss	0.9500
19:55228687:TCAC:T	donor_loss	0.9500
19:55228688:CACCT:C	donor_loss	0.9500
19:55228689:ACC:A	donor_loss	0.9500

AlphaMissense

1440 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:55227550:A:C	F104L	0.977
19:55227550:A:T	F104L	0.977
19:55227552:A:G	F104L	0.977
19:55227289:G:C	F191L	0.958
19:55227289:G:T	F191L	0.958
19:55227291:A:G	F191L	0.958
19:55227325:G:C	F179L	0.940
19:55227325:G:T	F179L	0.940
19:55227327:A:G	F179L	0.940
19:55228405:G:C	F28L	0.917
19:55228405:G:T	F28L	0.917
19:55228407:A:G	F28L	0.917
19:55228198:G:C	F97L	0.902
19:55228198:G:T	F97L	0.902
19:55228200:A:G	F97L	0.902
19:55228330:C:A	K53N	0.900
19:55228330:C:G	K53N	0.900
19:55228329:A:G	C54R	0.892
19:55228226:T:A	D88V	0.886
19:55227326:A:G	F179S	0.882
19:55228226:T:G	D88A	0.877
19:55228225:G:C	D88E	0.876
19:55228225:G:T	D88E	0.876
19:55228242:A:G	C83R	0.868
19:55228314:A:G	C59R	0.867
19:55227317:G:A	S182F	0.865
19:55227552:A:T	F104I	0.862
19:55228322:G:T	P56H	0.861
19:55227551:A:C	F104C	0.859
19:55228230:C:A	G87W	0.853

dbSNP variants (sampled 300 via entrez): RS1000070664 (19:55227215 G>A), RS1000668015 (19:55230441 G>A), RS1000786698 (19:55226286 G>T), RS1002041841 (19:55226462 G>A), RS1002142281 (19:55230633 C>A,T), RS1003528451 (19:55229066 C>T), RS1003534820 (19:55228338 G>C), RS1004029766 (19:55228914 G>A), RS1004742808 (19:55229964 G>A,C), RS1005293601 (19:55227665 G>A,C), RS1005546447 (19:55226682 C>A), RS1006424304 (19:55229703 C>A,T), RS1006713304 (19:55226899 T>C,G), RS1007001073 (19:55228980 CCTAT>C), RS1007660629 (19:55230121 G>C)

Disease associations

OMIM: gene MIM:617806 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST005752_167	Systemic lupus erythematosus	2.000000e-08
GCST008930_3	Phosphatidylethanolamine-ether levels	2.000000e-08
GCST011096_2	Systemic lupus erythematosus	4.000000e-08
GCST011097_4	Systemic lupus erythematosus	2.000000e-07
GCST012020_378	Serum metabolite levels	2.000000e-13
GCST012020_60	Serum metabolite levels	2.000000e-12
GCST012021_57	Serum metabolite levels	2.000000e-13
GCST90002396_46	Mean reticulocyte volume	2.000000e-25

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010229	phosphatidylethanolamine ether measurement
EFO:0010701	mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression	3
Cyclosporine	decreases expression	2
Aflatoxin B1	affects expression, decreases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluoro-n-nonanoic acid	decreases expression	1
abrine	decreases expression	1
Rosiglitazone	decreases expression	1
Temozolomide	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	affects methylation	1
Atrazine	increases expression	1
Estradiol	decreases expression	1
Ozone	affects expression, increases abundance	1
Quercetin	decreases expression	1
Smoke	decreases expression	1
Tetrachlorodibenzodioxin	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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