C5orf47

Summary

C5orf47 (chromosome 5 open reading frame 47, HGNC:27026) is a protein-coding gene on chromosome 5q35.2, encoding Uncharacterized protein C5orf47 (Q569G3).

At a glance

• Gene–disease (curated): neuromyelitis optica (Limited, GenCC)
• GWAS associations: 10
• Clinical variants (ClinVar): 4 total — 1 pathogenic
• MANE Select transcript: NM_001144954

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27026
Approved symbol	C5orf47
Name	chromosome 5 open reading frame 47
Location	5q35.2
Locus type	gene with protein product
Status	Approved
Aliases	LOC133491
Ensembl gene	ENSG00000185056
Ensembl biotype	protein_coding
OMIM	620002
Entrez	133491

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000340147, ENST00000522195

RefSeq mRNA: 1 — MANE Select: NM_001144954 NM_001144954

CCDS: CCDS47343

Canonical transcript exons

ENST00000340147 — 5 exons

Exon	Start	End
ENSE00001290978	173998153	173998238
ENSE00001370189	173989170	173989588
ENSE00001386012	173999700	173999799
ENSE00001434049	174004271	174006140
ENSE00003680731	174001196	174001231

Expression profiles

Bgee: expression breadth broad, 56 present calls, max score 88.16.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1914 / max 202.0861, expressed in 4 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
60317	0.0950	4
60316	0.0817	4
60315	0.0147	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.16	gold quality
right testis	UBERON:0004534	86.29	gold quality
left testis	UBERON:0004533	85.49	gold quality
secondary oocyte	CL:0000655	85.24	gold quality
testis	UBERON:0000473	84.36	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.09	gold quality
buccal mucosa cell	CL:0002336	79.21	gold quality
oocyte	CL:0000023	74.94	gold quality
adult organism	UBERON:0007023	68.82	gold quality
sperm	CL:0000019	49.06	silver quality
skin of hip	UBERON:0001554	48.57	silver quality
Brodmann (1909) area 9	UBERON:0013540	47.50	gold quality
anterior cingulate cortex	UBERON:0009835	47.36	gold quality
prefrontal cortex	UBERON:0000451	47.34	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	47.17	gold quality
islet of Langerhans	UBERON:0000006	46.26	gold quality
putamen	UBERON:0001874	46.14	gold quality
upper leg skin	UBERON:0004262	46.12	silver quality
nucleus accumbens	UBERON:0001882	46.04	gold quality
neocortex	UBERON:0001950	44.97	gold quality
frontal cortex	UBERON:0001870	44.96	gold quality
right frontal lobe	UBERON:0002810	44.26	gold quality
cerebral cortex	UBERON:0000956	43.95	gold quality
caudate nucleus	UBERON:0001873	43.86	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
amygdala	UBERON:0001876	42.68	gold quality
forebrain	UBERON:0001890	42.44	gold quality
skeletal muscle tissue	UBERON:0001134	41.99	gold quality
vastus lateralis	UBERON:0001379	41.87	gold quality
quadriceps femoris	UBERON:0001377	41.82	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

101 targeting C5orf47, 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-126-5P	100.00	72.71	3180
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-7-1-3P	99.91	71.53	4384

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	4930524B15Rik	ENSMUSG00000020299
rattus_norvegicus	C10h5orf47	ENSRNOG00000027852

Protein

Protein identifiers

Uncharacterized protein C5orf47 — Q569G3 (reviewed: Q569G3)

All UniProt accessions (1): Q569G3

RefSeq proteins (1): NP_001138426* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031464	DUF4680	Family

Pfam: PF15730

UniProt features (3 total): chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q569G3-F1	62.69	0.14

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, MEISSNER_BRAIN_HCP_WITH_H3_UNMETHYLATED, MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, FOSTER_KDM1A_TARGETS_UP, RYBP_TARGET_GENES, ZFP91_TARGET_GENES, ZNF10_TARGET_GENES, MIR5696, MIR340_5P, MIR7_1_3P, MIR7_2_3P, MIR126_5P, MIR587

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

130 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C5orf47	C10orf120	Q5SQS8	671
C5orf47	CCDC27	Q2M243	604
C5orf47	SAXO1	Q8IYX7	587
C5orf47	FAM194C	Q8ND61	576
C5orf47	CCDC185	Q8N715	571
C5orf47	TRIM42	Q8IWZ5	539
C5orf47	LYPD4	Q6UWN0	531
C5orf47	C14orf119	Q9NWQ9	515
C5orf47	CBY2	Q8NA61	489
C5orf47	ZPLD1	Q8TCW7	483
C5orf47	ZNF606	Q8WXB4	479
C5orf47	DMRTC2	Q8IXT2	477
C5orf47	CFAP299	Q6V702	477
C5orf47	INSL6	Q9Y581	445
C5orf47	TGIF2LX	Q8IUE1	431
C5orf47	ARB2A	Q8WUF8	431

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GUT2, A0A1B0GVM6, A0JNL8, A2RU37, A4D1N5, A6NF83, A8MU10, B1ANY3, D3ZF18, F1MQW7, F2Z3F1, O71302, O93195, O95411, P06926, P0C686, P0C689, P0DJI6, P20976, P20977, P24026, Q06250, Q24JP4, Q3ZN08, Q4R3X9, Q52M75, Q569G3, Q5PR19, Q5W5W9, Q66669, Q67923, Q69604, Q6DGF6, Q6NUI1, Q6UYE1, Q6ZP68, Q7L4S7, Q7Z4H9, Q80IU5, Q80IU8

Diamond homologs: Q24JP4, Q569G3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
146333	GRCh38/hg38 5q35.2(chr5:173949773-174900395)x1	Pathogenic

SpliceAI

920 predictions. Top by Δscore:

Variant	Effect	Δscore
5:173989338:G:GG	donor_gain	0.9900
5:173989429:G:GT	donor_gain	0.9900
5:173989429:G:T	donor_gain	0.9900
5:173989929:T:G	donor_gain	0.9900
5:173989976:G:GT	donor_gain	0.9900
5:173989977:A:T	donor_gain	0.9900
5:173998255:GAGAA:G	donor_gain	0.9900
5:174001184:T:G	acceptor_gain	0.9900
5:174001231:GGTAA:G	donor_loss	0.9900
5:174001232:GTA:G	donor_loss	0.9900
5:174001233:T:TC	donor_loss	0.9900
5:173989379:GCCTT:G	donor_gain	0.9800
5:174001183:ATGTT:A	acceptor_gain	0.9800
5:174001190:TTGCA:T	acceptor_loss	0.9800
5:174001191:TGCAG:T	acceptor_loss	0.9800
5:174001192:GCA:G	acceptor_loss	0.9800
5:174001193:CAGGC:C	acceptor_loss	0.9800
5:174001194:A:AC	acceptor_loss	0.9800
5:174001232:G:GG	donor_gain	0.9800
5:174001234:AA:A	donor_loss	0.9800
5:174001183:AT:A	acceptor_gain	0.9700
5:174001194:A:AG	acceptor_gain	0.9700
5:174001194:AGG:A	donor_loss	0.9700
5:174001195:G:GG	acceptor_gain	0.9700
5:174001228:TCTGG:T	acceptor_loss	0.9700
5:174001229:CTGG:C	acceptor_loss	0.9700
5:174001230:TGGTA:T	acceptor_loss	0.9700
5:174001232:G:T	acceptor_loss	0.9700
5:174001184:T:TA	acceptor_gain	0.9600
5:174001187:T:A	acceptor_loss	0.9600

AlphaMissense

1122 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:173999740:T:C	M151T	0.988
5:173989324:T:C	F21L	0.985
5:173989326:C:A	F21L	0.985
5:173989326:C:G	F21L	0.985
5:173999741:G:A	M151I	0.981
5:173999741:G:C	M151I	0.981
5:173999741:G:T	M151I	0.981
5:173999752:A:T	N155I	0.977
5:173999709:T:A	W141R	0.973
5:173999709:T:C	W141R	0.973
5:173999740:T:G	M151R	0.973
5:173999753:T:A	N155K	0.973
5:173999753:T:G	N155K	0.973
5:173999731:T:G	I148S	0.967
5:173999731:T:C	I148T	0.964
5:173999731:T:A	I148N	0.963
5:173999765:A:C	R159S	0.963
5:173999765:A:T	R159S	0.963
5:173998188:T:C	F121L	0.962
5:173998190:T:A	F121L	0.962
5:173998190:T:G	F121L	0.962
5:173999751:A:C	N155H	0.960
5:173999773:T:C	L162P	0.960
5:173998189:T:C	F121S	0.958
5:173999751:A:G	N155D	0.957
5:173999751:A:T	N155Y	0.956
5:173999752:A:C	N155T	0.950
5:173999764:G:C	R159T	0.947
5:173989306:T:C	F15L	0.944
5:173989308:C:A	F15L	0.944

dbSNP variants (sampled 300 via entrez): RS1000005521 (5:174005059 G>A), RS1000104273 (5:173988214 C>G,T), RS1000316627 (5:173998451 A>G), RS1000325513 (5:173992228 G>T), RS1000357360 (5:173992928 A>G), RS1000359588 (5:174003376 G>A), RS1000445967 (5:173989780 C>G,T), RS1000456000 (5:174008263 T>C,G), RS1000530666 (5:174000052 G>A), RS1000779166 (5:173989969 A>G), RS1000913301 (5:173994276 A>C,G), RS1000964828 (5:174001463 T>A,C), RS1001152025 (5:173993910 A>G), RS1001399626 (5:173996669 C>A), RS1001418969 (5:174001137 T>C)

Disease associations

OMIM: gene MIM:620002 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
neuromyelitis optica	Limited	Autosomal dominant

Mondo (1): neuromyelitis optica (MONDO:0019100)

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST009356_6	Nonsyndromic cleft palate	6.000000e-06
GCST009357_12	Nonsyndromic cleft lip	4.000000e-06
GCST90020024_936	A body shape index	3.000000e-09
GCST90020024_939	A body shape index	1.000000e-09
GCST90020024_940	A body shape index	2.000000e-09
GCST90020025_979	Waist-to-hip ratio adjusted for BMI	1.000000e-08
GCST90020027_708	Waist-hip index	6.000000e-09
GCST90020029_1493	Waist circumference adjusted for body mass index	2.000000e-08
GCST90020029_1496	Waist circumference adjusted for body mass index	3.000000e-08
GCST90020029_1497	Waist circumference adjusted for body mass index	3.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0003959	cleft lip
EFO:0007789	BMI-adjusted waist circumference
EFO:0007788	BMI-adjusted waist-hip ratio

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D009471	Neuromyelitis Optica	C10.114.375.600.500; C10.114.375.800; C10.292.700.550.500; C10.314.350.600.500; C10.314.350.800; C11.640.576.695; C20.111.258.250.550.500; C20.111.258.250.775

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases methylation	1
trichostatin A	increases expression	1
bisphenol S	increases methylation	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00304291	PHASE4	COMPLETED	A Pilot Study of Mitoxantrone for the Treatment of Recurrent Neuromyelitis Optica (Devic’s Disease)
NCT02021825	PHASE4	UNKNOWN	Efficacy and Safety of Mitoxantrone in Patients With Refractory Neuromyelitis Optica and Spectrum Disorders
NCT02809079	PHASE4	UNKNOWN	Mycophenolate Mofetil Treatment With Neuromyelitis Optica Spectrum Disorders in Chinese Patients
NCT04256252	PHASE4	COMPLETED	Rituximab at Low dosE for neuromyelitiS optiCa spectrUm disordEr (RESCUE)
NCT05269667	PHASE4	TERMINATED	A Study In Neuromyelitis Optica Spectrum Disorder (NMOSD) With Satralizumab As An Intervention
NCT06180278	PHASE4	ACTIVE_NOT_RECRUITING	Long-term, Open-label, Safety Study of Inebilizumab in Neuromyelitis Optica Spectrum Disorder (NMOSD)
NCT06212245	PHASE4	UNKNOWN	A Clinical Research Study of Inebilizumab in Neuromyelitis Optica Spectrum Disorders
NCT01892345	PHASE3	TERMINATED	A Randomized Controlled Trial of Eculizumab in AQP4 Antibody-positive Participants With NMO (PREVENT Study)
NCT02003144	PHASE3	COMPLETED	An Open Label Extension Trial of Eculizumab in Relapsing NMO Patients
NCT02028884	PHASE3	COMPLETED	Efficacy and Safety Study of Satralizumab (SA237) as Add-on Therapy to Treat Participants With Neuromyelitis Optica (NMO) and NMO Spectrum Disorder (NMOSD)
NCT02073279	PHASE3	COMPLETED	Efficacy and Safety Study of Satralizumab (SA237) as Monotherapy to Treat Participants With Neuromyelitis Optica (NMO) and Neuromyelitis Optica Spectrum Disorder (NMOSD)
NCT02398994	PHASE3	TERMINATED	A Multicentre randomiSed Controlled TRial of IntraVEnous Immunoglobulin Versus Standard Therapy for Transverse Myelitis
NCT03330418	PHASE3	TERMINATED	A Phase III Study of TACI-antibody Fusion Protein Injection (RC18) in Subjects With Neuromyelitis Optica Spectrum Disorders
NCT04201262	PHASE3	COMPLETED	An Efficacy and Safety Study of Ravulizumab in Adult Participants With NMOSD
NCT04660539	PHASE3	COMPLETED	A Study to Evaluate the Safety and Efficacy of Satralizumab in Participants With Neuromyelitis Optica Spectrum Disorder (NMOSD)
NCT05199688	PHASE3	RECRUITING	A Study To Evaluate Pharmacokinetics, Efficacy, Safety, Tolerability, And Pharmacodynamics Of Satralizumab In Pediatric Patients With Aquaporin-4 Antibody Positive Neuromyelitis Optica Spectrum Disorder (NMOSD)
NCT05314010	PHASE3	ACTIVE_NOT_RECRUITING	A Study of MIL62 in Patients With Neuromyelitis Optica Spectrum Disorder (NMOSD)
NCT05730699	PHASE3	ACTIVE_NOT_RECRUITING	Efficacy and Safety of Divozilimab in Patients With Neuromyelitis Optica Spectrum Disorders (AQUARELLE)
NCT06724809	PHASE3	ACTIVE_NOT_RECRUITING	Efficacy, Safety, PK, PD, and ADA of Eculizumab in Chinese Adults With NMOSD
NCT07132398	PHASE3	NOT_YET_RECRUITING	Slow vs. Rapid Glucocorticoids Tapering With Inebilizumab in NMOSD
NCT07557420	PHASE3	NOT_YET_RECRUITING	Efficacy, Safety, Pharmacokinetics, Pharmacodynamics, and Immunogenicity Study of Ravulizumab in Chinese Adults With Neuromyelitis Optica Spectrum Disorder (NMOSD)
NCT00716066	PHASE2	ACTIVE_NOT_RECRUITING	Autologous Stem Cell Transplant for Neurologic Autoimmune Diseases
NCT01845584	PHASE2	COMPLETED	Phase II Clinical Trial of NPB-01 in Patients With Anti-aquaporin 4 Antibody Positive Neuromyelitis Optica Spectrum Disorder Not Provided Adequate Effect of Therapy to Steroids Plus Therapy.
NCT02166346	PHASE2	COMPLETED	Safety and Efficacy of Sustained Release Dalfampridine in Transverse Myelitis (Re-Launch)
NCT02249676	PHASE2	COMPLETED	Autologous Mesenchymal Stem Cells for the Treatment of Neuromyelitis Optica Spectrum Disorders
NCT02893111	PHASE2	COMPLETED	Efficacy and Safety of Bortezomib as add-on Treatment in Relapsing Neuromyelitis Optica Spectrum Disorder
NCT04064944	PHASE2	UNKNOWN	Comparison of the Efficacy and Safety of Immunoadsorption and Plasma Exchange for Acute Attack of Refractory Neuromyelitis Optica Spectrum Disorders
NCT04614454	PHASE2	COMPLETED	High Frequency Impulse Therapy for Neuropathic Pain in NMOSD
NCT04670770	PHASE2	COMPLETED	An Open Label Study of the Effects of SHR1459 in NMOSDs Patients
NCT05356858	PHASE2	TERMINATED	An Open Label Study of the Effects and Safety of Zanubrutinib in NMOSDs Adult Patients
NCT05549258	PHASE2	RECRUITING	Study of Inebilizumab in Pediatric Subjects With Neuromyelitis Optica Spectrum Disorder
NCT05551598	PHASE2	COMPLETED	Efficacy and Safety of Mitoxantrone Hydrochloride Liposome Injection in the Treatment of Neuromyelitis Optica Spectrum Disorder (NMOSD)
NCT06497374	PHASE2	NOT_YET_RECRUITING	FcRn Antagonists (Efgartigimod) for Acute NMOSD Attack
NCT06697535	PHASE2	RECRUITING	A Study to Evaluate the Efficacy and Safety of JYP0061 in Patients With Acute Neuromyelitis Spectrum Disease (NMOSD)
NCT00501748	PHASE1	COMPLETED	Safety and Tolerability of Rituximab in Neuromyelitis Optica
NCT01759602	PHASE1	COMPLETED	C1-esterase Inhibitor (Cinryze) for Acute Treatment of Neuromyelitis Optica Exacerbation
NCT01777412	PHASE1	COMPLETED	Efficacy of Bevacizumab (Avastin) in Treatment of Acute NMO Exacerbations
NCT02087813	PHASE1	WITHDRAWN	Pilot Study of alpha1-antitrypsin to Treat Neuromyelitis Optica Relapses
NCT02276963	PHASE1	COMPLETED	Ublituximab for Acute Neuromyelitis Optica (NMO) Relapses
NCT02283671	PHASE1	COMPLETED	Treatment of Multiple Sclerosis and Neuromyelitis Optica With Regulatory Dendritic Cell: Clinical Trial Phase 1 B