C3orf22

Summary

C3orf22 (chromosome 3 open reading frame 22, HGNC:28534) is a protein-coding gene on chromosome 3q21.3, encoding Uncharacterized protein C3orf22 (Q8N5N4).

Located in cytoplasm.

Source: NCBI Gene 152065 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 66 total
• MANE Select transcript: NM_152533

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28534
Approved symbol	C3orf22
Name	chromosome 3 open reading frame 22
Location	3q21.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC34728
Ensembl gene	ENSG00000180697
Ensembl biotype	protein_coding
Entrez	152065

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 nonsense_mediated_decay

ENST00000318225, ENST00000505070

RefSeq mRNA: 1 — MANE Select: NM_152533 NM_152533

CCDS: CCDS3040

Canonical transcript exons

ENST00000318225 — 4 exons

Exon	Start	End
ENSE00001218978	126551997	126552122
ENSE00001218993	126549692	126550078
ENSE00001219000	126553302	126553430
ENSE00003842761	126558627	126558932

Expression profiles

Bgee: expression breadth broad, 25 present calls, max score 91.93.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0408 / max 32.4781, expressed in 3 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
44353	0.0241	3
44354	0.0064	3
44352	0.0061	3
44355	0.0042	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	91.93	gold quality
left testis	UBERON:0004533	91.20	gold quality
sperm	CL:0000019	88.43	gold quality
testis	UBERON:0000473	87.61	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.58	silver quality
adult organism	UBERON:0007023	62.31	silver quality
pancreatic ductal cell	CL:0002079	60.43	silver quality
endothelial cell	CL:0000115	58.93	gold quality
buccal mucosa cell	CL:0002336	56.59	gold quality
vena cava	UBERON:0004087	56.24	gold quality
kidney epithelium	UBERON:0004819	55.20	gold quality
epithelial cell of pancreas	CL:0000083	54.70	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
ileal mucosa	UBERON:0000331	52.87	silver quality
tibialis anterior	UBERON:0001385	51.20	silver quality
oocyte	CL:0000023	51.14	gold quality
myocardium	UBERON:0002349	50.25	gold quality
deltoid	UBERON:0001476	49.77	gold quality
cauda epididymis	UBERON:0004360	49.25	gold quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
quadriceps femoris	UBERON:0001377	46.72	gold quality
layer of synovial tissue	UBERON:0007616	46.62	gold quality
synovial joint	UBERON:0002217	46.45	gold quality
vastus lateralis	UBERON:0001379	45.40	gold quality
middle temporal gyrus	UBERON:0002771	45.04	gold quality
muscle tissue	UBERON:0002385	44.42	gold quality
amniotic fluid	UBERON:0000173	44.12	gold quality
skeletal muscle tissue	UBERON:0001134	44.09	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting C3orf22, 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-4267	99.96	66.53	2368
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-7109-5P	99.18	66.13	1057
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-4763-5P	98.75	63.89	854
HSA-MIR-548S	98.50	67.17	1213

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	BC048671	ENSMUSG00000049694
rattus_norvegicus	C4h3orf22	ENSRNOG00000025934

Protein

Protein identifiers

Uncharacterized protein C3orf22 — Q8N5N4 (reviewed: Q8N5N4)

All UniProt accessions (1): Q8N5N4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N5N4-1	1	yes
Q8N5N4-2	2

RefSeq proteins (1): NP_689746* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038782	C3orf22	Family

UniProt features (2 total): chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N5N4-F1	67.00	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): chr3q21, GSE13522_WT_VS_IFNG_KO_SKIN_DN, GSE14026_TH1_VS_TH17_UP, GSE15324_ELF4_KO_VS_WT_ACTIVATED_CD8_TCELL_DN, DESCARTES_MAIN_FETAL_THYMIC_EPITHELIAL_CELLS, GSE21033_CTRL_VS_POLYIC_STIM_DC_6H_DN, GSE22935_UNSTIM_VS_48H_MBOVIS_BCG_STIM_MYD88_KO_MACROPHAGE_DN, GSE22443_NAIVE_VS_ACT_AND_IL12_TREATED_CD8_TCELL_DN, GSE27241_WT_VS_RORGT_KO_TH17_POLARIZED_CD4_TCELL_UP, GSE21063_CTRL_VS_ANTI_IGM_STIM_BCELL_16H_DN, GSE46606_UNSTIM_VS_CD40L_IL2_IL5_3DAY_STIMULATED_IRF4HIGH_SORTED_BCELL_DN, GSE41176_WT_VS_TAK1_KO_ANTI_IGM_STIM_BCELL_1H_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

116 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C3orf22	RNASE12	Q5GAN4	621
C3orf22	C12orf56	Q8IXR9	620
C3orf22	SMIM17	P0DL12	608
C3orf22	SH2D7	A6NKC9	596
C3orf22	C1orf167	Q5SNV9	591
C3orf22	CC2D2B	Q6DHV5	591
C3orf22	C22orf42	Q6IC83	590
C3orf22	ANKRD62	A6NC57	583
C3orf22	SPDYE4	A6NLX3	581
C3orf22	CLPSL1	A2RUU4	578
C3orf22	EPCIP	Q9NYP8	576
C3orf22	RD3L	P0DJH9	574
C3orf22	SMIM21	Q3B7S5	572
C3orf22	MGAT4D	A6NG13	544
C3orf22	SPATA12	Q7Z6I5	541

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0B4J1N3, A0A1B0GTK4, A0A1B0GTR0, A0JNL8, A2RUT3, A4IFR0, C9JUS6, D3ZKM3, E9PXB6, F2Z3F1, O70899, O71302, O93195, O95411, P03165, P04610, P0C7M3, P12912, P13206, P20976, P20977, P29560, P47939, P47940, P69714, Q02919, Q08648, Q1RN00, Q1WG82, Q5PR19, Q66669, Q67923, Q69027, Q69604, Q6PDA7, Q6UWK7, Q80IU5, Q80IU8, Q8N5N4, Q913A9

Diamond homologs: Q32PB5, Q8C5S3, Q8N5N4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	60
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1350 predictions. Top by Δscore:

Variant	Effect	Δscore
3:126551995:A:AC	donor_gain	1.0000
3:126551995:AC:A	donor_gain	1.0000
3:126551996:C:CC	donor_gain	1.0000
3:126551996:CC:C	donor_gain	1.0000
3:126551996:CCCT:C	donor_gain	1.0000
3:126553315:T:TA	donor_gain	1.0000
3:126553426:CATGG:C	acceptor_gain	1.0000
3:126553427:ATGG:A	acceptor_gain	1.0000
3:126553428:TGG:T	acceptor_gain	1.0000
3:126553429:GG:G	acceptor_gain	1.0000
3:126553429:GGC:G	acceptor_loss	1.0000
3:126553431:C:CC	acceptor_gain	1.0000
3:126553432:T:G	acceptor_loss	1.0000
3:126541721:T:A	acceptor_gain	0.9900
3:126541724:C:A	acceptor_gain	0.9900
3:126541731:AG:A	acceptor_gain	0.9900
3:126541732:GG:G	acceptor_gain	0.9900
3:126541732:GGA:G	acceptor_gain	0.9900
3:126541732:GGACC:G	acceptor_gain	0.9900
3:126551990:GACTT:G	donor_loss	0.9900
3:126551991:ACTTA:A	donor_loss	0.9900
3:126551992:CTTAC:C	donor_loss	0.9900
3:126551994:T:TG	donor_loss	0.9900
3:126551995:A:C	donor_loss	0.9900
3:126552122:CCT:C	acceptor_loss	0.9900
3:126552123:C:CG	acceptor_loss	0.9900
3:126552124:TGCAA:T	acceptor_loss	0.9900
3:126553296:CCGCA:C	donor_loss	0.9900
3:126553297:CGCAC:C	donor_loss	0.9900
3:126553299:CACCT:C	donor_loss	0.9900

AlphaMissense

897 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:126549964:G:C	F110L	0.974
3:126549964:G:T	F110L	0.974
3:126549966:A:G	F110L	0.974
3:126549965:A:G	F110S	0.903
3:126552014:C:A	R66S	0.899
3:126552014:C:G	R66S	0.899
3:126552027:A:G	L62S	0.899
3:126553310:A:C	F27L	0.898
3:126553310:A:T	F27L	0.898
3:126553312:A:G	F27L	0.898
3:126549980:A:G	L105S	0.890
3:126552009:A:G	I68T	0.888
3:126549993:A:G	W101R	0.878
3:126549993:A:T	W101R	0.878
3:126549991:C:A	W101C	0.877
3:126549991:C:G	W101C	0.877
3:126553322:A:C	F23L	0.872
3:126553322:A:T	F23L	0.872
3:126553324:A:G	F23L	0.872
3:126549969:G:T	R109S	0.870
3:126549989:T:A	E102V	0.868
3:126549965:A:C	F110C	0.858
3:126552035:C:A	Q59H	0.848
3:126552035:C:G	Q59H	0.848
3:126552122:C:A	R30S	0.846
3:126552122:C:G	R30S	0.846
3:126549988:T:A	E102D	0.826
3:126549988:T:G	E102D	0.826
3:126552015:C:A	R66M	0.821
3:126549966:A:C	F110V	0.813

dbSNP variants (sampled 300 via entrez): RS1000045188 (3:126545734 T>C), RS1000072177 (3:126532101 T>G), RS1000190774 (3:126539558 T>TGC), RS1000300113 (3:126532789 A>G), RS1000316401 (3:126550122 G>A), RS1000342153 (3:126560614 T>C), RS1000395911 (3:126560926 C>A,T), RS1000486227 (3:126532537 A>G), RS1000533511 (3:126544234 C>T), RS1000549130 (3:126537597 C>T), RS1000843897 (3:126549878 C>A,G,T), RS1000915339 (3:126555639 T>G), RS1000977417 (3:126537777 A>G), RS1000996474 (3:126543861 C>T), RS1001045561 (3:126544115 C>G,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

1 associations (top):

Study	Trait	p-value
GCST90002393_246	Monocyte count	7.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005091	monocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs1054097	C3orf22, CHST13		0.00	0

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	2
Aflatoxin B1	decreases expression, increases methylation	2
terbufos	increases methylation	1
tebuconazole	decreases expression	1
Grape Seed Proanthocyanidins	increases expression, affects cotreatment	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Catechin	affects cotreatment, increases expression	1
Copper	affects cotreatment, decreases expression	1
Diazinon	increases methylation	1
Fonofos	increases methylation	1
Parathion	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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