C4orf17

Summary

C4orf17 (chromosome 4 open reading frame 17, HGNC:25274) is a protein-coding gene on chromosome 4q23, encoding Uncharacterized protein C4orf17 (Q53FE4).

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 6 total — 1 pathogenic
• MANE Select transcript: NM_032149

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25274
Approved symbol	C4orf17
Name	chromosome 4 open reading frame 17
Location	4q23
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP434G072
Ensembl gene	ENSG00000138813
Ensembl biotype	protein_coding
Entrez	84103

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000326581, ENST00000477187, ENST00000503257, ENST00000514652

RefSeq mRNA: 1 — MANE Select: NM_032149 NM_032149

CCDS: CCDS3649

Canonical transcript exons

ENST00000326581 — 9 exons

Exon	Start	End
ENSE00000969990	99529815	99529958
ENSE00001906628	99511021	99511272
ENSE00001947844	99541910	99542303
ENSE00002020086	99512989	99513208
ENSE00003468737	99522500	99522709
ENSE00003522143	99539163	99539370
ENSE00003576518	99537669	99537750
ENSE00003612044	99524521	99524585
ENSE00003680408	99540412	99540455

Expression profiles

Bgee: expression breadth broad, 28 present calls, max score 94.52.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0534 / max 41.9509, expressed in 3 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
49006	0.0393	3
49007	0.0070	3
49008	0.0070	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	94.52	silver quality
kidney epithelium	UBERON:0004819	92.55	gold quality
nasal cavity epithelium	UBERON:0005384	88.54	gold quality
buccal mucosa cell	CL:0002336	88.36	gold quality
sperm	CL:0000019	87.77	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	83.45	gold quality
superficial temporal artery	UBERON:0001614	82.93	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.60	gold quality
left testis	UBERON:0004533	80.33	gold quality
right testis	UBERON:0004534	79.79	gold quality
vastus lateralis	UBERON:0001379	79.22	gold quality
testis	UBERON:0000473	78.83	gold quality
quadriceps femoris	UBERON:0001377	78.53	gold quality
mucosa of paranasal sinus	UBERON:0005030	78.26	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	76.26	gold quality
lower lobe of lung	UBERON:0008949	75.96	silver quality
upper arm skin	UBERON:0004263	75.23	gold quality
epithelial cell of pancreas	CL:0000083	73.86	gold quality
biceps brachii	UBERON:0001507	73.13	gold quality
adult organism	UBERON:0007023	72.77	gold quality
deltoid	UBERON:0001476	71.42	gold quality
vena cava	UBERON:0004087	71.01	gold quality
body of tongue	UBERON:0011876	70.49	gold quality
epithelium of nasopharynx	UBERON:0001951	70.07	gold quality
germinal epithelium of ovary	UBERON:0001304	69.82	gold quality
tongue	UBERON:0001723	69.66	gold quality
cerebellar vermis	UBERON:0004720	69.30	gold quality
saphenous vein	UBERON:0007318	69.22	gold quality
substantia nigra pars compacta	UBERON:0001965	69.20	gold quality
superior surface of tongue	UBERON:0007371	68.90	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.91

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting C4orf17, 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-5692A	100.00	74.40	6850
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-4760-5P	99.80	69.88	1619
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-8061	99.63	69.44	1411
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-3171	99.49	69.06	776
HSA-MIR-145-3P	99.33	67.66	764
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-670-3P	99.03	68.88	2404
HSA-MIR-6074	98.89	69.64	2187
HSA-MIR-455-5P	98.74	67.31	795
HSA-MIR-3928-5P	98.50	67.48	980
HSA-MIR-6806-3P	98.50	67.31	980
HSA-MIR-376A-5P	97.70	65.61	863
HSA-MIR-1227-3P	97.36	66.94	834
HSA-MIR-500B-3P	96.49	65.40	1087

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	4930579F01Rik	ENSMUSG00000012042
rattus_norvegicus	C2h4orf17	ENSRNOG00000024623

Protein

Protein identifiers

Uncharacterized protein C4orf17 — Q53FE4 (reviewed: Q53FE4)

All UniProt accessions (2): D6RHU4, Q53FE4

Isoforms (2)

UniProt ID	Names	Canonical?
Q53FE4-1	1	yes
Q53FE4-2	2

RefSeq proteins (1): NP_115525* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037394	TBATA-like	Family

Pfam: PF15256

UniProt features (13 total): region of interest 3, sequence variant 3, compositionally biased region 3, splice variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q53FE4-F1	56.75	0.13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): TTTGTAG_MIR520D, MODULE_95, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, MODULE_163, FOXN3_TARGET_GENES, NME2_TARGET_GENES, MIR579_3P, MIR664B_3P, MIR664A_3P, MIR7154_5P, MIR6806_3P, MIR3928_5P, MIR1227_3P, GSE13306_RA_VS_UNTREATED_TCONV_DN, GSE16522_ANTI_CD3CD28_STIM_VS_UNSTIM_NAIVE_CD8_TCELL_UP

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

144 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C4orf17	LKAAEAR1	Q8TD35	670
C4orf17	ZNF512	Q96ME7	578
C4orf17	ARRDC5	A6NEK1	507
C4orf17	NT5C1B	Q96P26	433
C4orf17	DNAJC17	Q9NVM6	418
C4orf17	DIPK1C	Q0P6D2	397
C4orf17	TDRD12	Q587J7	391
C4orf17	TBCK	Q8TEA7	380
C4orf17	LRMDA	Q9H2I8	371
C4orf17	ZNF536	O15090	359
C4orf17	TREML4	Q6UXN2	348
C4orf17	ADH1C	P00326	330
C4orf17	ADH7	P40394	328
C4orf17	GAGE4	P0DSO3	327
C4orf17	PGAP1	Q75T13	324

IntAct

28 interactions, top by confidence:

A	B	Type	Score
NCK2	C4orf17	psi-mi:“MI:0915”(physical association)	0.560
GRN	C4orf17	psi-mi:“MI:0915”(physical association)	0.560
C4orf17	ZNF417	psi-mi:“MI:0915”(physical association)	0.560
LONRF1	C4orf17	psi-mi:“MI:0915”(physical association)	0.560
C4orf17	ABI2	psi-mi:“MI:0915”(physical association)	0.560
C4orf17	HOMER3	psi-mi:“MI:0915”(physical association)	0.560
C4orf17	CCN2	psi-mi:“MI:0915”(physical association)	0.400
CRK	C4orf17	psi-mi:“MI:0915”(physical association)	0.370
SUV39H1	C4orf17	psi-mi:“MI:0915”(physical association)	0.370
C4orf17	KDM1A	psi-mi:“MI:0915”(physical association)	0.370
C4orf17	PRMT1	psi-mi:“MI:0915”(physical association)	0.370
NCK2	C4orf17	psi-mi:“MI:0915”(physical association)	0.000
GRN	C4orf17	psi-mi:“MI:0915”(physical association)	0.000
ZNF417	C4orf17	psi-mi:“MI:0915”(physical association)	0.000
LONRF1	C4orf17	psi-mi:“MI:0915”(physical association)	0.000
ABI2	C4orf17	psi-mi:“MI:0915”(physical association)	0.000
C4orf17	HOMER3	psi-mi:“MI:0915”(physical association)	0.000
HOMER3	C4orf17	psi-mi:“MI:0915”(physical association)	0.000
C4orf17	CHD3	psi-mi:“MI:0915”(physical association)	0.000
C4orf17	COPS6	psi-mi:“MI:0915”(physical association)	0.000
C4orf17	SH3GL3	psi-mi:“MI:0915”(physical association)	0.000
C4orf17	TUBA4A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): C4orf17 (Two-hybrid), TUBA4A (Two-hybrid), C4orf17 (Two-hybrid), C4orf17 (Two-hybrid), C4orf17 (Two-hybrid), CHD3 (Two-hybrid), COPS6 (Two-hybrid), SH3GL3 (Two-hybrid), C4orf17 (Two-hybrid), LONRF1 (Two-hybrid), ZNF417 (Two-hybrid), CTGF (Affinity Capture-MS), SRRM1 (Cross-Linking-MS (XL-MS)), KDM1A (Two-hybrid), PRMT1 (Two-hybrid)

ESM2 similar proteins: A0JNF3, A4L9P8, A5WUN7, A6H5Y1, D4AEC2, E9PV87, E9Q309, H6D7E6, O54931, P28290, Q08AD1, Q09JY9, Q1G7G9, Q2KHM9, Q2MJV9, Q2T9X8, Q3KQW7, Q3MHH7, Q49A88, Q4KLH6, Q4KM62, Q53FE4, Q5PQL8, Q5RBY6, Q5RKG1, Q5VT06, Q66H16, Q66H35, Q6A000, Q6DF94, Q6NSV7, Q6ZQ06, Q7ZX27, Q80VP2, Q8BQ48, Q8C804, Q8K2J4, Q8N0Z3, Q8NA03, Q8R2H7

Diamond homologs: Q4R616, Q53FE4, Q7TSD4, Q32KL8, Q96M53

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2427353	NC_000004.11:g.(?100239320)(100528137_?)del	Pathogenic

SpliceAI

1214 predictions. Top by Δscore:

Variant	Effect	Δscore
4:99522681:TGCCA:T	donor_gain	1.0000
4:99522715:T:G	donor_gain	1.0000
4:99524519:A:AG	acceptor_gain	1.0000
4:99524520:G:GG	acceptor_gain	1.0000
4:99540404:T:A	acceptor_gain	1.0000
4:99540455:GGT:G	donor_gain	1.0000
4:99541908:A:AG	acceptor_gain	1.0000
4:99541909:G:GG	acceptor_gain	1.0000
4:99511105:G:GT	donor_gain	0.9900
4:99522483:A:AG	acceptor_gain	0.9900
4:99522490:A:AG	acceptor_gain	0.9900
4:99522496:CTAG:C	acceptor_loss	0.9900
4:99522497:TAGG:T	acceptor_loss	0.9900
4:99522498:A:AG	acceptor_gain	0.9900
4:99522499:G:A	acceptor_loss	0.9900
4:99522499:G:GG	acceptor_gain	0.9900
4:99522499:GGCTT:G	acceptor_gain	0.9900
4:99522707:CTGGT:C	donor_loss	0.9900
4:99522710:G:C	donor_loss	0.9900
4:99522711:T:A	donor_loss	0.9900
4:99524515:TTTCA:T	acceptor_loss	0.9900
4:99524516:TTCA:T	acceptor_loss	0.9900
4:99524518:CA:C	acceptor_loss	0.9900
4:99524519:A:AT	acceptor_loss	0.9900
4:99524520:GA:G	acceptor_gain	0.9900
4:99524584:AGGT:A	donor_loss	0.9900
4:99524585:GGTA:G	donor_loss	0.9900
4:99524586:G:GA	donor_loss	0.9900
4:99524587:T:A	donor_loss	0.9900
4:99529959:G:GG	donor_gain	0.9900

AlphaMissense

2348 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:99537726:T:A	W202R	0.996
4:99537726:T:C	W202R	0.996
4:99513208:G:C	G43R	0.992
4:99537730:T:C	L203P	0.991
4:99522520:T:C	C50R	0.990
4:99537728:G:C	W202C	0.990
4:99537728:G:T	W202C	0.990
4:99522522:T:G	C50W	0.988
4:99513199:C:G	H40D	0.987
4:99537705:T:C	S195P	0.986
4:99537727:G:C	W202S	0.986
4:99537682:T:C	L187P	0.985
4:99537694:T:C	L191S	0.985
4:99513171:G:C	R30S	0.984
4:99513171:G:T	R30S	0.984
4:99539175:T:A	V214D	0.984
4:99513194:T:A	V38D	0.983
4:99522503:T:C	L44S	0.983
4:99513170:G:T	R30M	0.982
4:99537738:G:C	A206P	0.982
4:99539167:A:C	K211N	0.982
4:99539167:A:T	K211N	0.982
4:99513201:C:A	H40Q	0.981
4:99513201:C:G	H40Q	0.981
4:99522520:T:A	C50S	0.981
4:99522521:G:A	C50Y	0.981
4:99522521:G:C	C50S	0.981
4:99537673:T:C	L184P	0.981
4:99537739:C:A	A206E	0.980
4:99513170:G:C	R30T	0.979

dbSNP variants (sampled 300 via entrez): RS10000018 (4:99537291 A>G), RS1000064080 (4:99525759 T>C), RS1000079019 (4:99519715 G>A), RS1000102870 (4:99516605 G>C), RS1000157121 (4:99535156 G>A), RS1000318707 (4:99528630 G>A), RS1000387175 (4:99528368 C>A,T), RS1000441915 (4:99535366 G>C), RS1000568404 (4:99521307 A>C), RS10005769 (4:99521683 C>T), RS1000673832 (4:99542520 C>A), RS1000709578 (4:99515187 A>C), RS1000777732 (4:99513566 A>G), RS10007975 (4:99527667 C>T), RS1000871894 (4:99523976 C>T)

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

9 associations (top):

Study	Trait	p-value
GCST001822_7	Metabolite levels (MHPG)	8.000000e-06
GCST001960_8	Eating disorders	8.000000e-06
GCST002112_3	Celiac disease	5.000000e-06
GCST005356_2	Severe malaria	4.000000e-07
GCST005357_12	Severe malaria (adjusted for sickle cell variant rs334)	9.000000e-07
GCST006921_3	Regular attendance at a pub or social club	4.000000e-25
GCST007328_36	Alcohol consumption (drinks per week)	3.000000e-10
GCST008758_23	Pre-treatment viral load in HIV-1 infection	2.000000e-16
GCST90011898_160	Alanine aminotransferase levels	2.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005133	MHPG measurement
EFO:0009592	social interaction measurement
EFO:0010125	viral load

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Rotenone	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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