C17orf58

Summary

C17orf58 (chromosome 17 open reading frame 58, HGNC:27568) is a protein-coding gene on chromosome 17q24.2, encoding UPF0450 protein C17orf58 (Q2M2W7). It is a selective cancer dependency (DepMap: 37.3% of cell lines).

Located in collagen-containing extracellular matrix.

Source: NCBI Gene 284018 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 8 total
• Cancer dependency (DepMap): dependent in 37.3% of screened cell lines
• MANE Select transcript: NM_001382359

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27568
Approved symbol	C17orf58
Name	chromosome 17 open reading frame 58
Location	17q24.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000186665
Ensembl biotype	protein_coding
Entrez	284018

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000334461, ENST00000449250, ENST00000536693, ENST00000580729, ENST00000912770

RefSeq mRNA: 3 — MANE Select: NM_001382359 NM_001382359, NM_181655, NM_181656

CCDS: CCDS42375, CCDS45765, CCDS92385

Canonical transcript exons

ENST00000580729 — 4 exons

Exon	Start	End
ENSE00002521700	67991099	67992103
ENSE00002685946	67993424	67993984
ENSE00002701134	67996123	67996469
ENSE00003796474	67993044	67993235

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 96.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.4453 / max 163.7675, expressed in 1690 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
167704	7.1294	1687
167709	0.3158	96

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
synovial joint	UBERON:0002217	96.53	gold quality
vena cava	UBERON:0004087	95.81	gold quality
mammalian vulva	UBERON:0000997	95.34	gold quality
epithelium of mammary gland	UBERON:0003244	94.35	gold quality
mammary duct	UBERON:0001765	94.31	gold quality
layer of synovial tissue	UBERON:0007616	93.62	gold quality
bronchial epithelial cell	CL:0002328	93.49	gold quality
bronchus	UBERON:0002185	93.08	gold quality
placenta	UBERON:0001987	92.33	gold quality
urethra	UBERON:0000057	91.05	gold quality
germinal epithelium of ovary	UBERON:0001304	90.85	gold quality
mammary gland	UBERON:0001911	90.82	gold quality
thoracic mammary gland	UBERON:0005200	90.81	gold quality
oviduct epithelium	UBERON:0004804	90.70	gold quality
Brodmann (1909) area 23	UBERON:0013554	90.58	gold quality
tibia	UBERON:0000979	89.83	gold quality
endometrium	UBERON:0001295	89.82	gold quality
parietal pleura	UBERON:0002400	89.79	gold quality
cortical plate	UBERON:0005343	89.54	gold quality
palpebral conjunctiva	UBERON:0001812	89.29	gold quality
penis	UBERON:0000989	89.13	gold quality
pericardium	UBERON:0002407	89.08	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.02	gold quality
decidua	UBERON:0002450	89.02	gold quality
secondary oocyte	CL:0000655	88.99	gold quality
esophagus squamous epithelium	UBERON:0006920	88.50	gold quality
epithelial cell of pancreas	CL:0000083	88.00	silver quality
pigmented layer of retina	UBERON:0001782	87.88	gold quality
oral cavity	UBERON:0000167	87.57	gold quality
middle temporal gyrus	UBERON:0002771	87.54	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	12.20
E-MTAB-6142	no	58.41

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 37.3% of screened cell lines.

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	1810010H24Rik	ENSMUSG00000078607
rattus_norvegicus	C10h17orf58	ENSRNOG00000043295

Protein

Protein identifiers

UPF0450 protein C17orf58 — Q2M2W7 (reviewed: Q2M2W7)

All UniProt accessions (3): A0A8J8YVE6, A0A8J8ZI57, Q2M2W7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the UPF0450 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q2M2W7-1	1	yes
Q2M2W7-2	2

RefSeq proteins (3): NP_001369288, NP_858041, NP_858042 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001134	Netrin_domain	Domain
IPR008993	TIMP-like_OB-fold	Homologous_superfamily

UniProt features (13 total): compositionally biased region 4, disulfide bond 3, signal peptide 1, chain 1, splice variant 1, sequence variant 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q2M2W7-F1	65.41	0.29

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (3): 208–338, 193–267, 197–271

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 116 (showing top): TAL1ALPHAE47_01, CAGGTCC_MIR492, FREAC3_01, OCT1_07, HIF1_Q3, TGGNNNNNNKCCAR_UNKNOWN, POU3F2_02, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, TAL1BETAE47_01, YGCGYRCGC_UNKNOWN, ZF5_01, GEORGES_TARGETS_OF_MIR192_AND_MIR215, TAL1BETAITF2_01, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_UP

GO Biological Process (0):

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

GO Cellular Component (1): extracellular matrix (GO:0031012)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
external encapsulating structure	1

Protein interactions and networks

STRING

660 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C17orf58	BPTF	Q12830	494
C17orf58	ANKFN1	Q8N957	447
C17orf58	SLC35G1	Q2M3R5	427
C17orf58	OR7D2	Q96RA2	401
C17orf58	C1QTNF4	Q9BXJ3	388
C17orf58	KLHL38	Q2WGJ6	357
C17orf58	KIF9	Q9HAQ2	337
C17orf58	GDPGP1	Q6ZNW5	336
C17orf58	Q53S48	Q53S48	324
C17orf58	CFAP46	Q8IYW2	322
C17orf58	ZZEF1	O43149	320
C17orf58	ERVV-2	B6SEH9	320
C17orf58	NPIPB11	E5RHQ5	313
C17orf58	PPM1D	O15297	310
C17orf58	ADPRHL1	Q8NDY3	303

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0U1RR11, A0A0U1RRI6, A6NCS6, A6NJG2, B0BN44, D3YXK1, E9PY61, E9Q0B3, F5H4A9, O00220, O00221, P09038, P0DPI3, P22083, P98077, Q08AU9, Q2M2W7, Q2M3V2, Q2TBI2, Q5F267, Q5FW56, Q5IS69, Q5R866, Q5T4W7, Q5TM52, Q5U4P2, Q5VTJ3, Q659K9, Q673H1, Q69ZB3, Q6AYE8, Q6IPT2, Q6PJ61, Q7RTU4, Q7TSX9, Q7YR31, Q80SU3, Q86SH2, Q86Y97, Q8NBR0

Diamond homologs: A2BDC9, Q08AU9, Q2M2W7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

477 predictions. Top by Δscore:

Variant	Effect	Δscore
17:67993056:CTGG:C	donor_gain	1.0000
17:67993243:C:CT	acceptor_gain	1.0000
17:67992100:CTGC:C	acceptor_gain	0.9900
17:67992102:GCCT:G	acceptor_gain	0.9900
17:67992965:A:AC	donor_gain	0.9900
17:67992965:ACAG:A	donor_gain	0.9900
17:67992965:ACAGC:A	donor_gain	0.9900
17:67992966:C:CC	donor_gain	0.9900
17:67992966:CAG:C	donor_gain	0.9900
17:67992966:CAGC:C	donor_gain	0.9900
17:67992966:CAGCC:C	donor_gain	0.9900
17:67993069:A:AC	donor_gain	0.9900
17:67993243:C:T	acceptor_gain	0.9900
17:67993244:G:T	acceptor_gain	0.9900
17:67992099:GCTGC:G	acceptor_gain	0.9800
17:67992100:CTGCC:C	acceptor_gain	0.9800
17:67992101:TGCC:T	acceptor_gain	0.9800
17:67992104:C:CC	acceptor_gain	0.9800
17:67993012:A:C	donor_gain	0.9800
17:67993014:ATG:A	donor_gain	0.9800
17:67993015:T:C	donor_gain	0.9800
17:67993098:TGTGG:T	donor_gain	0.9800
17:67993236:C:CC	acceptor_gain	0.9800
17:67992102:GCC:G	acceptor_loss	0.9700
17:67992104:C:CG	acceptor_loss	0.9700
17:67992105:T:A	acceptor_loss	0.9700
17:67992960:G:GT	donor_gain	0.9700
17:67993010:A:AC	donor_gain	0.9700
17:67993011:C:CC	donor_gain	0.9700
17:67993014:A:AC	donor_gain	0.9700

AlphaMissense

2164 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:67991967:A:C	F80L	0.973
17:67991967:A:T	F80L	0.973
17:67991969:A:G	F80L	0.973
17:67992091:A:T	I39N	0.955
17:67992063:T:A	R48S	0.948
17:67992063:T:G	R48S	0.948
17:67992084:C:A	M41I	0.947
17:67992084:C:G	M41I	0.947
17:67992084:C:T	M41I	0.947
17:67992066:C:A	K47N	0.942
17:67992066:C:G	K47N	0.942
17:67992083:C:G	G42R	0.941
17:67991970:C:A	R79S	0.928
17:67991970:C:G	R79S	0.928
17:67992004:C:T	G68E	0.921
17:67992007:T:A	D67V	0.921
17:67992010:C:A	G66V	0.921
17:67992082:C:A	G42V	0.910
17:67992064:C:G	R48T	0.908
17:67992011:C:A	G66W	0.907
17:67992064:C:A	R48I	0.906
17:67992082:C:T	G42D	0.903
17:67993114:G:C	F11L	0.901
17:67993114:G:T	F11L	0.901
17:67993116:A:G	F11L	0.901
17:67992005:C:G	G68R	0.900
17:67992005:C:T	G68R	0.900
17:67992008:C:G	D67H	0.898
17:67992076:A:T	I44N	0.898
17:67992074:A:C	Y45D	0.896

dbSNP variants (sampled 300 via entrez): RS11079714 (17:67997875 C>G,T), RS111275281 (17:67998400 G>A), RS111513436 (17:67996891 G>A,C,T), RS111513651 (17:67993106 C>A,T), RS111815984 (17:67998307 G>A,T), RS112215615 (17:67998291 G>C), RS112416132 (17:67998301 A>G), RS112612674 (17:67992964 T>C), RS112662999 (17:67996894 A>G,T), RS113012247 (17:67994514 G>A,T), RS113368729 (17:67997292 C>G,T), RS113421199 (17:67991385 A>G), RS113470373 (17:67996900 C>T), RS113985803 (17:67993855 G>A,C,T), RS115269584 (17:67991279 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

10 associations (top):

Study	Trait	p-value
GCST006922_1	Regular attendance at a religious group	2.000000e-06
GCST006923_7	Loneliness	6.000000e-09
GCST006924_5	Loneliness (MTAG)	1.000000e-09
GCST007326_95	Number of sexual partners	2.000000e-12
GCST007515_21	Type 2 diabetes	7.000000e-07
GCST007517_29	Type 2 diabetes	1.000000e-07
GCST008129_29	Body mass index	1.000000e-11
GCST008151_112	Waist circumference	3.000000e-06
GCST008160_64	Waist circumference	3.000000e-06
GCST010703_274	Brain morphology (MOSTest)	1.000000e-15

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0009592	social interaction measurement
EFO:0007865	loneliness measurement
EFO:0004340	body mass index
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases abundance, increases expression, decreases expression	2
Tretinoin	decreases expression	2
Cadmium Chloride	decreases expression	2
Particulate Matter	increases abundance, increases expression, decreases expression	2
aristolochic acid I	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
K 7174	decreases expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Doxorubicin	increases expression	1
Nickel	increases expression	1
Quercetin	decreases expression	1
Smoke	decreases expression	1
Tunicamycin	decreases expression	1
Urethane	increases expression	1
Valproic Acid	affects expression	1
1-Methyl-4-phenylpyridinium	increases expression	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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