C16orf87

Summary

C16orf87 (chromosome 16 open reading frame 87, HGNC:33754) is a protein-coding gene on chromosome 16q11.2, encoding UPF0547 protein C16orf87 (Q6PH81).

At a glance

• Clinical variants (ClinVar): 11 total
• MANE Select transcript: NM_001001436

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33754
Approved symbol	C16orf87
Name	chromosome 16 open reading frame 87
Location	16q11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000155330
Ensembl biotype	protein_coding
Entrez	388272

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000285697, ENST00000394806, ENST00000564250, ENST00000565112

RefSeq mRNA: 3 — MANE Select: NM_001001436 NM_001001436, NM_001348660, NM_001348661

CCDS: CCDS10724, CCDS86522

Canonical transcript exons

ENST00000285697 — 4 exons

Exon	Start	End
ENSE00001020407	46796603	46803070
ENSE00001862260	46831084	46831180
ENSE00003510892	46824386	46824482
ENSE00003648227	46809603	46809785

Expression profiles

Bgee: expression breadth ubiquitous, 236 present calls, max score 90.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.9106 / max 299.8505, expressed in 1759 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
157223	11.9380	1754
157224	0.5305	273
207865	0.4294	221
157222	0.0126	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	90.38	gold quality
buccal mucosa cell	CL:0002336	89.57	gold quality
ganglionic eminence	UBERON:0004023	85.10	gold quality
right testis	UBERON:0004534	84.83	gold quality
left testis	UBERON:0004533	84.64	gold quality
testis	UBERON:0000473	84.34	gold quality
gastrocnemius	UBERON:0001388	82.97	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.96	gold quality
muscle of leg	UBERON:0001383	82.85	gold quality
ventricular zone	UBERON:0003053	82.81	gold quality
secondary oocyte	CL:0000655	82.72	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.33	gold quality
hindlimb stylopod muscle	UBERON:0004252	82.27	gold quality
skeletal muscle organ	UBERON:0014892	82.04	gold quality
adrenal tissue	UBERON:0018303	81.94	gold quality
tibialis anterior	UBERON:0001385	81.41	gold quality
stromal cell of endometrium	CL:0002255	81.15	gold quality
skeletal muscle tissue	UBERON:0001134	80.99	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	80.93	gold quality
amniotic fluid	UBERON:0000173	80.88	gold quality
biceps brachii	UBERON:0001507	80.77	gold quality
deltoid	UBERON:0001476	79.95	silver quality
monocyte	CL:0000576	79.77	gold quality
leukocyte	CL:0000738	79.59	gold quality
sperm	CL:0000019	78.19	gold quality
bone marrow cell	CL:0002092	78.01	gold quality
muscle tissue	UBERON:0002385	77.85	gold quality
calcaneal tendon	UBERON:0003701	77.31	gold quality
quadriceps femoris	UBERON:0001377	76.72	gold quality
liver	UBERON:0002107	76.28	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-ENAD-17	yes	36.38
E-HCAD-10	yes	18.44
E-MTAB-9388	yes	5.85
E-ANND-3	yes	4.77
E-GEOD-110499	no	147.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

76 targeting C16orf87, 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-1277-5P	100.00	73.95	5056
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5011-5P	100.00	83.46	5820
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-548N	99.98	71.94	4170
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	C7H16orf87	ENSDARG00000002506
mus_musculus	4921524J17Rik	ENSMUSG00000036934
rattus_norvegicus	C19h16orf87	ENSRNOG00000017090

Protein

Protein identifiers

UPF0547 protein C16orf87 — Q6PH81 (reviewed: Q6PH81)

All UniProt accessions (2): Q6PH81, H3BQL3

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the UPF0547 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6PH81-1	1	yes
Q6PH81-2	2

RefSeq proteins (3): NP_001001436, NP_001335589, NP_001335590 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018886	UPF0547	Domain
IPR040246	C16orf87-like	Family

Pfam: PF10571

UniProt features (7 total): compositionally biased region 2, chain 1, region of interest 1, coiled-coil region 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PH81-F1	70.97	0.27

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 (1): 91

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 90 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, CUI_TCF21_TARGETS_2_DN, AHR_Q5, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP, CAGTGTT_MIR141_MIR200A, chr16q11, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, BRUINS_UVC_RESPONSE_EARLY_LATE, KRIEG_KDM3A_TARGETS_NOT_HYPOXIA, NRF1_Q6, ID2_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

212 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C16orf87	ZNF727	A8MUV8	571
C16orf87	PWWP2A	Q96N64	498
C16orf87	BBX	Q8WY36	475
C16orf87	ZNF215	Q9UL58	474
C16orf87	SINHCAF	Q9NP50	452
C16orf87	FAM90A1	Q86YD7	447
C16orf87	A0A0G2JH32	A0A0G2JH32	446
C16orf87	ZFP41	Q8N8Y5	446
C16orf87	ADNP	Q9H2P0	413
C16orf87	ANKRD9	Q96BM1	396
C16orf87	FAM170A	A1A519	369
C16orf87	GEMIN4	P57678	369
C16orf87	ZGPAT	Q8N5A5	355
C16orf87	ARID5B	Q14865	346
C16orf87	DPYSL4	O14531	307

IntAct

60 interactions, top by confidence:

A	B	Type	Score
HDAC1	CDK2AP1	psi-mi:“MI:0914”(association)	0.840
C16orf87	HDAC1	psi-mi:“MI:0915”(physical association)	0.820
HDAC1	TNRC18	psi-mi:“MI:0914”(association)	0.790
H2AZ1	ZNHIT1	psi-mi:“MI:0914”(association)	0.770
H2AX	PPM1G	psi-mi:“MI:0914”(association)	0.730
MAGEA12	C16orf87	psi-mi:“MI:0915”(physical association)	0.720
C16orf87	MAGEA12	psi-mi:“MI:0915”(physical association)	0.720
H2BC1	PPM1G	psi-mi:“MI:0914”(association)	0.640
C16orf87	CDC27	psi-mi:“MI:0914”(association)	0.640
SRRM4	C16orf87	psi-mi:“MI:0915”(physical association)	0.560
C16orf87	PPIA	psi-mi:“MI:0915”(physical association)	0.560
C16orf87	YWHAG	psi-mi:“MI:0915”(physical association)	0.560
C16orf87	SETDB1	psi-mi:“MI:0915”(physical association)	0.560
C16orf87	KAT5	psi-mi:“MI:0915”(physical association)	0.560
LMO3	C16orf87	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (72): C16orf87 (Two-hybrid), C16orf87 (Affinity Capture-RNA), C16orf87 (Affinity Capture-MS), MIER3 (Affinity Capture-MS), ANAPC2 (Affinity Capture-MS), MIER1 (Affinity Capture-MS), CDC16 (Affinity Capture-MS), ARID5B (Affinity Capture-MS), NEK2 (Affinity Capture-MS), ANAPC4 (Affinity Capture-MS), CDC23 (Affinity Capture-MS), CDC27 (Affinity Capture-MS), MIER2 (Affinity Capture-MS), HDAC1 (Affinity Capture-MS), ANAPC5 (Affinity Capture-MS)

ESM2 similar proteins: A4IGK3, B7ZAP0, O08609, O54941, O55047, O60519, P18847, P26801, P28574, P29596, P37285, P52161, P52162, P52164, P60762, P61244, P61245, P97875, Q07016, Q07866, Q08CW1, Q08DJ0, Q0VCP9, Q0VD32, Q13330, Q28772, Q2KII1, Q32KT0, Q32M00, Q3T0B9, Q56A18, Q5BJU6, Q5R581, Q5ZIL4, Q60765, Q62599, Q642H2, Q6PH81, Q78E65, Q7TMY4

Diamond homologs: Q32KT0, Q5XG50, Q6DGQ4, Q6PH81, Q9CR55

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 35 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.

Reactome pathways:

Pathway	Partners	Fold	FDR
Packaging Of Telomere Ends	6	50.7×	3e-08
NuRD complex assembly	9	48.8×	3e-11
Recognition and association of DNA glycosylase with site containing an affected purine	6	47.1×	4e-08
Cleavage of the damaged purine	6	47.1×	4e-08
ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression	8	46.9×	3e-10
FXIIa activates plasma kallikrein-kinin system	7	46.6×	3e-09
Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3	7	45.2×	4e-09
Interaction of NuRD complexes with transcription factors	9	43.9×	4e-11

GO biological processes:

GO term	Partners	Fold	FDR
heterochromatin formation	8	61.9×	2e-10

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

772 predictions. Top by Δscore:

Variant	Effect	Δscore
16:46803066:TTTCT:T	acceptor_gain	1.0000
16:46803067:TTCT:T	acceptor_gain	1.0000
16:46803069:CT:C	acceptor_gain	1.0000
16:46803071:C:CC	acceptor_gain	1.0000
16:46824381:GTTA:G	donor_loss	1.0000
16:46824382:TTACC:T	donor_loss	1.0000
16:46824383:TACCT:T	donor_loss	1.0000
16:46824385:C:CT	donor_loss	1.0000
16:46824479:GAACC:G	acceptor_loss	1.0000
16:46824480:AACC:A	acceptor_loss	1.0000
16:46824481:AC:A	acceptor_gain	1.0000
16:46824481:ACCTG:A	acceptor_loss	1.0000
16:46824482:CC:C	acceptor_gain	1.0000
16:46824482:CCT:C	acceptor_loss	1.0000
16:46824483:C:A	acceptor_loss	1.0000
16:46824483:C:CC	acceptor_gain	1.0000
16:46824484:T:A	acceptor_loss	1.0000
16:46831081:CACC:C	donor_loss	1.0000
16:46831082:ACCTG:A	donor_loss	1.0000
16:46831083:C:A	donor_loss	1.0000
16:46824378:A:AC	donor_gain	0.9900
16:46824379:C:CC	donor_gain	0.9900
16:46824478:GGAAC:G	acceptor_gain	0.9900
16:46824479:GAAC:G	acceptor_gain	0.9900
16:46803074:T:C	acceptor_gain	0.9800
16:46803074:T:TC	acceptor_gain	0.9800
16:46809602:CCT:C	donor_gain	0.9800
16:46809611:T:TA	donor_gain	0.9800
16:46824485:G:C	acceptor_gain	0.9700
16:46824485:G:GC	acceptor_gain	0.9700

AlphaMissense

1006 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:46802989:A:C	I143R	1.000
16:46802989:A:G	I143T	1.000
16:46802989:A:T	I143K	1.000
16:46802996:C:G	A141P	1.000
16:46802998:A:C	L140W	1.000
16:46802998:A:G	L140S	1.000
16:46803001:G:T	A139D	1.000
16:46803002:C:G	A139P	1.000
16:46803004:A:T	V138D	1.000
16:46824441:A:C	F36L	1.000
16:46824441:A:T	F36L	1.000
16:46824442:A:G	F36S	1.000
16:46824443:A:G	F36L	1.000
16:46824453:A:C	C32W	1.000
16:46824454:C:T	C32Y	1.000
16:46824455:A:G	C32R	1.000
16:46824459:A:C	C30W	1.000
16:46824460:C:T	C30Y	1.000
16:46824461:A:G	C30R	1.000
16:46824465:T:A	K28N	1.000
16:46824465:T:G	K28N	1.000
16:46824472:G:T	A26E	1.000
16:46824475:A:T	V25D	1.000
16:46831103:C:T	C16Y	1.000
16:46831104:A:G	C16R	1.000
16:46831108:T:A	K14N	1.000
16:46831108:T:G	K14N	1.000
16:46831115:G:T	A12D	1.000
16:46802977:A:C	I147S	0.999
16:46802977:A:G	I147T	0.999

dbSNP variants (sampled 300 via entrez): RS1000035424 (16:46814961 T>C), RS1000366018 (16:46828361 TAAAA>T,TAAA,TAAAAA), RS1000369868 (16:46798641 G>C), RS1000401246 (16:46820344 T>C), RS1000432264 (16:46820673 A>G), RS1000443336 (16:46798921 T>C), RS1000609758 (16:46813727 A>G), RS1000683158 (16:46806189 C>T), RS1000701334 (16:46800547 A>C), RS1000837245 (16:46821298 C>G,T), RS1000977863 (16:46826648 T>C), RS1001397266 (16:46796724 A>C), RS1001408691 (16:46797247 T>C), RS1001423275 (16:46828798 A>T), RS1001516280 (16:46817949 T>A,G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D018270	Carcinoma, Ductal, Breast	C04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases expression	5
trichostatin A	decreases expression, affects expression, affects cotreatment	4
sodium arsenite	decreases expression, increases abundance, increases expression	3
Arsenic	affects methylation, increases abundance, increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
FR900359	increases phosphorylation	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
butyraldehyde	increases expression	1
manganese chloride	increases abundance, increases expression	1
coumarin	increases phosphorylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Irinotecan	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Leflunomide	increases expression	1
Panobinostat	affects cotreatment, decreases expression	1
Manganese	increases abundance, increases expression	1
Quercetin	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Vanadates	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Cyclosporine	increases expression	1
Antirheumatic Agents	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03414970	PHASE3	ACTIVE_NOT_RECRUITING	Hypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344	PHASE2	TERMINATED	Docetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999	PHASE2	NOT_YET_RECRUITING	Randomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364	PHASE1/PHASE2	SUSPENDED	High Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855	PHASE1/PHASE2	COMPLETED	Talimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908	EARLY_PHASE1	COMPLETED	Broccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041	EARLY_PHASE1	COMPLETED	Intraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974	Not specified	ACTIVE_NOT_RECRUITING	Nipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198	Not specified	TERMINATED	Oncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397	Not specified	UNKNOWN	MRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532	Not specified	COMPLETED	Living Well After Breast Surgery