C1orf87

Summary

C1orf87 (chromosome 1 open reading frame 87, HGNC:28547) is a protein-coding gene on chromosome 1p32.1, encoding Uncharacterized protein C1orf87 (Q8N0U7).

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 11 total — 1 pathogenic
• MANE Select transcript: NM_152377

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28547
Approved symbol	C1orf87
Name	chromosome 1 open reading frame 87
Location	1p32.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC34837, CREF
Ensembl gene	ENSG00000162598
Ensembl biotype	protein_coding
OMIM	618860
Entrez	127795

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000371201, ENST00000450089, ENST00000486478, ENST00000488027, ENST00000491817, ENST00000957187

RefSeq mRNA: 1 — MANE Select: NM_152377 NM_152377

CCDS: CCDS614

Canonical transcript exons

ENST00000371201 — 12 exons

Exon	Start	End
ENSE00001066704	60037992	60038107
ENSE00001066705	60055204	60055438
ENSE00001066706	60040991	60041131
ENSE00001066707	60039917	60040180
ENSE00001173639	60025401	60025498
ENSE00001266678	60033476	60033641
ENSE00001454606	60072537	60072670
ENSE00001454607	60073690	60073770
ENSE00001809459	59990394	59990833
ENSE00003467850	60010392	60010456
ENSE00003577672	59997609	59997816
ENSE00003690313	60001077	60001156

Expression profiles

Bgee: expression breadth ubiquitous, 110 present calls, max score 96.64.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2186 / max 47.0922, expressed in 64 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12593	0.1579	56
12592	0.0606	31

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	96.64	gold quality
bronchus	UBERON:0002185	95.15	gold quality
right uterine tube	UBERON:0001302	94.91	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.44	gold quality
mucosa of paranasal sinus	UBERON:0005030	84.81	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	83.64	gold quality
oviduct epithelium	UBERON:0004804	83.39	gold quality
left testis	UBERON:0004533	79.99	gold quality
fallopian tube	UBERON:0003889	79.68	gold quality
right testis	UBERON:0004534	78.92	gold quality
epithelium of nasopharynx	UBERON:0001951	78.41	gold quality
buccal mucosa cell	CL:0002336	78.11	gold quality
testis	UBERON:0000473	77.57	gold quality
caudate nucleus	UBERON:0001873	70.60	gold quality
right lung	UBERON:0002167	70.29	gold quality
sperm	CL:0000019	68.06	gold quality
kidney epithelium	UBERON:0004819	66.77	gold quality
nasal cavity mucosa	UBERON:0001826	66.66	gold quality
cardiac muscle of right atrium	UBERON:0003379	64.31	gold quality
nucleus accumbens	UBERON:0001882	64.22	gold quality
hypothalamus	UBERON:0001898	64.21	gold quality
left ventricle myocardium	UBERON:0006566	64.08	gold quality
amygdala	UBERON:0001876	61.60	gold quality
left uterine tube	UBERON:0001303	60.89	gold quality
caput epididymis	UBERON:0004358	60.87	gold quality
descending thoracic aorta	UBERON:0002345	60.41	gold quality
trachea	UBERON:0003126	60.03	silver quality
adult organism	UBERON:0007023	59.30	silver quality
tibialis anterior	UBERON:0001385	57.93	silver quality
superior vestibular nucleus	UBERON:0007227	57.85	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.86

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting C1orf87, 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-3064-3P	100.00	70.09	1254
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-6760-5P	98.87	66.73	1515
HSA-MIR-26B-3P	98.71	67.49	1102
HSA-MIR-6780A-3P	98.42	67.49	1518
HSA-MIR-10226	98.25	66.50	811
HSA-MIR-203B-3P	97.82	66.27	979
HSA-MIR-4676-5P	97.54	65.29	715
HSA-MIR-575	97.54	65.18	718
HSA-MIR-6858-3P	96.37	64.41	771
HSA-MIR-6861-5P	96.23	67.19	800
HSA-MIR-103B	95.51	66.85	441
HSA-MIR-4765	93.11	66.17	737

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gm12695	ENSMUSG00000078639
rattus_norvegicus	C5h1orf87	ENSRNOG00000026169

Protein

Protein identifiers

Uncharacterized protein C1orf87 — Q8N0U7 (reviewed: Q8N0U7)

All UniProt accessions (2): C9JPP7, Q8N0U7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell projection. Cilium. Cytoplasm. Cytoskeleton. Cilium axoneme.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N0U7-1	1	yes
Q8N0U7-2	2
Q8N0U7-3	3

RefSeq proteins (1): NP_689590* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR040774	DUF5580	Family
IPR048316	DUF5580_N	Domain
IPR049246	DUF5580_M	Domain
IPR049247	DUF5580_C	Domain

Pfam: PF17743, PF20742, PF20743

UniProt features (15 total): sequence variant 5, region of interest 3, compositionally biased region 3, splice variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N0U7-F1	63.36	0.13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 40 (showing top): LHX3_01, FREAC3_01, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, FOXJ2_02, GOCC_CYTOPLASMIC_REGION, TAATTA_CHX10_01, GOCC_CILIUM, DODD_NASOPHARYNGEAL_CARCINOMA_DN, TST1_01, RAO_BOUND_BY_SALL4_ISOFORM_A, PRDM12_TARGET_GENES, ZNF213_TARGET_GENES, ZNF577_TARGET_GENES, ZNF781_TARGET_GENES, MIR6861_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): cilium (GO:0005929), axoneme (GO:0005930)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cytoskeleton	1
microtubule	1
ciliary plasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

410 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C1orf87	SHISA9	B4DS77	425
C1orf87	ZWINT	O95229	382
C1orf87	CFAP210	Q0VFZ6	308
C1orf87	CDC50A	Q9NV96	301
C1orf87	CFAP77	Q6ZQR2	297
C1orf87	TRDN	Q13061	291
C1orf87	CCDC17	Q96LX7	287
C1orf87	C1orf141	Q5JVX7	267
C1orf87	LOX	P28300	266
C1orf87	NES	P48681	250
C1orf87	GJB2	P29033	248
C1orf87	FYB2	Q5VWT5	247
C1orf87	GAPDH	P00354	247
C1orf87	SPACA9	Q96E40	247
C1orf87	ZP3	P21754	246
C1orf87	C9orf40	Q8IXQ3	246

IntAct

6 interactions, top by confidence:

A	B	Type	Score
C1orf87	LRRK2	psi-mi:“MI:0407”(direct interaction)	0.440
C1orf87	RPS16	psi-mi:“MI:0915”(physical association)	0.400
C1orf87	SNX2	psi-mi:“MI:0914”(association)	0.350
MINPP1	MGAT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (35): C1orf87 (Reconstituted Complex), SNX5 (Affinity Capture-MS), SNX1 (Affinity Capture-MS), CDK5RAP2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), HEPACAM (Affinity Capture-MS), SARM1 (Affinity Capture-MS), PCNT (Affinity Capture-MS), C1orf87 (Affinity Capture-MS), AKAP9 (Affinity Capture-MS), HERC1 (Affinity Capture-MS), PDE4DIP (Affinity Capture-MS), PPM1B (Affinity Capture-MS), UBR4 (Affinity Capture-MS), PPP2R2D (Affinity Capture-MS)

ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A2AGB2, A2ALV5, A3KMW7, A6NM62, A8MT70, A9JRX0, D3Z987, P15975, P56716, P70347, Q0P5X5, Q0VET5, Q28FY7, Q2M2Z5, Q3MHT3, Q3U0P1, Q3U3V8, Q3UXL4, Q3V089, Q5SXH7, Q5T1N1, Q5T4T6, Q5VXU9, Q68CR7, Q6NZK5, Q6P2D8, Q7M6U3, Q7Z4H7, Q7Z572, Q7ZYI3, Q7ZZH7, Q80VP2, Q86T90, Q86YC2, Q8BG34, Q8BL06, Q8CCC3, Q8MJ03

Diamond homologs: A2AGB2, Q8N0U7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	6
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
3063410	GRCh37/hg19 1p32.1-31.3(chr1:59121165-62057570)x1	Pathogenic

SpliceAI

1935 predictions. Top by Δscore:

Variant	Effect	Δscore
1:60025399:A:AC	donor_gain	1.0000
1:60025400:C:CC	donor_gain	1.0000
1:60033646:T:TC	acceptor_gain	1.0000
1:60040012:G:C	donor_gain	1.0000
1:60055202:A:AC	donor_gain	1.0000
1:60055203:C:CC	donor_gain	1.0000
1:60072530:GACTT:G	donor_loss	1.0000
1:60072531:ACTT:A	donor_loss	1.0000
1:60072532:CTTA:C	donor_loss	1.0000
1:60072533:TTA:T	donor_loss	1.0000
1:60072534:TA:T	donor_loss	1.0000
1:60072535:A:AC	donor_gain	1.0000
1:60072535:ACAT:A	donor_gain	1.0000
1:60072536:C:CC	donor_gain	1.0000
1:60072536:CA:C	donor_gain	1.0000
1:60072536:CAT:C	donor_gain	1.0000
1:60072536:CATC:C	donor_gain	1.0000
1:60072536:CATCT:C	donor_gain	1.0000
1:60072575:T:TA	donor_gain	1.0000
1:60072668:TCC:T	acceptor_gain	1.0000
1:60072668:TCCC:T	acceptor_loss	1.0000
1:60072669:CC:C	acceptor_gain	1.0000
1:60072669:CCC:C	acceptor_gain	1.0000
1:60072670:CC:C	acceptor_gain	1.0000
1:60072670:CCTAG:C	acceptor_loss	1.0000
1:60072671:C:CC	acceptor_gain	1.0000
1:60072671:C:CG	acceptor_loss	1.0000
1:59990865:T:C	acceptor_gain	0.9900
1:59990865:T:TC	acceptor_gain	0.9900
1:59997621:G:C	donor_gain	0.9900

AlphaMissense

3618 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:59990730:G:C	F528L	0.975
1:59990730:G:T	F528L	0.975
1:59990732:A:G	F528L	0.975
1:60039941:A:C	F241L	0.964
1:60039941:A:T	F241L	0.964
1:60039943:A:G	F241L	0.964
1:59990686:A:G	L543S	0.957
1:59990803:A:G	L504P	0.955
1:60010455:A:G	W377R	0.950
1:60010455:A:T	W377R	0.950
1:59997647:A:G	L481P	0.948
1:59997669:A:G	W474R	0.948
1:59997669:A:T	W474R	0.948
1:59997635:A:G	L485P	0.945
1:59997656:A:G	F478S	0.945
1:60033522:A:G	F328S	0.942
1:59990677:A:G	L546P	0.941
1:60025486:A:G	C348R	0.939
1:59990695:A:G	L540P	0.936
1:59990787:A:C	N509K	0.936
1:59990787:A:T	N509K	0.936
1:59990682:C:A	K544N	0.934
1:59990682:C:G	K544N	0.934
1:59990773:A:G	L514P	0.930
1:59997635:A:T	L485H	0.928
1:59997639:C:G	A484P	0.927
1:59997655:G:C	F478L	0.927
1:59997655:G:T	F478L	0.927
1:59997657:A:G	F478L	0.927
1:59997667:C:A	W474C	0.925

dbSNP variants (sampled 300 via entrez): RS1000046124 (1:60008490 G>A,C), RS1000093610 (1:60062741 T>A,G), RS1000148257 (1:60020802 C>T), RS1000157856 (1:60059083 TA>T,TAA), RS1000168857 (1:60065574 T>A), RS1000204666 (1:60014754 T>C), RS1000205704 (1:60073184 C>A), RS1000223113 (1:60026978 C>G), RS1000225283 (1:60075688 C>T), RS1000280535 (1:60069572 C>T), RS1000282559 (1:60056159 G>A,T), RS1000283306 (1:60065331 G>C), RS1000288469 (1:60028359 T>C), RS1000315650 (1:60008724 T>C), RS1000363361 (1:60075196 T>G)

Disease associations

OMIM: gene MIM:618860 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): primary ovarian failure (MONDO:0005387)

Orphanet (1): NON RARE IN EUROPE: Primary ovarian failure (Orphanet:619)

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST002136_4	Periodontitis (PAL4Q3)	4.000000e-06
GCST002930_4	Cobalt levels	1.000000e-06
GCST003542_146	Night sleep phenotypes	2.000000e-06
GCST003628_9	Clozapine-induced agranulocytosis/granulocytopenia in treatment-resistant schizophrenia	8.000000e-06
GCST003997_9	Myopia	6.000000e-13
GCST004860_98	Alcoholic chronic pancreatitis	1.000000e-06
GCST007692_124	Chronic obstructive pulmonary disease	4.000000e-09
GCST012309_14	Schizophrenia	9.000000e-07

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D016649	Primary Ovarian Insufficiency	C12.050.351.500.056.630.750; C12.100.250.056.630.750; C19.391.630.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases methylation, affects cotreatment	1
kojic acid	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Arbutin	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00417066	PHASE4	COMPLETED	Flexible GnRH Antagonist vs Flare up GnRH Agonist Protocol in Poor Responders
NCT00732693	PHASE4	COMPLETED	Evaluation of Physiologic and Standard Sex Steroid Replacement Regimens in Women With Premature Ovarian Failure
NCT00837616	PHASE4	COMPLETED	Estrogen Dosing in Turner Syndrome: Pharmacology and Metabolism
NCT01853501	PHASE4	UNKNOWN	Effects of ADSC Therapy in Women With POF
NCT02783937	PHASE4	COMPLETED	Filgrastim for Premature Ovarian Insufficiency
NCT03535480	PHASE4	UNKNOWN	Autologous Bone Marrow Stem Cell Ovarian Transplantation to Restore Ovarian Function in Premature Ovarian Failure
NCT00140998	PHASE3	COMPLETED	Estrogen Treatment (Oral vs. Patches) in Turner Syndrome
NCT00001951	PHASE2	COMPLETED	Hormone Replacement in Young Women With Premature Ovarian Failure
NCT00370019	PHASE2	WITHDRAWN	Effects of an Estrogen Replacement Therapy Skin Patch on Ovulation in Women With Premature Ovarian Failure
NCT00429494	PHASE2	COMPLETED	GnRH Analogue for Ovarian Function Preservation in Hematopoietic Stem Cell Transplantation Patients
NCT03816852	PHASE2	SUSPENDED	The Safety and Efficiency Study of Mesenchymal Stem Cell (19#iSCLife®-POI) in Premature Ovarian Insufficiency
NCT04536467	PHASE2	UNKNOWN	Prevention of Chemotherapy-Induced Ovarian Failure With Goserelin in Premenopausal Lymphoma Patients
NCT06117982	PHASE2	COMPLETED	The Impact of Granulocyte Colony Stimulating Factor on Premature Ovarian Insufficiency
NCT02912104	PHASE1	COMPLETED	A Therapeutic Trial of Human Amniotic Epithelial Cells Transplantation for Primary Ovarian Failure
NCT03178695	PHASE1	COMPLETED	Inovium Ovarian Rejuvenation Trials
NCT04815213	PHASE1	ACTIVE_NOT_RECRUITING	The Use of Expandeded Mesenchymal Stromal Cells (MSC) in Premature Ovarian Failure (POF) in Adult Humans
NCT05138367	PHASE1	COMPLETED	Effects of UCA-PSCs in Women With POF
NCT06132542	PHASE1	UNKNOWN	Autologous ADMSC Transplantation in Patients With POI
NCT00948857	PHASE2/PHASE3	TERMINATED	Dehydroepiandrosterone (DHEA) Treatment and Premature Ovarian Failure (POF)
NCT04031456	PHASE2/PHASE3	RECRUITING	Autologous PRP Infusion May Restore Ovarian Function and May Promote Folliculogenesis in POI Patients
NCT02043743	PHASE1/PHASE2	UNKNOWN	Autologous Stem Cells Transplantation in Patients With Idiopathic and Drug Induced Premature Ovarian Failure
NCT02062931	PHASE1/PHASE2	UNKNOWN	Autologous Mesenchymal Stem Cells Transplantation In Women With Premature Ovarian Failure
NCT02151890	PHASE1/PHASE2	COMPLETED	Pregnancy After Stem Cell Transplantation in Premature Ovarian Failure
NCT02372474	PHASE1/PHASE2	COMPLETED	It is a Real The First Baby Of Autologous Stem Cell Therapy in Premature Ovarian Failure
NCT02603744	PHASE1/PHASE2	UNKNOWN	Autologous Adipose Derived Mesenchymal Stromal Cells Transplantation in Women With Premature Ovarian Failure (POF)
NCT02644447	PHASE1/PHASE2	COMPLETED	Transplantation of HUC-MSCs With Injectable Collagen Scaffold for POF
NCT03069209	PHASE1/PHASE2	UNKNOWN	Autologous Bone Marrow-Derived Stem Cell Transplantation in Patients With Premature Ovarian Failure (POF)
NCT03985462	PHASE1/PHASE2	WITHDRAWN	Very Small Embryonic-like Stem Cells for Ovary
NCT04009473	PHASE1/PHASE2	UNKNOWN	Stem Cell Therapy and Growth Factor Ovarian in Vitro Activation
NCT04071574	PHASE1/PHASE2	COMPLETED	Comparative Study on the Efficacy of Ovarian Stimulation Protocols on the Success Rate of ICSI in Female Infertility
NCT04922398	PHASE1/PHASE2	UNKNOWN	Ovarian Injection of PRP (Platelet -Rich Plasma) Vs Normal Saline in Premature Ovarian Insufficiency
NCT05462379	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	Autologous Heterotopic Fresh Ovarian Graft in Woman With LACC Eligible for Pelvic Radiotherapy Treatment.
NCT06202547	PHASE1/PHASE2	UNKNOWN	Intra-ovarian Injection of MSC-EVs in Idiopathic Premature Ovarian Failure
NCT01129947	EARLY_PHASE1	WITHDRAWN	The Use of DHEA in Women With Premature Ovarian Failure
NCT05522634	EARLY_PHASE1	UNKNOWN	A Clinical Study of Chinese Herbal Compound TJAOA101 in the Treatment of Premature Ovarian Insufficiency
NCT07308327	EARLY_PHASE1	ACTIVE_NOT_RECRUITING	The Influence of Gut Microbiota on Ovarian Function: A Single-center, Randomized,Double Blind, Parallel-controlled, Exploratory Clinical Trial
NCT00001275	Not specified	COMPLETED	Ovarian Follicle Function in Patients With Primary Ovarian Failure
NCT00001306	Not specified	COMPLETED	Steroid Therapy in Autoimmune Premature Ovarian Failure
NCT00006156	Not specified	COMPLETED	Feasibility Study for Development of an Early Test for Ovarian Failure
NCT00119925	Not specified	UNKNOWN	‘SPRING’-Study: Subfertility Guidelines: Patient Related Implementation in the Netherlands Among Gynaecologists