C9orf85

Summary

C9orf85 (chromosome 9 open reading frame 85, HGNC:28784) is a protein-coding gene on chromosome 9q21.13, encoding Uncharacterized protein C9orf85 (Q96MD7).

At a glance

• Clinical variants (ClinVar): 13 total
• MANE Select transcript: NM_182505

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28784
Approved symbol	C9orf85
Name	chromosome 9 open reading frame 85
Location	9q21.13
Locus type	gene with protein product
Status	Approved
Aliases	MGC61599
Ensembl gene	ENSG00000155621
Ensembl biotype	protein_coding
OMIM	620761
Entrez	138241

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 3 nonsense_mediated_decay

ENST00000334731, ENST00000377027, ENST00000377031, ENST00000473252, ENST00000479413, ENST00000486911, ENST00000897315, ENST00000924626

RefSeq mRNA: 4 — MANE Select: NM_182505 NM_001365053, NM_001365055, NM_001365057, NM_182505

CCDS: CCDS6639, CCDS94421

Canonical transcript exons

ENST00000334731 — 4 exons

Exon	Start	End
ENSE00001337850	71972692	71973457
ENSE00003504987	71971505	71971618
ENSE00003549933	71947006	71947112
ENSE00003843190	71911639	71911836

Expression profiles

Bgee: expression breadth ubiquitous, 244 present calls, max score 97.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.0702 / max 217.0966, expressed in 1783 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
96898	8.5531	1742
96899	4.4614	1560
96897	1.0557	630

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelial cell of pancreas	CL:0000083	97.20	silver quality
amniotic fluid	UBERON:0000173	94.15	gold quality
pancreatic ductal cell	CL:0002079	93.50	silver quality
gingival epithelium	UBERON:0001949	90.82	gold quality
gingiva	UBERON:0001828	87.92	gold quality
mucosa of paranasal sinus	UBERON:0005030	87.91	gold quality
oral cavity	UBERON:0000167	87.90	gold quality
epithelium of nasopharynx	UBERON:0001951	87.88	gold quality
upper arm skin	UBERON:0004263	87.74	silver quality
jejunal mucosa	UBERON:0000399	87.30	gold quality
superficial temporal artery	UBERON:0001614	86.40	gold quality
duodenum	UBERON:0002114	86.07	gold quality
parotid gland	UBERON:0001831	85.57	gold quality
esophagus squamous epithelium	UBERON:0006920	85.04	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	83.81	gold quality
lower esophagus mucosa	UBERON:0035834	83.63	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.48	gold quality
seminal vesicle	UBERON:0000998	83.48	gold quality
calcaneal tendon	UBERON:0003701	83.38	gold quality
leukocyte	CL:0000738	83.36	gold quality
monocyte	CL:0000576	83.34	gold quality
vastus lateralis	UBERON:0001379	83.12	silver quality
palpebral conjunctiva	UBERON:0001812	82.94	gold quality
popliteal artery	UBERON:0002250	82.70	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.69	gold quality
tibial artery	UBERON:0007610	82.69	gold quality
mucosa of transverse colon	UBERON:0004991	82.53	gold quality
esophagus mucosa	UBERON:0002469	82.37	gold quality
ileal mucosa	UBERON:0000331	82.32	gold quality
spinal cord	UBERON:0002240	82.29	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting C9orf85, 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-4425	100.00	67.59	1049
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-122B-5P	99.46	70.81	1457
HSA-MIR-208A-5P	99.42	70.83	1913
HSA-MIR-208B-5P	99.42	70.83	1952
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-888-5P	99.30	70.15	1855
HSA-MIR-5584-3P	99.23	68.79	1351
HSA-MIR-2054	99.20	68.89	1699
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-670-3P	99.03	68.88	2404
HSA-MIR-1304-5P	98.90	68.58	1054
HSA-MIR-5089-5P	98.45	66.06	1388
HSA-MIR-876-5P	97.99	68.49	1345
HSA-MIR-8055	97.62	66.09	1023
HSA-MIR-937-5P	97.43	68.39	667
HSA-MIR-5187-3P	97.28	67.10	1037
HSA-MIR-122-5P	97.23	64.92	1024
HSA-MIR-5694	97.06	67.70	682

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	C5H9orf85	ENSDARG00000035570
mus_musculus	1110059E24Rik	ENSMUSG00000035171
rattus_norvegicus	C1h9orf85	ENSRNOG00000027161
rattus_norvegicus		ENSRNOG00000083026
drosophila_melanogaster	CG8675	FBGN0030834

Protein

Protein identifiers

Uncharacterized protein C9orf85 — Q96MD7 (reviewed: Q96MD7)

All UniProt accessions (4): Q96MD7, E9PN32, F6X0R3, H3BLX8

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt ID	Names	Canonical?
Q96MD7-3	1	yes
Q96MD7-1	2
Q96MD7-2	3

RefSeq proteins (4): NP_001351982, NP_001351984, NP_001351986, NP_872311* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019351	DUF2039	Family

Pfam: PF10217

UniProt features (8 total): modified residue 3, splice variant 3, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96MD7-F1	75.66	0.30

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 (3): 2, 137, 137

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 118 (showing top): RNGTGGGC_UNKNOWN, AP1_01, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, TGACCTY_ERR1_Q2, WANG_LMO4_TARGETS_DN, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, NF1_Q6_01, TGCTGAY_UNKNOWN, USF_01, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, AACTTT_UNKNOWN, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

340 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C9orf85	CCDC28A-AS1	A0A096LPI5	717
C9orf85	C9orf57	Q5W0N0	716
C9orf85	ZFAND5	O76080	610
C9orf85	CEMIP2	Q9UHN6	527
C9orf85	HIGD2B	Q4VC39	500
C9orf85	C16orf89	Q6UX73	474
C9orf85	ABHD17B	Q5VST6	368
C9orf85	SLC4A2	P04920	350
C9orf85	KIF27	Q86VH2	348
C9orf85	CPNE8	Q86YQ8	348
C9orf85	RSRC2	Q7L4I2	347
C9orf85	NOC4L	Q9BVI4	346
C9orf85	TRPM3	Q9HCF6	345
C9orf85	TMC1	Q8TDI8	343
C9orf85	MIPOL1	Q8TD10	324
C9orf85	NPAP1	Q9NZP6	324

IntAct

5 interactions, top by confidence:

A	B	Type	Score
C9orf85	BRCC3	psi-mi:“MI:0914”(association)	0.530
LAGE3	CTSA	psi-mi:“MI:0914”(association)	0.530
C9orf85	HBB	psi-mi:“MI:0914”(association)	0.350
C9orf85	MPO	psi-mi:“MI:0914”(association)	0.350

BioGRID (12): C9orf85 (Affinity Capture-RNA), HBA2 (Affinity Capture-MS), HBB (Affinity Capture-MS), ANKHD1 (Affinity Capture-MS), PRTFDC1 (Affinity Capture-MS), BABAM1 (Affinity Capture-MS), FAM175B (Affinity Capture-MS), BRE (Affinity Capture-MS), BRCC3 (Affinity Capture-MS), C9orf85 (Affinity Capture-MS), C9orf85 (Affinity Capture-MS), C9orf85 (Affinity Capture-RNA)

ESM2 similar proteins: A8MR21, B2RXH8, B7ZW38, F4JGB7, F4K3M6, O60812, O82312, O82387, O82391, P0DMR1, P83946, P93422, P93831, Q0DZT4, Q0WVE8, Q10MI4, Q149N8, Q3ED78, Q5RBK9, Q5VN06, Q66GQ6, Q680I0, Q6K1U0, Q6K1U4, Q6K5I0, Q6NKT5, Q7TP98, Q7X7E9, Q7ZXY4, Q84JE8, Q84UI6, Q8GW46, Q8GYY5, Q8GZ42, Q8L925, Q8N9N2, Q8NCT3, Q8RXT5, Q8S4P4, Q8S4P5

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, A7MB40, P78312, Q8CGI1, A2RRD8, A6NHJ4, P0CJ79, P17035, P51522, Q08AN1, Q0VGE8, Q3MIS6, Q5HY98, Q5R8X1, Q5RER9, Q5VIY5, Q6PDB4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1468 predictions. Top by Δscore:

Variant	Effect	Δscore
9:71918423:A:G	acceptor_gain	1.0000
9:71947003:A:AG	acceptor_gain	1.0000
9:71947004:A:G	acceptor_gain	1.0000
9:71947005:G:GG	acceptor_gain	1.0000
9:71947005:GA:G	acceptor_gain	1.0000
9:71947005:GAAA:G	acceptor_gain	1.0000
9:71947110:GTG:G	donor_gain	1.0000
9:71971503:A:AG	acceptor_gain	1.0000
9:71971504:G:GG	acceptor_gain	1.0000
9:71971504:GT:G	acceptor_gain	1.0000
9:71971504:GTGTT:G	acceptor_gain	1.0000
9:71971619:G:GG	donor_gain	1.0000
9:71911662:G:GT	donor_gain	0.9900
9:71911832:CCAAG:C	donor_loss	0.9900
9:71911833:CAAGG:C	donor_loss	0.9900
9:71911834:AAG:A	donor_loss	0.9900
9:71911837:GTA:G	donor_loss	0.9900
9:71911838:T:G	donor_loss	0.9900
9:71946992:T:TA	acceptor_loss	0.9900
9:71947000:TTTAA:T	acceptor_loss	0.9900
9:71947001:TTAAG:T	acceptor_loss	0.9900
9:71947002:TAAGA:T	acceptor_loss	0.9900
9:71947003:AAG:A	acceptor_loss	0.9900
9:71947004:AGAA:A	acceptor_loss	0.9900
9:71947005:G:GA	acceptor_loss	0.9900
9:71947005:GAA:G	acceptor_gain	0.9900
9:71947005:GAAAA:G	acceptor_gain	0.9900
9:71947118:T:G	donor_gain	0.9900
9:71971500:TTTA:T	acceptor_loss	0.9900
9:71971504:GTGT:G	acceptor_gain	0.9900

AlphaMissense

1071 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:71911798:T:C	F22L	0.991
9:71911800:C:A	F22L	0.991
9:71911800:C:G	F22L	0.991
9:71947063:T:A	W54R	0.991
9:71947063:T:C	W54R	0.991
9:71947065:G:C	W54C	0.991
9:71947065:G:T	W54C	0.991
9:71947066:C:A	R55S	0.985
9:71947067:G:C	R55P	0.982
9:71947045:T:A	C48S	0.981
9:71947046:G:C	C48S	0.981
9:71947083:A:C	K60N	0.981
9:71947083:A:T	K60N	0.981
9:71947036:T:C	C45R	0.979
9:71947111:T:C	C70R	0.977
9:71947045:T:C	C48R	0.974
9:71971589:A:C	K98N	0.974
9:71971589:A:T	K98N	0.974
9:71971528:T:A	V78E	0.973
9:71971551:T:C	C86R	0.973
9:71971581:T:C	C96R	0.973
9:71947075:T:G	Y58D	0.972
9:71947064:G:C	W54S	0.969
9:71947111:T:A	C70S	0.969
9:71947112:G:C	C70S	0.969
9:71947058:T:A	L52H	0.968
9:71947089:A:C	K62N	0.968
9:71947089:A:T	K62N	0.968
9:71911776:G:C	Q14H	0.967
9:71911776:G:T	Q14H	0.967

dbSNP variants (sampled 300 via entrez): RS1000000863 (9:71925504 A>C), RS1000079004 (9:71977992 A>G), RS1000116613 (9:71925212 A>G,T), RS1000153171 (9:71971133 T>C), RS1000180607 (9:71972668 A>G), RS1000195600 (9:71930676 A>G), RS1000202451 (9:71956840 A>G), RS1000328349 (9:71960241 A>G), RS1000376389 (9:71922927 A>C), RS1000392385 (9:71918039 C>G), RS1000405366 (9:71978894 G>A,T), RS1000428824 (9:71922744 A>C,G), RS1000530956 (9:71939007 C>T), RS1000591141 (9:71962026 C>T), RS1000643417 (9:71961638 T>C)

Disease associations

OMIM: gene MIM:620761 | 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

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

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	3
Formaldehyde	decreases expression, increases expression	2
Nickel	decreases expression	2
Valproic Acid	decreases methylation, increases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Bortezomib	increases expression	1
Sunitinib	decreases expression	1
Vorinostat	affects cotreatment, increases expression	1
Acetaminophen	decreases expression	1
Cadmium	decreases expression, increases abundance	1
Calcitriol	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Folic Acid	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	increases expression	1

Clinical trials (associated diseases)

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