TMEM87B

Summary

TMEM87B (transmembrane protein 87B, HGNC:25913) is a protein-coding gene on chromosome 2q13, encoding Transmembrane protein 87B (Q96K49). May be involved in retrograde transport from endosomes to the trans-Golgi network (TGN).

This gene encodes a protein that may interact with human papillomavirus type 18 E6 oncogene. The protein is also likely to be involved in endosome-to-trans-Golgi network retrograde transport. The gene is expressed in adult and fetal tissues, including brain and heart. This gene is a component of the 2q13 deletion syndrome. Mutations in this gene may be associated with congenital heart defects.

Source: NCBI Gene 84910 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 87 total — 1 likely-pathogenic
• MANE Select transcript: NM_032824

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25913
Approved symbol	TMEM87B
Name	transmembrane protein 87B
Location	2q13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ14681
Ensembl gene	ENSG00000153214
Ensembl biotype	protein_coding
OMIM	617203
Entrez	84910

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000283206, ENST00000452029, ENST00000452614, ENST00000463427, ENST00000471632, ENST00000649734, ENST00000650799, ENST00000879173, ENST00000879174, ENST00000879175

RefSeq mRNA: 2 — MANE Select: NM_032824 NM_001329914, NM_032824

CCDS: CCDS33275, CCDS92843

Canonical transcript exons

ENST00000283206 — 19 exons

Exon	Start	End
ENSE00001009494	112112899	112112929
ENSE00001009495	112106002	112106075
ENSE00001009498	112074912	112074962
ENSE00001009500	112064162	112064253
ENSE00001009501	112066936	112067067
ENSE00001009502	112107788	112107840
ENSE00001009503	112059977	112060037
ENSE00001009504	112086005	112086104
ENSE00001009505	112077192	112077282
ENSE00001009506	112055269	112055756
ENSE00001009508	112081335	112081518
ENSE00003460296	112091712	112091783
ENSE00003460570	112097044	112097152
ENSE00003494538	112098595	112098698
ENSE00003494970	112089625	112089718
ENSE00003623422	112100622	112100695
ENSE00003655677	112097233	112097291
ENSE00003663033	112081057	112081118
ENSE00003851097	112116084	112119314

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 94.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.8186 / max 489.7264, expressed in 1823 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
21969	18.9145	1803
21971	5.5806	1022
21968	5.2663	1661
21972	1.6925	617
21970	1.5227	878
21967	0.8420	482

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of sigmoid colon	UBERON:0004993	94.62	gold quality
corpus epididymis	UBERON:0004359	94.46	gold quality
rectum	UBERON:0001052	94.37	gold quality
colonic mucosa	UBERON:0000317	94.18	gold quality
palpebral conjunctiva	UBERON:0001812	93.76	gold quality
jejunal mucosa	UBERON:0000399	93.53	gold quality
islet of Langerhans	UBERON:0000006	93.45	gold quality
duodenum	UBERON:0002114	93.39	gold quality
ileal mucosa	UBERON:0000331	93.02	gold quality
epithelial cell of pancreas	CL:0000083	92.25	gold quality
stromal cell of endometrium	CL:0002255	92.21	gold quality
cauda epididymis	UBERON:0004360	91.98	gold quality
calcaneal tendon	UBERON:0003701	91.87	gold quality
seminal vesicle	UBERON:0000998	91.57	gold quality
adrenal tissue	UBERON:0018303	91.49	gold quality
mucosa of transverse colon	UBERON:0004991	91.00	gold quality
epithelium of nasopharynx	UBERON:0001951	90.79	gold quality
mucosa of paranasal sinus	UBERON:0005030	90.44	gold quality
decidua	UBERON:0002450	90.41	gold quality
caput epididymis	UBERON:0004358	90.31	gold quality
vermiform appendix	UBERON:0001154	89.65	gold quality
nasal cavity mucosa	UBERON:0001826	89.62	gold quality
monocyte	CL:0000576	89.52	gold quality
esophagus squamous epithelium	UBERON:0006920	89.43	gold quality
leukocyte	CL:0000738	89.41	gold quality
pancreas	UBERON:0001264	89.36	gold quality
endometrium	UBERON:0001295	89.28	gold quality
smooth muscle tissue	UBERON:0001135	88.94	gold quality
nasal cavity epithelium	UBERON:0005384	88.81	gold quality
superficial temporal artery	UBERON:0001614	88.40	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-11	no	479.73
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

109 targeting TMEM87B, 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-4262	100.00	73.26	3931
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819

Literature-anchored findings (GeneRIF, showing 1)

• Heterozygous loss of FBLN7 and TMEM87B account for some of the clinical features, including cardiac defects and craniofacial abnormalities associated with 2q13 deletion syndrome. (PMID:24694933)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	TMEM87B	ENSDARG00000112581
mus_musculus	Tmem87b	ENSMUSG00000014353
rattus_norvegicus	Tmem87b	ENSRNOG00000017443
drosophila_melanogaster	CG12121	FBGN0030109
drosophila_melanogaster	CG17660	FBGN0031356
caenorhabditis_elegans		WBGENE00015801
caenorhabditis_elegans		WBGENE00016867

Paralogs (3): TMEM87A (ENSG00000103978), GPR108 (ENSG00000125734), GPR107 (ENSG00000148358)

Protein

Protein identifiers

Transmembrane protein 87B — Q96K49 (reviewed: Q96K49)

All UniProt accessions (5): Q96K49, A0A3B3IU29, A0A494BZZ8, A0A994J791, H7C0B3

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in retrograde transport from endosomes to the trans-Golgi network (TGN).

Subcellular location. Golgi apparatus membrane.

Disease relevance. TMEM87B mutations may be involved in restrictive cardiomyopathy (RCM), a rare non-ischemic myocardial disease. RCM is characterized by restrictive ventricular-filling physiology in the presence of normal or reduced diastolic and/or systolic volumes (of 1 or both ventricles), biatrial enlargement, and normal ventricular wall thickness.

Similarity. Belongs to the LU7TM family. TMEM87 subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96K49-1	1	yes
Q96K49-2	2

RefSeq proteins (2): NP_001316843, NP_116213* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009637	GPR107/GPR108-like	Family
IPR053937	GOST_TM	Domain
IPR054101	TMEM87A/B_GOLD	Domain

Pfam: PF06814, PF21901

UniProt features (26 total): topological domain 8, transmembrane region 7, modified residue 4, glycosylation site 3, signal peptide 1, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96K49-F1	74.41	0.26

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 (4): 469, 494, 496, 534

Glycosylation sites (3): 68, 197, 272

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 121 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, GSE45365_NK_CELL_VS_BCELL_UP, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_VESICLE_MEDIATED_TRANSPORT, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, GOBP_RETROGRADE_TRANSPORT_ENDOSOME_TO_GOLGI, GOBP_CYTOSOLIC_TRANSPORT, GOCC_GOLGI_STACK, GOCC_GOLGI_CISTERNA, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, GOCC_GOLGI_CISTERNA_MEMBRANE, GOCC_ORGANELLE_SUBCOMPARTMENT, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP

GO Biological Process (1): retrograde transport, endosome to Golgi (GO:0042147)

GO Molecular Function (0):

GO Cellular Component (5): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), cytosol (GO:0005829), Golgi cisterna membrane (GO:0032580), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	2
cellular anatomical structure	2
intercellular transport	1
endosomal transport	1
cytosolic transport	1
Golgi apparatus	1
bounding membrane of organelle	1
endomembrane system	1
intracellular membrane-bounded organelle	1
organelle membrane	1
Golgi cisterna	1

Protein interactions and networks

STRING

684 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM87B	FBLN7	Q53RD9	638
TMEM87B	ZC3H6	P61129	565
TMEM87B	ACOXL	Q9NUZ1	503
TMEM87B	ANAPC1	Q9H1A4	500
TMEM87B	ZC3H8	Q8N5P1	470
TMEM87B	ZNHIT1	O43257	415
TMEM87B	GPR107	Q5VW38	406
TMEM87B	MERTK	Q12866	394
TMEM87B	VWA5B1	Q5TIE3	379
TMEM87B	PLEKHB2	Q96CS7	378
TMEM87B	ATOSB	Q7L5A3	370
TMEM87B	RHNO1	Q9BSD3	359
TMEM87B	GPR137	Q96N19	355
TMEM87B	LRRIQ4	A6NIV6	348
TMEM87B	XKR5	Q6UX68	348

IntAct

15 interactions, top by confidence:

A	B	Type	Score
IPPK	TMEM223	psi-mi:“MI:0914”(association)	0.530
TMEM87B	RRBP1	psi-mi:“MI:0915”(physical association)	0.400
	ESYT2	psi-mi:“MI:0914”(association)	0.350
CANX	HLA-A	psi-mi:“MI:0914”(association)	0.350
CHRNB2	TMEM131L	psi-mi:“MI:0914”(association)	0.350
ST14	LIPT2	psi-mi:“MI:0914”(association)	0.350
CHRNB4	GPR89A	psi-mi:“MI:0914”(association)	0.350
HFE	PODXL	psi-mi:“MI:0914”(association)	0.350
KLRC2	CLGN	psi-mi:“MI:0914”(association)	0.350
CD3D	CLGN	psi-mi:“MI:0914”(association)	0.350
ENTPD7	TMEM120B	psi-mi:“MI:0914”(association)	0.350
VIPR1	SLC33A1	psi-mi:“MI:0914”(association)	0.350
MFSD5	ILVBL	psi-mi:“MI:0914”(association)	0.350
SLC22A14	CLGN	psi-mi:“MI:0914”(association)	0.350

BioGRID (30): TMEM87B (Affinity Capture-MS), TMEM87B (Affinity Capture-MS), TMEM87B (Affinity Capture-MS), TMEM87B (Affinity Capture-MS), TMEM87B (Positive Genetic), TMEM87B (Synthetic Lethality), RRBP1 (Proximity Label-MS), TMEM87B (Proximity Label-MS), TMEM87B (Proximity Label-MS), TMEM87B (Proximity Label-MS), TMEM87B (Proximity Label-MS), TMEM87B (Proximity Label-MS), TMEM87B (Proximity Label-MS), TMEM87B (Proximity Label-MS), TMEM87B (Affinity Capture-MS)

ESM2 similar proteins: A3KNK1, A4FUY9, A5D6V4, A5PN43, A8DZH4, D3ZWZ9, E1BY51, E7EYQ9, F4JTN2, O14524, P51811, Q28CV2, Q3T124, Q3TPR7, Q3ZBX1, Q49LS5, Q4R8A8, Q4V8X0, Q502E0, Q5F3F5, Q5GH61, Q5HZD4, Q5HZE5, Q5PQQ4, Q5PR61, Q5RDB4, Q5U4X7, Q5YCC5, Q68DH5, Q6AXF6, Q6GQE1, Q6P4P2, Q6Q3F5, Q7ZX75, Q7ZYA0, Q810F5, Q86UW1, Q86X19, Q8BKU8, Q8C561

Diamond homologs: Q28EW0, Q8BKU8, Q8BXN9, Q8NBN3, Q96K49

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	56
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
223092	NM_032824.3(TMEM87B):c.1366A>G (p.Asn456Asp)	Likely pathogenic

SpliceAI

3090 predictions. Top by Δscore:

Variant	Effect	Δscore
2:112066935:G:T	acceptor_loss	1.0000
2:112067064:GAAT:G	donor_gain	1.0000
2:112067068:G:GG	donor_gain	1.0000
2:112081051:TCCTA:T	acceptor_loss	1.0000
2:112081052:CCTA:C	acceptor_loss	1.0000
2:112081053:CTA:C	acceptor_loss	1.0000
2:112081055:A:AG	acceptor_gain	1.0000
2:112081055:A:AT	acceptor_loss	1.0000
2:112081056:G:GA	acceptor_gain	1.0000
2:112081056:GTTT:G	acceptor_gain	1.0000
2:112081115:GATT:G	donor_gain	1.0000
2:112081116:ATTG:A	donor_loss	1.0000
2:112081117:TT:T	donor_gain	1.0000
2:112081117:TTGTG:T	donor_loss	1.0000
2:112081118:TGT:T	donor_loss	1.0000
2:112081119:G:GG	donor_gain	1.0000
2:112081119:GTG:G	donor_loss	1.0000
2:112081120:TGA:T	donor_loss	1.0000
2:112081121:GAG:G	donor_loss	1.0000
2:112086001:TCAG:T	acceptor_gain	1.0000
2:112086002:CAGC:C	acceptor_gain	1.0000
2:112086003:A:AG	acceptor_gain	1.0000
2:112086004:G:GA	acceptor_gain	1.0000
2:112086004:GCCC:G	acceptor_gain	1.0000
2:112086004:GCCCA:G	acceptor_gain	1.0000
2:112086100:GTGAA:G	donor_gain	1.0000
2:112086101:TGAA:T	donor_gain	1.0000
2:112086102:GAA:G	donor_gain	1.0000
2:112086102:GAAG:G	donor_gain	1.0000
2:112086104:AGT:A	donor_loss	1.0000

AlphaMissense

3669 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:112107805:G:C	W514C	0.999
2:112107805:G:T	W514C	0.999
2:112081380:T:A	W234R	0.997
2:112081380:T:C	W234R	0.997
2:112107803:T:A	W514R	0.997
2:112107803:T:C	W514R	0.997
2:112086082:A:C	S306R	0.996
2:112086084:C:A	S306R	0.996
2:112086084:C:G	S306R	0.996
2:112100629:T:C	F462L	0.996
2:112100631:C:A	F462L	0.996
2:112100631:C:G	F462L	0.996
2:112098673:T:A	W451R	0.994
2:112098673:T:C	W451R	0.994
2:112086088:G:C	G308R	0.993
2:112086089:G:T	G308V	0.992
2:112098640:T:C	F440L	0.992
2:112098642:T:A	F440L	0.992
2:112098642:T:G	F440L	0.992
2:112098679:C:T	P453S	0.992
2:112098680:C:A	P453Q	0.992
2:112098693:T:A	N457K	0.991
2:112098693:T:G	N457K	0.991
2:112100627:C:A	A461D	0.991
2:112086089:G:A	G308D	0.990
2:112097103:A:C	K388N	0.990
2:112097103:A:T	K388N	0.990
2:112098682:T:C	S454P	0.990
2:112086048:G:C	K294N	0.987
2:112086048:G:T	K294N	0.987

dbSNP variants (sampled 300 via entrez): RS1000057611 (2:112115731 G>A), RS1000070192 (2:112113088 A>G), RS1000083914 (2:112093464 A>G), RS1000108786 (2:112069416 C>A,T), RS1000136369 (2:112093173 C>T), RS1000177222 (2:112107336 C>T), RS1000182737 (2:112057583 G>A), RS1000241096 (2:112064085 T>C), RS1000298703 (2:112107155 C>G,T), RS1000312182 (2:112062917 A>G), RS1000392804 (2:112080414 C>T), RS1000453812 (2:112099758 T>G), RS1000458351 (2:112069692 A>G), RS1000563120 (2:112108964 G>A), RS1000649682 (2:112088115 T>C)

Disease associations

OMIM: gene MIM:617203 | 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
GCST007267_116	Systolic blood pressure	9.000000e-11
GCST009391_1630	Metabolite levels	7.000000e-06
GCST010481_7	Acute anterior uveitis in ankylosing spondylitis	3.000000e-06
GCST90002398_345	Neutrophil count	2.000000e-13

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0006335	systolic blood pressure
EFO:0010465	beta-hydroxybutyric acid measurement
EFO:0004833	neutrophil count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	4
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, increases expression	2
Tretinoin	increases expression	2
Cyclosporine	decreases expression	2
FR900359	increases phosphorylation	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	increases oxidation, increases abundance, affects cotreatment	1
sulforaphane	increases expression	1
perfluorooctanoic acid	increases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
abrine	decreases expression	1
Zoledronic Acid	increases expression	1
Acetaminophen	decreases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Benzo(a)pyrene	increases expression	1
Caffeine	increases phosphorylation	1
Calcitriol	increases expression, affects cotreatment	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Doxorubicin	decreases expression	1
Folic Acid	decreases expression	1
Formaldehyde	increases expression	1
Hydrogen Peroxide	affects cotreatment, increases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression, affects cotreatment	1
Ozone	increases oxidation, increases abundance, affects cotreatment	1
Dihydrotestosterone	increases expression	1
Testosterone	affects cotreatment, increases expression	1
Theophylline	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	increases expression	1

Clinical trials (associated diseases)

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