C17orf78

Summary

C17orf78 (chromosome 17 open reading frame 78, HGNC:26831) is a protein-coding gene on chromosome 17q12, encoding Uncharacterized protein C17orf78 (Q8N4C9).

Predicted to be located in membrane.

Source: NCBI Gene 284099 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_173625

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26831
Approved symbol	C17orf78
Name	chromosome 17 open reading frame 78
Location	17q12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ39647
Ensembl gene	ENSG00000278505
Ensembl biotype	protein_coding
Entrez	284099

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000611038, ENST00000615133

RefSeq mRNA: 2 — MANE Select: NM_173625 NM_001321399, NM_173625

CCDS: CCDS45655, CCDS82110

Canonical transcript exons

ENST00000615133 — 7 exons

Exon	Start	End
ENSE00003714848	37389246	37389362
ENSE00003718626	37377879	37377965
ENSE00003720651	37386009	37386125
ENSE00003727173	37391647	37392708
ENSE00003727610	37375985	37376150
ENSE00003728941	37379137	37379382
ENSE00003746091	37388670	37388794

Expression profiles

Bgee: expression breadth broad, 27 present calls, max score 98.77.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2255 / max 237.2137, expressed in 7 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
160455	0.1671	7
160456	0.0519	6
160454	0.0065	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
duodenum	UBERON:0002114	98.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.16	gold quality
small intestine	UBERON:0002108	78.93	gold quality
small intestine Peyer’s patch	UBERON:0003454	78.04	gold quality
colonic epithelium	UBERON:0000397	56.40	gold quality
testis	UBERON:0000473	49.50	gold quality
left testis	UBERON:0004533	49.43	gold quality
right testis	UBERON:0004534	48.23	gold quality
intestine	UBERON:0000160	47.46	gold quality
endometrium	UBERON:0001295	44.92	silver quality
corpus callosum	UBERON:0002336	44.92	silver quality
adrenal tissue	UBERON:0018303	43.88	silver quality
lymph node	UBERON:0000029	43.68	gold quality
tonsil	UBERON:0002372	43.34	gold quality
apex of heart	UBERON:0002098	43.19	silver quality
bone marrow cell	CL:0002092	42.97	gold quality
skeletal muscle tissue	UBERON:0001134	42.75	gold quality
ganglionic eminence	UBERON:0004023	41.24	silver quality
hindlimb stylopod muscle	UBERON:0004252	41.18	silver quality
kidney	UBERON:0002113	40.95	gold quality
muscle tissue	UBERON:0002385	40.47	gold quality
lower esophagus mucosa	UBERON:0035834	40.43	silver quality
ventricular zone	UBERON:0003053	40.16	gold quality
stromal cell of endometrium	CL:0002255	39.25	gold quality
right ovary	UBERON:0002118	38.99	silver quality
liver	UBERON:0002107	37.62	gold quality
bone marrow	UBERON:0002371	37.54	gold quality
islet of Langerhans	UBERON:0000006	36.87	silver quality
right uterine tube	UBERON:0001302	36.84	silver quality
adult mammalian kidney	UBERON:0000082	36.48	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting C17orf78, 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-3646	100.00	73.56	5283
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-6753-3P	99.93	66.57	637
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-520F-3P	99.82	71.32	1216
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-7156-5P	99.64	68.81	1369
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-6513-3P	99.59	69.77	1102
HSA-MIR-4688	99.48	64.68	828
HSA-MIR-6743-5P	99.48	63.60	721
HSA-MIR-657	99.48	66.02	848
HSA-MIR-4273	99.45	67.93	1206
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-8085	99.28	67.56	2362
HSA-MIR-6731-5P	99.28	67.42	2375
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-4795-5P	99.11	66.90	876
HSA-MIR-4699-5P	98.99	67.50	1210

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gm11437	ENSMUSG00000051452
rattus_norvegicus	C10h17orf78	ENSRNOG00000028116

Protein

Protein identifiers

Uncharacterized protein C17orf78 — Q8N4C9 (reviewed: Q8N4C9)

All UniProt accessions (1): Q8N4C9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N4C9-1	1	yes
Q8N4C9-2	2

RefSeq proteins (2): NP_001308328, NP_775896* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031668	DUF4711	Family

Pfam: PF15829

UniProt features (9 total): region of interest 2, compositionally biased region 2, splice variant 2, chain 1, transmembrane region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N4C9-F1	46.08	0.03

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (showing top): MIDORIKAWA_AMPLIFIED_IN_LIVER_CANCER, RYTTCCTG_ETS2_B, FREAC7_01, MIR5003_3P, MIR24_3P, MIR552_5P, GSE10463_CD40L_AND_VA347_VS_CD40L_IN_DC_UP, MIR4456, MIR6734_5P, chr17q12, NIKOLSKY_BREAST_CANCER_17Q11_Q21_AMPLICON, GAO_SMALL_INTESTINE_24W_C3_ENTEROCYTE_PROGENITOR_SUBTYPE_1, BUSSLINGER_DUODENAL_LATE_IMMATURE_ENTEROCYTES, WP_17Q12_COPY_NUMBER_VARIATION_SYNDROME, GSE2706_UNSTIM_VS_2H_LPS_DC_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

254 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C17orf78	SYNRG	Q9UMZ2	690
C17orf78	TADA2A	O75478	652
C17orf78	MRM1	Q6IN84	621
C17orf78	GGNBP2	Q9H3C7	604
C17orf78	PIGW	Q7Z7B1	600
C17orf78	DUSP14	O95147	599
C17orf78	DDX52	Q9Y2R4	594
C17orf78	ZNHIT3	Q15649	581
C17orf78	MYO19	Q96H55	575
C17orf78	OR6T1	Q8NGN1	540
C17orf78	AATF	Q9NY61	478
C17orf78	A0A087WT91	A0A087WT91	470
C17orf78	FAM221A	A4D161	434
C17orf78	DHRS11	Q6UWP2	419
C17orf78	TBC1D3G	Q6DHY5	418

IntAct

4 interactions, top by confidence:

A	B	Type	Score
C17orf78	ATP2B1	psi-mi:“MI:0914”(association)	0.350
C17orf78	SRC	psi-mi:“MI:0914”(association)	0.350

BioGRID (11): ZYX (Affinity Capture-MS), GBF1 (Affinity Capture-MS), ATP2A3 (Affinity Capture-MS), ATP2B1 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B3 (Affinity Capture-MS), ATP2B4 (Affinity Capture-MS), CELSR2 (Affinity Capture-MS), PRKAR1B (Affinity Capture-MS), NPTN (Affinity Capture-MS), SRC (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTR0, A0A1B0GTY4, A0A1B0GVD1, A7WNB0, A8R0V4, E9Q7F5, O55779, O70552, O75818, O93036, P01586, P03212, P03319, P03321, P04823, P0DOE0, P10260, P13206, P16837, P20880, P28907, P36340, P47939, P47940, Q02484, Q03233, Q1HVF6, Q2HRD2, Q3KSS3, Q3TTJ4, Q5BK38, Q5QR91, Q5VAN0, Q64277, Q66669, Q66672, Q6GQU0, Q6GVM5, Q6UWF9, Q86WR6

Diamond homologs: A6H7F9, Q5QR91, Q8N4C9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

956 predictions. Top by Δscore:

Variant	Effect	Δscore
17:37376146:GAAAG:G	donor_gain	1.0000
17:37376149:AGG:A	donor_loss	1.0000
17:37376151:G:GA	donor_loss	1.0000
17:37391642:TCTAG:T	acceptor_loss	1.0000
17:37391643:CTAG:C	acceptor_loss	1.0000
17:37391644:TA:T	acceptor_loss	1.0000
17:37376151:G:GG	donor_gain	0.9900
17:37376152:T:G	donor_loss	0.9900
17:37384705:T:TA	acceptor_gain	0.9900
17:37384714:T:A	acceptor_gain	0.9900
17:37384722:T:G	acceptor_gain	0.9900
17:37388790:GTCCT:G	donor_gain	0.9900
17:37388795:G:GG	donor_gain	0.9900
17:37391638:A:AG	acceptor_gain	0.9900
17:37391639:A:G	acceptor_gain	0.9900
17:37391641:CTCTA:C	acceptor_loss	0.9900
17:37391645:A:AG	acceptor_gain	0.9900
17:37391646:G:GG	acceptor_gain	0.9900
17:37391646:GGTT:G	acceptor_gain	0.9900
17:37384708:A:AG	acceptor_gain	0.9800
17:37384736:A:AG	acceptor_gain	0.9800
17:37391645:AGGTT:A	acceptor_gain	0.9800
17:37391646:GGTTG:G	acceptor_gain	0.9800
17:37376149:AG:A	donor_gain	0.9700
17:37376150:GG:G	donor_gain	0.9700
17:37384709:C:G	acceptor_gain	0.9700
17:37388926:C:G	donor_gain	0.9700
17:37389380:G:GA	donor_gain	0.9700
17:37376148:AAG:A	donor_gain	0.9600
17:37379135:A:AG	acceptor_gain	0.9600

AlphaMissense

1787 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:37376114:A:C	S8R	0.975
17:37376116:C:A	S8R	0.975
17:37376116:C:G	S8R	0.975
17:37376111:T:C	F7L	0.920
17:37376113:C:A	F7L	0.920
17:37376113:C:G	F7L	0.920
17:37379199:T:C	C70R	0.889
17:37388768:T:C	F203L	0.887
17:37388770:T:A	F203L	0.887
17:37388770:T:G	F203L	0.887
17:37388777:T:C	F206L	0.886
17:37388779:T:A	F206L	0.886
17:37388779:T:G	F206L	0.886
17:37391719:T:C	F275L	0.873
17:37391721:C:A	F275L	0.873
17:37391721:C:G	F275L	0.873
17:37379199:T:A	C70S	0.859
17:37379200:G:C	C70S	0.859
17:37388718:A:T	K186I	0.853
17:37388719:A:C	K186N	0.852
17:37388719:A:T	K186N	0.852
17:37379328:T:C	C113R	0.840
17:37379328:T:A	C113S	0.821
17:37379329:G:C	C113S	0.821
17:37386032:T:A	C139S	0.815
17:37386033:G:C	C139S	0.815
17:37388730:C:A	A190D	0.812
17:37388702:T:A	W181R	0.809
17:37388702:T:C	W181R	0.809
17:37386011:T:C	F132L	0.801

dbSNP variants (sampled 300 via entrez): RS1000054688 (17:37385952 C>A,T), RS1000118931 (17:37382590 G>A), RS1000176942 (17:37376835 A>G,T), RS1000195567 (17:37393137 T>C), RS1000319941 (17:37380657 G>A,C,T), RS1000405518 (17:37382284 T>C), RS1000442148 (17:37374916 C>T), RS1000474828 (17:37374654 TA>T), RS1000651047 (17:37380949 C>A), RS1000699745 (17:37377301 T>C), RS1001062952 (17:37387740 A>G), RS1001252309 (17:37379615 G>A), RS1001304735 (17:37375490 A>G), RS1001337268 (17:37380149 A>G), RS1001605484 (17:37375320 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001941_16	Ovarian cancer	8.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
fluorene-9-bisphenol	increases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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