C3orf80

Summary

C3orf80 (chromosome 3 open reading frame 80, HGNC:40048) is a protein-coding gene on chromosome 3q25.33, encoding Uncharacterized membrane protein C3orf80 (F5H4A9).

Predicted to be located in membrane.

Source: NCBI Gene 401097 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_001168214

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40048
Approved symbol	C3orf80
Name	chromosome 3 open reading frame 80
Location	3q25.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000180044
Ensembl biotype	protein_coding
Entrez	401097

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 nonsense_mediated_decay

ENST00000326474, ENST00000490320

RefSeq mRNA: 1 — MANE Select: NM_001168214 NM_001168214

CCDS: CCDS54667

Canonical transcript exons

ENST00000326474 — 1 exons

Exon	Start	End
ENSE00001230110	160225422	160228213

Expression profiles

Bgee: expression breadth ubiquitous, 160 present calls, max score 90.33.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2063 / max 64.1693, expressed in 298 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
39574	0.7633	165
39573	0.2486	139
203003	0.1064	30
39572	0.0586	21
39575	0.0294	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	90.33	gold quality
Brodmann (1909) area 23	UBERON:0013554	88.87	gold quality
Brodmann (1909) area 46	UBERON:0006483	87.03	gold quality
prefrontal cortex	UBERON:0000451	85.10	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	83.51	gold quality
Brodmann (1909) area 9	UBERON:0013540	83.44	gold quality
frontal cortex	UBERON:0001870	82.18	gold quality
middle temporal gyrus	UBERON:0002771	81.79	silver quality
neocortex	UBERON:0001950	80.75	gold quality
primary visual cortex	UBERON:0002436	80.27	gold quality
right frontal lobe	UBERON:0002810	78.81	gold quality
superior frontal gyrus	UBERON:0002661	78.72	gold quality
occipital lobe	UBERON:0002021	78.59	gold quality
anterior cingulate cortex	UBERON:0009835	78.56	gold quality
cerebral cortex	UBERON:0000956	77.64	gold quality
lower esophagus mucosa	UBERON:0035834	77.60	gold quality
muscle layer of sigmoid colon	UBERON:0035805	75.51	gold quality
esophagus squamous epithelium	UBERON:0006920	72.85	silver quality
parietal lobe	UBERON:0001872	72.08	gold quality
dorsal root ganglion	UBERON:0000044	71.71	gold quality
entorhinal cortex	UBERON:0002728	71.47	silver quality
islet of Langerhans	UBERON:0000006	71.02	gold quality
postcentral gyrus	UBERON:0002581	70.61	gold quality
temporal lobe	UBERON:0001871	70.26	gold quality
esophagus mucosa	UBERON:0002469	69.18	gold quality
cerebellum	UBERON:0002037	68.61	gold quality
amygdala	UBERON:0001876	68.46	gold quality
cerebellar cortex	UBERON:0002129	68.45	gold quality
cerebellar hemisphere	UBERON:0002245	68.42	gold quality
stromal cell of endometrium	CL:0002255	67.56	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

67 targeting C3orf80, 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-4795-3P	100.00	74.62	4024
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	1110032F04Rik	ENSMUSG00000046999
rattus_norvegicus	C2h3orf80	ENSRNOG00000009803

Protein

Protein identifiers

Uncharacterized membrane protein C3orf80 — F5H4A9 (reviewed: F5H4A9)

All UniProt accessions (2): F5H4A9, A0A1W2PNY3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001161686* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031696	DUF4719	Family

Pfam: PF15843

UniProt features (6 total): signal peptide 1, chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-F5H4A9-F1	60.73	0.01

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (1): 57

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 77 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP, GAVIN_FOXP3_TARGETS_CLUSTER_T4, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP, CHEN_METABOLIC_SYNDROM_NETWORK, chr3q25, CHYLA_CBFA2T3_TARGETS_DN, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP, STK33_DN, STK33_SKM_DN, GSE13522_CTRL_VS_T_CRUZI_G_STRAIN_INF_SKIN_UP, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNAR_KO_DN, GSE13522_WT_VS_IFNAR_KO_SKING_T_CRUZI_Y_STRAIN_INF_UP, ZNF596_TARGET_GENES, ZSCAN30_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

198 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C3orf80	REDIC1	Q86WS4	595
C3orf80	CLMB	Q96GX8	503
C3orf80	RPP21	Q9H633	479
C3orf80	OTOL1	A6NHN0	447
C3orf80	TMEM51	Q9NW97	447
C3orf80	TRMT44	Q8IYL2	446
C3orf80	LRRC49	Q8IUZ0	444
C3orf80	RNF225	M0QZC1	402
C3orf80	SLC35B3	Q9H1N7	372
C3orf80	BCAS4	Q8TDM0	366
C3orf80	ZNF584	Q8IVC4	355
C3orf80	COLGALT1	Q8NBJ5	350
C3orf80	SNTG2	Q9NY99	348
C3orf80	RSPH3	Q86UC2	323
C3orf80	RNF126	Q9BV68	323

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0U1RR11, A0A0U1RRI6, A6NCS6, A6NJG2, B0BN44, D3YXK1, E9PY61, E9Q0B3, F5H4A9, O00220, O00221, P09038, P0DPI3, P22083, P98077, Q08AU9, Q2M2W7, Q2M3V2, Q2TBI2, Q5F267, Q5FW56, Q5IS69, Q5R866, Q5T4W7, Q5TM52, Q5U4P2, Q5VTJ3, Q659K9, Q673H1, Q69ZB3, Q6AYE8, Q6IPT2, Q6PJ61, Q7RTU4, Q7TSX9, Q7YR31, Q80SU3, Q86SH2, Q86Y97, Q8NBR0

Diamond homologs: E9Q0B3, F5H4A9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

346 predictions. Top by Δscore:

Variant	Effect	Δscore
3:160227829:A:AG	acceptor_gain	0.9900
3:160227830:G:GG	acceptor_gain	0.9900
3:160227830:GTTT:G	acceptor_gain	0.9900
3:160227722:CCTT:C	acceptor_gain	0.9800
3:160227150:A:AG	acceptor_gain	0.9700
3:160226287:G:T	donor_gain	0.9500
3:160227721:CCCTT:C	acceptor_gain	0.9300
3:160227725:T:TC	acceptor_gain	0.9300
3:160227720:GCCC:G	acceptor_loss	0.9200
3:160227721:CCC:C	acceptor_loss	0.9200
3:160227723:CTTT:C	acceptor_loss	0.9200
3:160227724:T:A	acceptor_loss	0.9200
3:160226291:T:TA	donor_gain	0.9100
3:160227719:CGCC:C	acceptor_gain	0.9000
3:160227738:A:C	acceptor_loss	0.9000
3:160226231:TC:T	donor_gain	0.8900
3:160227830:GTT:G	acceptor_gain	0.8700
3:160226287:G:GT	donor_gain	0.8600
3:160226641:G:GT	donor_gain	0.8600
3:160227163:T:G	acceptor_gain	0.8600
3:160227721:CC:C	acceptor_gain	0.8600
3:160227676:T:TG	acceptor_gain	0.8400
3:160227725:T:C	acceptor_gain	0.8400
3:160226570:C:CA	acceptor_gain	0.8300
3:160227743:A:C	acceptor_loss	0.8300
3:160227723:C:CC	acceptor_gain	0.7700
3:160227724:T:C	acceptor_gain	0.7700
3:160227741:A:C	acceptor_loss	0.7600
3:160226227:G:GT	donor_gain	0.7500
3:160227151:A:G	acceptor_gain	0.7500

AlphaMissense

1522 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:160225907:T:A	L91H	1.000
3:160225919:G:A	G95D	1.000
3:160225885:G:A	G84R	0.999
3:160225885:G:C	G84R	0.999
3:160225886:G:A	G84E	0.999
3:160225895:T:A	I87N	0.999
3:160225913:C:A	A93D	0.999
3:160225918:G:C	G95R	0.999
3:160225871:T:A	V79D	0.998
3:160225880:T:A	L82H	0.998
3:160225880:T:C	L82P	0.998
3:160225892:T:A	L86H	0.998
3:160225895:T:C	I87T	0.998
3:160225898:T:A	L88Q	0.998
3:160225909:T:C	F92L	0.998
3:160225910:T:C	F92S	0.998
3:160225911:C:A	F92L	0.998
3:160225911:C:G	F92L	0.998
3:160225928:T:C	L98P	0.998
3:160226240:T:C	L202P	0.998
3:160225846:T:C	F71L	0.997
3:160225848:C:A	F71L	0.997
3:160225848:C:G	F71L	0.997
3:160225876:A:G	K81E	0.997
3:160225889:T:C	L85P	0.997
3:160225892:T:C	L86P	0.997
3:160225898:T:C	L88P	0.997
3:160225898:T:G	L88R	0.997
3:160225901:T:A	L89Q	0.997
3:160225901:T:C	L89P	0.997

dbSNP variants (sampled 300 via entrez): RS1000138680 (3:160227489 T>C), RS1000564985 (3:160224295 T>C), RS1002137719 (3:160225470 C>G), RS1002232580 (3:160225665 C>A,T), RS1002462425 (3:160226566 A>G,T), RS1003265767 (3:160228237 T>C), RS1003471952 (3:160227887 A>G), RS1003501483 (3:160227553 T>C,G), RS1004146625 (3:160225360 C>A,G), RS1004600749 (3:160223684 C>A,T), RS1005393651 (3:160227934 A>G), RS1006228681 (3:160224770 G>A), RS1006281048 (3:160225117 C>T), RS1006897324 (3:160227544 T>C), RS1006948382 (3:160227878 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

5 associations (top):

Study	Trait	p-value
GCST005531_91	Multiple sclerosis	5.000000e-07
GCST010725_1	Malaria	3.000000e-09
GCST010725_57	Malaria	2.000000e-08
GCST010725_87	Malaria	3.000000e-09
GCST90016667_2	Spleen volume	3.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Nickel	decreases expression	2
butyraldehyde	decreases expression	1
benzo(e)pyrene	decreases methylation	1
abrine	decreases expression	1
eprenetapopt	affects expression, affects reaction	1
jinfukang	affects cotreatment, decreases expression	1
Arsenic Trioxide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Coal	decreases expression, increases abundance	1
Estradiol	increases expression	1
Hydrogen Peroxide	increases expression	1
Malathion	decreases expression	1
Methapyrilene	decreases methylation	1
Smoke	decreases expression, increases abundance	1
Tretinoin	increases expression	1
Triclosan	decreases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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