C5orf24

Summary

C5orf24 (chromosome 5 open reading frame 24, HGNC:26746) is a protein-coding gene on chromosome 5q31.1, encoding UPF0461 protein C5orf24 (Q7Z6I8).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001135586

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26746
Approved symbol	C5orf24
Name	chromosome 5 open reading frame 24
Location	5q31.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ37562
Ensembl gene	ENSG00000181904
Ensembl biotype	protein_coding
Entrez	134553

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 10 protein_coding

ENST00000338051, ENST00000394976, ENST00000435259, ENST00000504727, ENST00000507390, ENST00000508791, ENST00000890487, ENST00000918493, ENST00000918494, ENST00000956993

RefSeq mRNA: 3 — MANE Select: NM_001135586 NM_001135586, NM_001300894, NM_152409

CCDS: CCDS4179, CCDS75307

Canonical transcript exons

ENST00000394976 — 2 exons

Exon	Start	End
ENSE00001520208	134845968	134846212
ENSE00001865658	134854898	134859735

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 99.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 46.8478 / max 304.5932, expressed in 1820 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
58613	41.1498	1820
58615	5.2024	1603
58617	0.4956	203

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	99.11	gold quality
visceral pleura	UBERON:0002401	98.78	gold quality
tibia	UBERON:0000979	98.51	gold quality
parietal pleura	UBERON:0002400	98.47	gold quality
renal medulla	UBERON:0000362	98.37	gold quality
cardiac muscle of right atrium	UBERON:0003379	98.33	gold quality
urethra	UBERON:0000057	98.24	gold quality
epithelium of mammary gland	UBERON:0003244	98.14	gold quality
mammary duct	UBERON:0001765	98.13	gold quality
cardia of stomach	UBERON:0001162	97.90	gold quality
epithelial cell of pancreas	CL:0000083	97.77	gold quality
postcentral gyrus	UBERON:0002581	97.77	gold quality
parietal lobe	UBERON:0001872	97.71	gold quality
layer of synovial tissue	UBERON:0007616	97.66	gold quality
subthalamic nucleus	UBERON:0001906	97.63	gold quality
medulla oblongata	UBERON:0001896	97.60	gold quality
left ventricle myocardium	UBERON:0006566	97.60	gold quality
pons	UBERON:0000988	97.58	gold quality
trigeminal ganglion	UBERON:0001675	97.52	gold quality
pericardium	UBERON:0002407	97.48	gold quality
deltoid	UBERON:0001476	97.41	gold quality
inferior vagus X ganglion	UBERON:0005363	97.39	gold quality
synovial joint	UBERON:0002217	97.38	gold quality
pylorus	UBERON:0001166	97.34	gold quality
dorsal plus ventral thalamus	UBERON:0001897	97.30	gold quality
dorsal root ganglion	UBERON:0000044	97.19	gold quality
superior vestibular nucleus	UBERON:0007227	97.19	gold quality
saphenous vein	UBERON:0007318	97.11	gold quality
tibialis anterior	UBERON:0001385	97.05	gold quality
cauda epididymis	UBERON:0004360	96.97	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

344 targeting C5orf24, 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-3163	100.00	77.23	8605
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-511-3P	99.99	68.85	1467

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch1073-44g3.1	ENSDARG00000060018
danio_rerio	C21H5orf24	ENSDARG00000113250
mus_musculus	B230219D22Rik	ENSMUSG00000045767
rattus_norvegicus	C17h5orf24	ENSRNOG00000063300

Protein

Protein identifiers

UPF0461 protein C5orf24 — Q7Z6I8 (reviewed: Q7Z6I8)

All UniProt accessions (3): Q7Z6I8, A0A1Y8EJU8, H0YAE0

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the UPF0461 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q7Z6I8-1	1	yes
Q7Z6I8-2	2

RefSeq proteins (3): NP_001129058, NP_001287823, NP_689622 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040419	DUF5568	Family

Pfam: PF17724

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z6I8-F1	54.79	0.00

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 (5): 184, 37, 121, 180, 75

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 215 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GCM_GSPT1, GTTAAAG_MIR302B, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, TGTGTGA_MIR377, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, ATTCTTT_MIR186, PARK_HSC_AND_MULTIPOTENT_PROGENITORS, BASAKI_YBX1_TARGETS_DN, FISCHER_DREAM_TARGETS, TGCCTTA_MIR124A, ATGTTTC_MIR494, chr5q31

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

424 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C5orf24	LSMEM2	Q8N112	506
C5orf24	CATSPER3	Q86XQ3	447
C5orf24	ZNF551	P17034	431
C5orf24	ANKRD13C	Q8N6S4	400
C5orf24	ZCCHC10	Q8TBK6	391
C5orf24	ZSCAN23	Q3MJ62	370
C5orf24	FAM171A2	A8MVW0	370
C5orf24	ATAD3C	Q5T2N8	369
C5orf24	RPL15	P39030	362
C5orf24	KLHL23	Q8NBE8	358
C5orf24	A0A0A6YYG8	A0A0A6YYG8	357
C5orf24	PHYHIPL	Q96FC7	349
C5orf24	ZC3H11A	O75152	343
C5orf24	PRRG4	Q9BZD6	337
C5orf24	GBF1	Q92538	324

IntAct

24 interactions, top by confidence:

A	B	Type	Score
C5orf24	EFEMP2	psi-mi:“MI:0915”(physical association)	0.560
EFEMP2	C5orf24	psi-mi:“MI:0915”(physical association)	0.560
PIAS2	C5orf24	psi-mi:“MI:0915”(physical association)	0.560
C5orf24		psi-mi:“MI:0915”(physical association)	0.560
C5orf24	MEIS1	psi-mi:“MI:0914”(association)	0.530
Naa10	MYO9A	psi-mi:“MI:0914”(association)	0.350
PCDHB15	HLA-A	psi-mi:“MI:0914”(association)	0.350
Cdkn2aip	SF1	psi-mi:“MI:0914”(association)	0.350
MMGT1	DERL1	psi-mi:“MI:0914”(association)	0.350
CREB1	NFIX	psi-mi:“MI:0914”(association)	0.350
FOXC1	NFIX	psi-mi:“MI:0914”(association)	0.350
FOXC2	ZNF536	psi-mi:“MI:0914”(association)	0.350
ARHGEF19	NUP42	psi-mi:“MI:0914”(association)	0.350
C5orf24	MYH7B	psi-mi:“MI:0914”(association)	0.350
AIM2	DDX39A	psi-mi:“MI:0914”(association)	0.350
PYHIN1	SUPT5H	psi-mi:“MI:0914”(association)	0.350
BUD13	RPSA2	psi-mi:“MI:2364”(proximity)	0.270
C5orf24	PIAS2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (65): C5orf24 (Two-hybrid), C5orf24 (Affinity Capture-MS), C5orf24 (Affinity Capture-MS), C5orf24 (Affinity Capture-MS), C5orf24 (Affinity Capture-MS), C5orf24 (Affinity Capture-MS), C5orf24 (Affinity Capture-MS), C5orf24 (Affinity Capture-MS), PKNOX2 (Affinity Capture-MS), GOPC (Affinity Capture-MS), STK11 (Affinity Capture-MS), STRADA (Affinity Capture-MS), CHFR (Affinity Capture-MS), PBX2 (Affinity Capture-MS), PBX3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2L7I0, F4JYG0, O64571, P01103, P06876, P10242, P13007, P46200, P97868, Q0E2F9, Q0WWX5, Q2HJG4, Q32KY7, Q38796, Q3T026, Q4R361, Q4R731, Q5HYM0, Q5PPV5, Q5XF11, Q641W3, Q66H65, Q66HC1, Q680Q4, Q6A037, Q6ASW7, Q6DJS0, Q6E3D4, Q6E3D5, Q6L4L4, Q71RC2, Q7Z6E9, Q7Z6I8, Q7ZXG4, Q801E2, Q80X32, Q8BWW4, Q8JZS6, Q8K3Y6, Q8L793

Diamond homologs: Q0II29, Q0V9N5, Q5NVP2, Q6INB0, Q6NXA8, Q7Z6I8, Q80X32

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	0
Likely pathogenic	0
Uncertain significance	1
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

675 predictions. Top by Δscore:

Variant	Effect	Δscore
5:134854892:T:TA	acceptor_gain	0.9900
5:134854897:GAAA:G	acceptor_gain	0.9900
5:134847078:A:AG	acceptor_gain	0.9800
5:134847079:G:GG	acceptor_gain	0.9800
5:134847079:GTAAT:G	acceptor_gain	0.9800
5:134854896:A:AG	acceptor_gain	0.9800
5:134854897:G:GG	acceptor_gain	0.9800
5:134854897:GA:G	acceptor_gain	0.9800
5:134854897:GAAAA:G	acceptor_gain	0.9800
5:134846212:GGTA:G	donor_loss	0.9700
5:134846213:G:A	donor_loss	0.9700
5:134846214:T:G	donor_loss	0.9700
5:134851266:ATTT:A	acceptor_gain	0.9700
5:134854893:G:A	acceptor_gain	0.9600
5:134854897:GAA:G	acceptor_gain	0.9600
5:134847079:GTA:G	acceptor_gain	0.9500
5:134851266:ATTTG:A	acceptor_gain	0.9500
5:134845743:G:GT	donor_gain	0.9400
5:134845981:G:GA	donor_gain	0.9400
5:134846213:G:GG	donor_gain	0.9400
5:134846210:GAG:G	donor_gain	0.9200
5:134847079:GT:G	acceptor_gain	0.9200
5:134857432:G:GG	donor_gain	0.9200
5:134845738:G:GG	donor_gain	0.9100
5:134845823:GCT:G	donor_gain	0.9100
5:134847183:GGATG:G	donor_gain	0.9100
5:134847184:GATGG:G	donor_gain	0.9100
5:134854753:AAGT:A	acceptor_gain	0.9100
5:134847079:GTAA:G	acceptor_gain	0.9000
5:134845980:T:TA	donor_gain	0.8900

AlphaMissense

1230 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:134855184:G:A	G95E	1.000
5:134855202:G:A	G101E	1.000
5:134855204:T:C	Y102H	1.000
5:134855213:A:C	S105R	1.000
5:134855215:C:A	S105R	1.000
5:134855215:C:G	S105R	1.000
5:134855220:G:A	G107D	1.000
5:134855223:G:C	R108T	1.000
5:134855224:A:C	R108S	1.000
5:134855224:A:T	R108S	1.000
5:134855232:G:A	G111E	1.000
5:134855250:G:A	G117E	1.000
5:134855252:T:C	F118L	1.000
5:134855253:T:C	F118S	1.000
5:134855253:T:G	F118C	1.000
5:134855254:T:A	F118L	1.000
5:134855254:T:G	F118L	1.000
5:134855261:A:C	S121R	1.000
5:134855263:T:A	S121R	1.000
5:134855263:T:G	S121R	1.000
5:134855268:G:A	G123D	1.000
5:134855271:G:C	R124T	1.000
5:134855272:A:C	R124S	1.000
5:134855272:A:T	R124S	1.000
5:134855280:G:A	G127E	1.000
5:134855298:G:A	G133E	1.000
5:134855309:A:C	S137R	1.000
5:134855311:C:A	S137R	1.000
5:134855311:C:G	S137R	1.000
5:134855172:G:A	G91D	0.999

dbSNP variants (sampled 300 via entrez): RS1000037532 (5:134845575 G>C), RS1000252595 (5:134842720 A>G), RS1000462474 (5:134836793 C>T), RS1000653374 (5:134853504 A>ACTT), RS1000711425 (5:134832971 G>A), RS1001081100 (5:134838851 C>T), RS1001175504 (5:134839689 A>G,T), RS1001283697 (5:134836373 A>G), RS1001471399 (5:134845478 A>G), RS1001472454 (5:134835168 T>C), RS1001526305 (5:134847892 T>G), RS1001789264 (5:134842067 G>A), RS1001957051 (5:134841923 G>C), RS1001989695 (5:134853468 A>C,G), RS1002000573 (5:134860061 G>A)

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

1 associations (top):

Study	Trait	p-value
GCST009325_87	Parkinson’s disease or first degree relation to individual with Parkinson’s disease	7.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

36 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	5
Air Pollutants	affects cotreatment, decreases expression, increases abundance	4
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
Smoke	decreases expression, increases abundance	3
trichostatin A	affects cotreatment, decreases expression	2
entinostat	decreases expression, affects cotreatment	2
Cadmium Chloride	decreases expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
FR900359	affects phosphorylation	1
TAK-243	decreases sumoylation	1
geldanamycin	increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
cobaltous chloride	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
methacrylaldehyde	increases abundance, affects cotreatment, decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
torcetrapib	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Vorinostat	decreases expression	1
Acrolein	affects cotreatment, decreases expression, increases abundance	1
Arsenic	increases abundance, affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Coal	decreases expression, increases abundance	1
Endosulfan	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Hydrogen Peroxide	increases expression	1
Manganese	decreases expression, increases abundance, affects cotreatment	1
Ozone	affects cotreatment, decreases expression, increases abundance	1

Clinical trials (associated diseases)

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