C1orf174

Summary

C1orf174 (chromosome 1 open reading frame 174, HGNC:27915) is a protein-coding gene on chromosome 1p36.32, encoding UPF0688 protein C1orf174 (Q8IYL3).

Located in nucleoplasm.

Source: NCBI Gene 339448 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 18 total — 2 pathogenic
• MANE Select transcript: NM_207356

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27915
Approved symbol	C1orf174
Name	chromosome 1 open reading frame 174
Location	1p36.32
Locus type	gene with protein product
Status	Approved
Aliases	RP13-531C17.2
Ensembl gene	ENSG00000198912
Ensembl biotype	protein_coding
Entrez	339448

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 5 nonsense_mediated_decay, 3 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000361605, ENST00000474140, ENST00000486765, ENST00000679703, ENST00000679929, ENST00000679946, ENST00000680054, ENST00000680169, ENST00000680279, ENST00000680535, ENST00000681823

RefSeq mRNA: 1 — MANE Select: NM_207356 NM_207356

CCDS: CCDS53

Canonical transcript exons

ENST00000361605 — 4 exons

Exon	Start	End
ENSE00001891341	3900172	3900272
ENSE00003466374	3890569	3891057
ENSE00003548802	3892883	3892996
ENSE00003665457	3889133	3890073

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 98.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.8755 / max 108.5483, expressed in 1813 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
9966	19.8755	1813

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	98.21	gold quality
secondary oocyte	CL:0000655	96.54	gold quality
gingival epithelium	UBERON:0001949	89.91	gold quality
skin of hip	UBERON:0001554	89.87	gold quality
blood vessel layer	UBERON:0004797	88.81	gold quality
nephron tubule	UBERON:0001231	88.78	gold quality
hair follicle	UBERON:0002073	88.25	gold quality
granulocyte	CL:0000094	88.04	gold quality
upper leg skin	UBERON:0004262	87.86	gold quality
gingiva	UBERON:0001828	87.83	gold quality
mucosa of sigmoid colon	UBERON:0004993	87.78	gold quality
colonic mucosa	UBERON:0000317	87.52	gold quality
pylorus	UBERON:0001166	87.19	gold quality
urethra	UBERON:0000057	87.15	gold quality
seminal vesicle	UBERON:0000998	87.09	gold quality
saphenous vein	UBERON:0007318	87.01	gold quality
renal glomerulus	UBERON:0000074	86.94	gold quality
renal medulla	UBERON:0000362	86.76	gold quality
penis	UBERON:0000989	86.65	gold quality
synovial joint	UBERON:0002217	86.63	gold quality
right lobe of liver	UBERON:0001114	86.55	gold quality
superficial temporal artery	UBERON:0001614	86.55	gold quality
spleen	UBERON:0002106	86.51	gold quality
lower esophagus mucosa	UBERON:0035834	86.51	gold quality
mucosa of transverse colon	UBERON:0004991	86.39	gold quality
metanephric glomerulus	UBERON:0004736	86.37	gold quality
duodenum	UBERON:0002114	86.36	gold quality
superior surface of tongue	UBERON:0007371	86.33	gold quality
oviduct epithelium	UBERON:0004804	86.31	gold quality
lower esophagus	UBERON:0013473	86.30	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.17

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting C1orf174, 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-1277-5P	100.00	73.95	5056
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-1251-3P	99.64	67.21	1408
HSA-MIR-4452	99.50	68.45	1493
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-569	99.42	66.32	1009
HSA-MIR-4666A-5P	99.41	69.72	1887
HSA-MIR-297	99.40	69.58	1418
HSA-MIR-4426	99.17	66.74	1949

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-147a11.3	ENSDARG00000069009
mus_musculus	A430005L14Rik	ENSMUSG00000047613
rattus_norvegicus	C5h1orf174	ENSRNOG00000025034

Protein

Protein identifiers

UPF0688 protein C1orf174 — Q8IYL3 (reviewed: Q8IYL3)

All UniProt accessions (7): Q8IYL3, A0A7P0T887, A0A7P0T8I3, A0A7P0T8M5, A0A7P0TAC3, A0A7P0TAV4, A0A7P0Z4H8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Similarity. Belongs to the UPF0688 family.

RefSeq proteins (1): NP_997239* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031530	UPF0688	Family

Pfam: PF15772

UniProt features (10 total): sequence variant 3, region of interest 2, compositionally biased region 2, modified residue 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IYL3-F1	61.92	0.06

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 (2): 148, 189

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 119 (showing top): BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP, FISCHER_DREAM_TARGETS, HAN_SATB1_TARGETS_DN, MARSON_BOUND_BY_E2F4_UNSTIMULATED, MULLIGHAN_MLL_SIGNATURE_1_DN, chr1p36, JOHNSTONE_PARVB_TARGETS_3_DN, GCNP_SHH_UP_LATE.V1_UP, ATF5_TARGET_GENES, CIITA_TARGET_GENES, COBLL1_TARGET_GENES, E2F2_TARGET_GENES, E2F5_TARGET_GENES, HES2_TARGET_GENES, NFE2L1_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (2): nucleoplasm (GO:0005654), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
nuclear lumen	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

538 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C1orf174	CCDC27	Q2M243	575
C1orf174	CEP104	O60308	506
C1orf174	MRPS16	Q9Y3D3	494
C1orf174	HAGHL	Q6PII5	447
C1orf174	LRRC47	Q8N1G4	447
C1orf174	PPP1R2C	O14990	393
C1orf174	SPANXN1	Q5VSR9	390
C1orf174	DENND10	Q8TCE6	379
C1orf174	EFCAB14	O75071	377
C1orf174	BRD10	Q5HYC2	374
C1orf174	CXorf38	Q8TB03	370
C1orf174	TPRG1L	Q5T0D9	370
C1orf174	SPATA25	Q9BR10	370
C1orf174	ARL16	Q0P5N6	357
C1orf174	OSER1	Q9NX31	354

IntAct

47 interactions, top by confidence:

A	B	Type	Score
C1orf174	PDIK1L	psi-mi:“MI:0915”(physical association)	0.900
PDIK1L	CTDSPL2	psi-mi:“MI:0914”(association)	0.840
C1orf174	IKZF1	psi-mi:“MI:0915”(physical association)	0.670
IKZF1	C1orf174	psi-mi:“MI:0915”(physical association)	0.670
DCK	DGUOK	psi-mi:“MI:0914”(association)	0.620
IKZF1	C1orf174	psi-mi:“MI:0915”(physical association)	0.560
MEOX2	C1orf174	psi-mi:“MI:0915”(physical association)	0.560
STK35	HSP90AA1	psi-mi:“MI:0914”(association)	0.530
C1orf174	AHCYL1	psi-mi:“MI:0914”(association)	0.530
C1orf174	TERF2IP	psi-mi:“MI:0915”(physical association)	0.510
C1orf174	SRPK2	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
C1orf174	MYH9	psi-mi:“MI:0915”(physical association)	0.400
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
PDIK1L	HSP90AA1	psi-mi:“MI:0914”(association)	0.350
STK35	HSP90AA1	psi-mi:“MI:0914”(association)	0.350
PDIK1L	CSTB	psi-mi:“MI:0914”(association)	0.350
C1orf174	H2AC11	psi-mi:“MI:0914”(association)	0.350
EGLN3	KLK3	psi-mi:“MI:0914”(association)	0.350
C1orf174	POLRMT	psi-mi:“MI:0914”(association)	0.350

BioGRID (65): C1orf174 (Two-hybrid), C1orf174 (Two-hybrid), C1orf174 (Affinity Capture-MS), C1orf174 (Affinity Capture-MS), C1orf174 (Affinity Capture-MS), C1orf174 (Affinity Capture-MS), C1orf174 (Affinity Capture-MS), C1orf174 (Proximity Label-MS), C1orf174 (Affinity Capture-MS), C1orf174 (Two-hybrid), COPS6 (Two-hybrid), EEF1G (Two-hybrid), KAT5 (Two-hybrid), C1orf174 (Two-hybrid), C1orf174 (Two-hybrid)

ESM2 similar proteins: A0A087WXM9, A0A2K1JJ00, A0JM83, A4IGL8, E1BC15, E9Q5F9, O14513, O35923, O60673, O88491, P46013, P97929, Q14B71, Q28DZ0, Q29RT4, Q3MHH3, Q3TNU4, Q3ZBP0, Q4QY64, Q4V7J0, Q5DTT3, Q5E9A0, Q5F2C3, Q5RD08, Q5VWN6, Q5VYV7, Q61493, Q69YH5, Q6NS59, Q703I1, Q80U59, Q86XD8, Q8IXS0, Q8IYL3, Q8L7I1, Q8N7Z5, Q8NFU7, Q8TEP8, Q92628, Q96BU1

Diamond homologs: A0JM83, Q1L9C7, Q32PF7, Q3KQW6, Q5M951, Q80WR5, Q8IYL3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	9
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
144175	GRCh38/hg38 1p36.32(chr1:3712088-4027367)x4	Pathogenic
974581	Single allele	Pathogenic

SpliceAI

460 predictions. Top by Δscore:

Variant	Effect	Δscore
1:3890075:T:C	acceptor_gain	1.0000
1:3900166:CCTCA:C	donor_loss	1.0000
1:3900167:CTCAC:C	donor_loss	1.0000
1:3900168:TCAC:T	donor_loss	1.0000
1:3900169:CACC:C	donor_loss	1.0000
1:3890073:CCT:C	acceptor_gain	0.9900
1:3890078:G:GC	acceptor_gain	0.9900
1:3891053:GAAGT:G	acceptor_gain	0.9900
1:3891058:C:CC	acceptor_gain	0.9900
1:3900174:T:TA	donor_gain	0.9900
1:3890563:TCTTA:T	donor_loss	0.9800
1:3890564:CTTA:C	donor_loss	0.9800
1:3890565:TTA:T	donor_loss	0.9800
1:3890566:TACC:T	donor_loss	0.9800
1:3890568:C:A	donor_loss	0.9800
1:3891056:GT:G	acceptor_gain	0.9800
1:3891057:TCT:T	acceptor_loss	0.9800
1:3900170:A:AC	donor_gain	0.9800
1:3900170:ACCTT:A	donor_gain	0.9800
1:3900171:C:CC	donor_gain	0.9800
1:3900171:CCTT:C	donor_gain	0.9800
1:3900171:CCTTC:C	donor_gain	0.9800
1:3890072:TCC:T	acceptor_loss	0.9700
1:3890073:CC:C	acceptor_loss	0.9700
1:3890074:C:CC	acceptor_gain	0.9700
1:3890074:CTT:C	acceptor_loss	0.9700
1:3890075:T:TC	acceptor_gain	0.9700
1:3890078:G:C	acceptor_gain	0.9700
1:3891055:AGT:A	acceptor_gain	0.9700
1:3892920:T:TA	donor_gain	0.9700

AlphaMissense

1596 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:3890008:G:C	F228L	0.998
1:3890008:G:T	F228L	0.998
1:3890010:A:G	F228L	0.998
1:3890020:T:A	R224S	0.998
1:3890020:T:G	R224S	0.998
1:3890021:C:G	R224T	0.998
1:3890009:A:G	F228S	0.996
1:3890013:G:C	H227D	0.996
1:3890021:C:A	R224I	0.996
1:3890594:A:G	F198S	0.996
1:3890620:G:C	S189R	0.995
1:3890620:G:T	S189R	0.995
1:3890622:T:G	S189R	0.995
1:3890590:A:C	F199L	0.994
1:3890590:A:T	F199L	0.994
1:3890592:A:G	F199L	0.994
1:3890593:G:C	F198L	0.993
1:3890593:G:T	F198L	0.993
1:3890595:A:G	F198L	0.993
1:3890022:T:C	R224G	0.992
1:3890032:T:A	R220S	0.992
1:3890032:T:G	R220S	0.992
1:3890009:A:C	F228C	0.991
1:3890033:C:G	R220T	0.991
1:3890011:A:C	H227Q	0.988
1:3890011:A:T	H227Q	0.988
1:3890035:G:C	S219R	0.988
1:3890035:G:T	S219R	0.988
1:3890037:T:G	S219R	0.988
1:3889999:T:A	K231N	0.987

dbSNP variants (sampled 300 via entrez): RS1000177534 (1:3891773 T>A,C), RS1000256530 (1:3900384 G>C,T), RS1000329359 (1:3897389 A>G), RS1000386651 (1:3897049 G>A), RS1000543148 (1:3901240 C>A,T), RS1000998172 (1:3896751 T>C), RS1001133448 (1:3897008 T>C), RS1001236082 (1:3893412 A>T), RS1001388692 (1:3898202 T>C), RS1001949083 (1:3902177 C>A,T), RS1002172475 (1:3894707 T>C), RS1002374851 (1:3899547 C>T), RS1002525992 (1:3894030 A>G), RS1002631261 (1:3894424 A>G,T), RS1002952320 (1:3894242 T>A,C)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:607872

GenCC curated gene-disease

Mondo (2): chromosome 1p36 deletion syndrome (MONDO:0011929), megacolon (MONDO:0001273)

Orphanet (1): 1p36 deletion syndrome (Orphanet:1606)

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST002701_10	Verbal declarative memory	3.000000e-06
GCST002701_34	Verbal declarative memory	3.000000e-07
GCST002701_9	Verbal declarative memory	2.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004874	memory performance
EFO:0006805	word list delayed recall measurement

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D008531	Megacolon	C06.405.469.158.701
C535362	Chromosome 1p36 Deletion Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression, increases methylation	4
sodium arsenite	decreases expression, increases abundance	2
Arsenic	affects methylation, decreases expression, increases abundance	2
GSK-J4	increases expression	1
coumarin	decreases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Vorinostat	increases expression	1
Leflunomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Caffeine	increases phosphorylation	1
Diazinon	increases methylation	1
Diuron	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Formaldehyde	decreases expression	1
Ketoconazole	increases expression	1
Thimerosal	increases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01793168	Not specified	RECRUITING	Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT02381457	Not specified	COMPLETED	SNP-based Microdeletion and Aneuploidy RegisTry (SMART)
NCT04340856	Not specified	COMPLETED	Retrospective, Uncontrolled Cohort Study on the Therapy of Chronic Megalon
NCT07470892	Not specified	NOT_YET_RECRUITING	Preoperative Fish Oil PN and Prognosis After Constipation Surgery