C16orf89

Summary

C16orf89 (chromosome 16 open reading frame 89, HGNC:28687) is a protein-coding gene on chromosome 16p13.3, encoding UPF0764 protein C16orf89 (Q6UX73).

This gene is expressed predominantly in the thyroid. Based on expression patterns similar to thyroid transcription factors and proteins, this gene may function in the development and function of the thyroid. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 146556 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 20 total
• MANE Select transcript: NM_001098514

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28687
Approved symbol	C16orf89
Name	chromosome 16 open reading frame 89
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC45438
Ensembl gene	ENSG00000153446
Ensembl biotype	protein_coding
OMIM	621148
Entrez	146556

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 3 retained_intron

ENST00000315997, ENST00000472572, ENST00000474471, ENST00000586629, ENST00000591875, ENST00000592343, ENST00000857150, ENST00000857151, ENST00000857152, ENST00000946892

RefSeq mRNA: 2 — MANE Select: NM_001098514 NM_001098514, NM_152459

CCDS: CCDS42116, CCDS45404

Canonical transcript exons

ENST00000472572 — 8 exons

Exon	Start	End
ENSE00002772906	5058493	5058610
ENSE00002820137	5065701	5065956
ENSE00002866551	5060286	5060436
ENSE00003534672	5055246	5055350
ENSE00003577213	5044122	5044478
ENSE00003607747	5047878	5047964
ENSE00003638444	5062425	5062574
ENSE00003662147	5056053	5056188

Expression profiles

Bgee: expression breadth ubiquitous, 208 present calls, max score 98.73.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9829 / max 286.3379, expressed in 234 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156144	1.9657	233
156143	0.0173	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left lobe of thyroid gland	UBERON:0001120	98.73	gold quality
thyroid gland	UBERON:0002046	98.68	gold quality
right lobe of thyroid gland	UBERON:0001119	98.58	gold quality
gall bladder	UBERON:0002110	95.15	gold quality
bronchial epithelial cell	CL:0002328	94.98	gold quality
body of stomach	UBERON:0001161	94.30	gold quality
bronchus	UBERON:0002185	94.13	gold quality
lower lobe of lung	UBERON:0008949	93.90	gold quality
upper lobe of lung	UBERON:0008948	93.45	gold quality
upper lobe of left lung	UBERON:0008952	93.39	gold quality
stomach	UBERON:0000945	93.36	gold quality
kidney epithelium	UBERON:0004819	93.01	gold quality
lung	UBERON:0002048	92.46	gold quality
putamen	UBERON:0001874	89.80	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.33	gold quality
amygdala	UBERON:0001876	89.27	gold quality
parotid gland	UBERON:0001831	89.26	gold quality
pylorus	UBERON:0001166	88.99	gold quality
caudate nucleus	UBERON:0001873	88.90	gold quality
right lung	UBERON:0002167	88.74	gold quality
nucleus accumbens	UBERON:0001882	88.31	gold quality
fundus of stomach	UBERON:0001160	87.99	gold quality
right frontal lobe	UBERON:0002810	87.50	gold quality
anterior cingulate cortex	UBERON:0009835	87.02	gold quality
cardia of stomach	UBERON:0001162	86.83	gold quality
mucosa of paranasal sinus	UBERON:0005030	86.44	gold quality
visceral pleura	UBERON:0002401	86.40	gold quality
nerve	UBERON:0001021	86.15	gold quality
tibial nerve	UBERON:0001323	86.15	gold quality
right atrium auricular region	UBERON:0006631	85.94	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-1	yes	94.81
E-GEOD-130148	yes	14.24
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting C16orf89, 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-671-5P	99.52	67.11	1277
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-4727-5P	99.23	67.55	1154
HSA-MIR-6738-3P	99.03	67.14	1326
HSA-MIR-5006-5P	98.79	66.92	1246
HSA-MIR-4272	98.76	68.74	1810
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-4290	98.51	65.17	907
HSA-MIR-1265	98.36	66.46	598
HSA-MIR-1291	96.28	65.89	1224
HSA-MIR-6775-3P	95.76	65.91	982
HSA-MIR-6851-3P	95.73	65.11	688
HSA-MIR-328-3P	92.82	64.37	521

Literature-anchored findings (GeneRIF, showing 1)

• characterization of C16orf89; mRNA and translated protein sequences (signal peptide, O-glycosylation sites); mRNA expression in various tissues primarily thyroid (PMID:20578903)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	C3H16orf89	ENSDARG00000075345
mus_musculus	AU021092	ENSMUSG00000051669
rattus_norvegicus	C10h16orf89	ENSRNOG00000021796

Protein

Protein identifiers

UPF0764 protein C16orf89 — Q6UX73 (reviewed: Q6UX73)

All UniProt accessions (2): Q6UX73, A0A0A0MT71

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Homodimer.

Subcellular location. Secreted.

Tissue specificity. Predominantly expressed in thyroid tissue.

Post-translational modifications. Glycosylated.

Miscellaneous. Major isoform, represents 80% of transcripts.

Similarity. Belongs to the UPF0764 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6UX73-1	1	yes
Q6UX73-2	2

RefSeq proteins (2): NP_001091984, NP_689672 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031751	DUF4735	Family

Pfam: PF15882

UniProt features (8 total): sequence variant 3, sequence conflict 2, signal peptide 1, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UX73-F1	71.13	0.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 65 (showing top): GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_6, ABBUD_LIF_SIGNALING_1_DN, TGGNNNNNNKCCAR_UNKNOWN, VECCHI_GASTRIC_CANCER_EARLY_DN, BURTON_ADIPOGENESIS_9, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_DN, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, GOMF_PROTEIN_HOMODIMERIZATION_ACTIVITY, DODD_NASOPHARYNGEAL_CARCINOMA_DN, SWEET_LUNG_CANCER_KRAS_UP, MIKKELSEN_MEF_LCP_WITH_H3K27ME3, KARLSSON_TGFB1_TARGETS_UP, LEE_BMP2_TARGETS_UP, WNT_UP.V1_DN

GO Biological Process (0):

GO Molecular Function (1): protein homodimerization activity (GO:0042803)

GO Cellular Component (4): cytosol (GO:0005829), membrane (GO:0016020), extracellular exosome (GO:0070062), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
identical protein binding	1
protein dimerization activity	1
cytoplasm	1
extracellular vesicle	1

Protein interactions and networks

STRING

278 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C16orf89	HIGD2B	Q4VC39	532
C16orf89	PEBP4	Q96S96	504
C16orf89	DRICH1	Q6PGQ1	491
C16orf89	C9orf85	Q96MD7	474
C16orf89	PLK5	Q496M5	406
C16orf89	WDR86	Q86TI4	399
C16orf89	GLRA3	O75311	398
C16orf89	KLHL18	O94889	395
C16orf89	DHRS7B	Q6IAN0	393
C16orf89	STATH	P02808	387
C16orf89	HTN3	P15516	377
C16orf89	LRRC19	Q9H756	374
C16orf89	LCN9	Q8WX39	370
C16orf89	IYD	Q6PHW0	366
C16orf89	GLRA2	P23416	339

IntAct

3 interactions, top by confidence:

A	B	Type	Score
DCUN1D1	RGSL1	psi-mi:“MI:0914”(association)	0.350
		psi-mi:“MI:0914”(association)	0.350

BioGRID (1): C16orf89 (Affinity Capture-MS)

ESM2 similar proteins: A0A8M9PDM1, A2BD09, A2RU67, A7MCS3, D3ZWJ9, E1B9E5, E9Q8Q8, O43278, O88968, P20062, P35054, P51642, P70277, Q0VCT2, Q32P28, Q3UST5, Q3V1T4, Q3V5L5, Q5F3L3, Q5HZE8, Q5REL7, Q64375, Q68BL7, Q6DFV8, Q6P7C7, Q6TMA8, Q6UX73, Q70D51, Q765H6, Q7TNI2, Q86XM0, Q8BHP7, Q8BYI8, Q8C7B8, Q8K2B0, Q92184, Q95JI2, Q99P91, Q9CYD3, Q9GMB2

Diamond homologs: A0A096LPI5, A6NIU2, A6NJG6, F2Z398, P0DTE4, P51957, Q09FC8, Q5H9K5, Q5T7P6, Q68CZ1, Q6B4Z3, Q6UX73, Q86U02, Q8IV13, Q8N7M2, Q8N9N2, Q8NDZ0, Q8NEM8, Q8TDM0, Q92918, Q96J02, Q96MD7, Q9BUA6, Q9NXG0, A7MCS3, Q3UST5, O00592, Q04864, Q3ZCU0, Q6ZUF6, Q7JQ07, Q8N769, Q9H2J1, O14607, O14628, O15054, O15550, O70546, P79457, Q5NCY0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	5
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1033 predictions. Top by Δscore:

Variant	Effect	Δscore
16:5055266:T:TA	donor_gain	1.0000
16:5056051:A:AC	donor_gain	1.0000
16:5056052:C:CT	donor_gain	1.0000
16:5056184:CCCCT:C	acceptor_gain	1.0000
16:5056185:CCCT:C	acceptor_gain	1.0000
16:5056185:CCCTC:C	acceptor_gain	1.0000
16:5056186:CCTC:C	acceptor_gain	1.0000
16:5056187:CT:C	acceptor_gain	1.0000
16:5062421:TCA:T	donor_loss	1.0000
16:5062423:A:T	donor_loss	1.0000
16:5062424:C:T	donor_loss	1.0000
16:5062424:CCT:C	donor_gain	1.0000
16:5062449:G:C	donor_gain	1.0000
16:5062570:CTGCT:C	acceptor_gain	1.0000
16:5062571:TGCT:T	acceptor_gain	1.0000
16:5062573:CT:C	acceptor_gain	1.0000
16:5062575:C:CC	acceptor_gain	1.0000
16:5056014:C:CA	donor_gain	0.9900
16:5056020:T:TA	donor_gain	0.9900
16:5056052:CTG:C	donor_gain	0.9900
16:5056058:T:A	donor_gain	0.9900
16:5056187:CTCTG:C	acceptor_loss	0.9900
16:5056189:C:CA	acceptor_loss	0.9900
16:5056189:C:CC	acceptor_gain	0.9900
16:5056190:T:A	acceptor_loss	0.9900
16:5058486:CACT:C	donor_loss	0.9900
16:5058487:ACTC:A	donor_loss	0.9900
16:5058488:CTCA:C	donor_loss	0.9900
16:5058489:TCACC:T	donor_loss	0.9900
16:5058490:CA:C	donor_loss	0.9900

AlphaMissense

2338 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:5055325:G:C	F263L	0.987
16:5055325:G:T	F263L	0.987
16:5055327:A:G	F263L	0.987
16:5060432:G:C	F121L	0.981
16:5060432:G:T	F121L	0.981
16:5060434:A:G	F121L	0.981
16:5055316:G:C	F266L	0.980
16:5055316:G:T	F266L	0.980
16:5055318:A:G	F266L	0.980
16:5055341:C:T	C258Y	0.978
16:5060405:C:A	W130C	0.977
16:5060405:C:G	W130C	0.977
16:5055256:G:C	F286L	0.974
16:5055256:G:T	F286L	0.974
16:5055258:A:G	F286L	0.974
16:5055277:C:A	Q279H	0.974
16:5055277:C:G	Q279H	0.974
16:5056133:C:G	C228S	0.972
16:5056134:A:T	C228S	0.972
16:5056133:C:T	C228Y	0.971
16:5060407:A:G	W130R	0.971
16:5060407:A:T	W130R	0.971
16:5055341:C:G	C258S	0.970
16:5055342:A:T	C258S	0.970
16:5065762:G:C	F49L	0.969
16:5065762:G:T	F49L	0.969
16:5065764:A:G	F49L	0.969
16:5055303:A:G	W271R	0.968
16:5055303:A:T	W271R	0.968
16:5058525:G:C	H199D	0.968

dbSNP variants (sampled 300 via entrez): RS1000098359 (16:5046010 C>T), RS1000295240 (16:5057951 C>T), RS1000461395 (16:5067343 A>AGC), RS1000503720 (16:5044826 A>C,G), RS1000587852 (16:5045605 C>A,G), RS1000619006 (16:5045733 T>C,G), RS1000627818 (16:5058201 A>G), RS1000673057 (16:5054271 A>G), RS1000787140 (16:5053979 A>C,G,T), RS1000871077 (16:5065536 C>T), RS1000888468 (16:5051413 A>G), RS1001059303 (16:5049432 C>T), RS1001100046 (16:5045087 C>G), RS1001234963 (16:5062790 G>A), RS1001415897 (16:5066822 A>C)

Disease associations

OMIM: gene MIM:621148 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
entinostat	increases expression, affects cotreatment	2
Benzo(a)pyrene	decreases expression, decreases methylation	2
Nickel	decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
Valproic Acid	affects expression, increases methylation	2
2,5,2’,5’-tetrachlorobiphenyl	decreases expression, increases expression	1
benzo(e)pyrene	increases methylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Acetaminophen	decreases expression	1
Methapyrilene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases expression	1

Clinical trials (associated diseases)

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