C2orf80

Summary

C2orf80 (chromosome 2 open reading frame 80, HGNC:34352) is a protein-coding gene on chromosome 2q33.3, encoding Uncharacterized protein C2orf80 (Q0P641).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 13 total — 2 pathogenic
• MANE Select transcript: NM_001099334

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34352
Approved symbol	C2orf80
Name	chromosome 2 open reading frame 80
Location	2q33.3
Locus type	gene with protein product
Status	Approved
Aliases	LOC389073, GONDA1
Ensembl gene	ENSG00000188674
Ensembl biotype	protein_coding
OMIM	615536
Entrez	389073

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 10 protein_coding

ENST00000341287, ENST00000423952, ENST00000428015, ENST00000449053, ENST00000451342, ENST00000451346, ENST00000453017, ENST00000962799, ENST00000962800, ENST00000962801

RefSeq mRNA: 1 — MANE Select: NM_001099334 NM_001099334

CCDS: CCDS42809

Canonical transcript exons

ENST00000341287 — 9 exons

Exon	Start	End
ENSE00001364961	208165347	208165815
ENSE00001366383	208180745	208180816
ENSE00001372513	208171988	208172075
ENSE00001376813	208170945	208171063
ENSE00001381887	208189953	208190030
ENSE00001526393	208184951	208185032
ENSE00001526394	208186946	208187061
ENSE00003515774	208182965	208183047
ENSE00003645676	208181218	208181305

Expression profiles

Bgee: expression breadth ubiquitous, 125 present calls, max score 96.39.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 2.2243 / max 215.3042, expressed in 156 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
33435	0.8017	105
33438	0.7206	93
33436	0.5605	100
33440	0.0969	49
33437	0.0252	9
33439	0.0194	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	96.39	gold quality
middle temporal gyrus	UBERON:0002771	93.15	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	93.15	gold quality
prefrontal cortex	UBERON:0000451	93.12	gold quality
anterior cingulate cortex	UBERON:0009835	92.67	gold quality
Brodmann (1909) area 23	UBERON:0013554	92.29	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.14	gold quality
amygdala	UBERON:0001876	92.07	gold quality
nucleus accumbens	UBERON:0001882	91.89	gold quality
frontal cortex	UBERON:0001870	91.81	gold quality
neocortex	UBERON:0001950	91.41	gold quality
temporal lobe	UBERON:0001871	91.28	gold quality
right frontal lobe	UBERON:0002810	91.09	gold quality
entorhinal cortex	UBERON:0002728	91.04	gold quality
cerebral cortex	UBERON:0000956	90.89	gold quality
Brodmann (1909) area 46	UBERON:0006483	90.82	gold quality
superior frontal gyrus	UBERON:0002661	90.01	gold quality
hypothalamus	UBERON:0001898	88.98	gold quality
cortical plate	UBERON:0005343	88.53	gold quality
caudate nucleus	UBERON:0001873	88.29	gold quality
Ammon’s horn	UBERON:0001954	87.98	gold quality
primary visual cortex	UBERON:0002436	87.40	gold quality
putamen	UBERON:0001874	87.09	gold quality
forebrain	UBERON:0001890	86.28	gold quality
postcentral gyrus	UBERON:0002581	86.06	gold quality
parietal lobe	UBERON:0001872	85.50	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.49	gold quality
occipital lobe	UBERON:0002021	85.22	gold quality
brain	UBERON:0000955	82.13	gold quality
substantia nigra	UBERON:0002038	81.72	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.56
E-HCAD-30	no	97.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting C2orf80, 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-4775	99.98	75.00	6394
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703
HSA-MIR-5007-3P	99.51	68.14	1242
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-103A-1-5P	99.39	67.78	1545
HSA-MIR-103A-2-5P	99.39	67.72	1577
HSA-MIR-155-5P	99.35	70.16	1509

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	D630023F18Rik	ENSMUSG00000044816

Protein

Protein identifiers

Uncharacterized protein C2orf80 — Q0P641 (reviewed: Q0P641)

All UniProt accessions (7): C9J2L1, C9J2S2, C9JAS9, C9JTX0, Q0P641, H7BZF5, H7C2Y3

RefSeq proteins (1): NP_001092804* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038776	C2orf80	Family

Pfam: PF17718

UniProt features (6 total): sequence variant 3, 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-Q0P641-F1	53.43	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 29 (showing top): MCGOWAN_RSP6_TARGETS_UP, MIKKELSEN_MCV6_LCP_WITH_H3K4ME3, MIR153_5P, MIR3658, MIR203A_3P, MIR548AN, MIR155_5P, QUINTENS_EMBRYONIC_BRAIN_RESPONSE_TO_IR, FAN_EMBRYONIC_CTX_OPC, ZHONG_PFC_MAJOR_TYPES_OPC, DESCARTES_MAIN_FETAL_OLIGODENDROCYTES, ZNF490_TARGET_GENES, OSMAN_BLOOD_CHAD63_KH_AGE_18_50YO_HIGH_DOSE_SUBJECTS_24HR_UP, GSE14413_UNSTIM_VS_IFNB_STIM_RAW264_CELLS_UP, GSE29614_DAY3_VS_DAY7_TIV_FLU_VACCINE_PBMC_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

215 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C2orf80	MGAT4D	A6NG13	662
C2orf80	SCOC	Q9UIL1	527
C2orf80	ARHGAP42	A6NI28	513
C2orf80	STMN3	Q9NZ72	498
C2orf80	BRINP1	O60477	491
C2orf80	ASTN1	O14525	488
C2orf80	ENTREP1	Q15884	479
C2orf80	PHLDB1	Q86UU1	433
C2orf80	ASTN2	O75129	432
C2orf80	TMEM25	Q86YD3	419
C2orf80	SUPT3H	O75486	417
C2orf80	HEATR3	Q7Z4Q2	403
C2orf80	SEC14L5	O43304	400
C2orf80	EPHA6	Q9UF33	399
C2orf80	INKA2	Q9NTI7	395

IntAct

0 interactions, top by confidence:

BioGRID (1): C2orf80 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GUC4, A1STV0, A6NGY3, B8NI18, O54842, O84275, O89085, P03238, P03331, P05911, P11888, P26548, P26549, P27224, P56555, P87318, Q08270, Q08588, Q0P641, Q1KN10, Q1KN12, Q1KN16, Q1KN19, Q1KN23, Q1X6X9, Q1X6Y0, Q1X6Y1, Q1X6Y7, Q1X6Z0, Q1X6Z2, Q1X6Z3, Q1X700, Q1X711, Q2YDL7, Q5BL73, Q5RDL5, Q6AY31, Q6W0C5, Q84295, Q86W67

Diamond homologs: Q0P641, Q5RDL5, Q8C3M9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	9
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
2426035	NC_000002.11:g.(?208986397)(209220029_?)del	Pathogenic
58819	GRCh38/hg38 2q33.3-34(chr2:208179265-209331482)x1	Pathogenic

SpliceAI

1468 predictions. Top by Δscore:

Variant	Effect	Δscore
2:208180739:CCTTA:C	donor_loss	1.0000
2:208180740:CTTAC:C	donor_loss	1.0000
2:208180741:TTACC:T	donor_loss	1.0000
2:208180742:TACC:T	donor_loss	1.0000
2:208180812:CTGTT:C	acceptor_gain	1.0000
2:208180817:C:CC	acceptor_gain	1.0000
2:208165813:GACC:G	acceptor_loss	0.9900
2:208165816:C:CA	acceptor_loss	0.9900
2:208165817:T:G	acceptor_loss	0.9900
2:208171987:CT:C	donor_gain	0.9900
2:208179610:C:G	acceptor_gain	0.9900
2:208180813:TGTT:T	acceptor_gain	0.9900
2:208180813:TGTTC:T	acceptor_loss	0.9900
2:208180814:GTT:G	acceptor_gain	0.9900
2:208180815:TT:T	acceptor_gain	0.9900
2:208180816:TC:T	acceptor_loss	0.9900
2:208180818:T:A	acceptor_loss	0.9900
2:208182953:A:AC	donor_gain	0.9900
2:208182954:C:CC	donor_gain	0.9900
2:208187962:C:A	donor_gain	0.9900
2:208189952:CCAA:C	donor_gain	0.9900
2:208165816:C:CC	acceptor_gain	0.9800
2:208187961:T:TA	donor_gain	0.9800
2:208189951:A:AC	donor_gain	0.9800
2:208189952:C:CC	donor_gain	0.9800
2:208171986:A:AC	donor_gain	0.9700
2:208171987:C:CC	donor_gain	0.9700
2:208182963:A:AC	donor_gain	0.9700
2:208182964:C:CC	donor_gain	0.9700
2:208165812:TGAC:T	acceptor_gain	0.9600

AlphaMissense

1250 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:208184993:A:C	F27L	0.989
2:208184993:A:T	F27L	0.989
2:208184995:A:G	F27L	0.989
2:208181258:C:G	R85P	0.972
2:208181253:C:G	A87P	0.970
2:208181231:G:T	A94D	0.947
2:208181232:C:G	A94P	0.941
2:208181243:A:G	L90S	0.938
2:208172026:A:G	L139S	0.936
2:208184994:A:G	F27S	0.931
2:208181235:A:C	Y93D	0.929
2:208181246:A:G	I89T	0.929
2:208185009:A:G	L22P	0.928
2:208181246:A:C	I89S	0.922
2:208185003:T:A	E24V	0.921
2:208186966:C:A	K7N	0.920
2:208186966:C:G	K7N	0.920
2:208184991:T:C	D28G	0.916
2:208185006:C:G	R23P	0.916
2:208183011:A:G	W54R	0.915
2:208183011:A:T	W54R	0.915
2:208184994:A:C	F27C	0.911
2:208172040:G:C	H134Q	0.909
2:208172040:G:T	H134Q	0.909
2:208181222:A:G	L97S	0.898
2:208184983:C:G	G31R	0.896
2:208184983:C:T	G31R	0.896
2:208172032:G:T	A137D	0.894
2:208181218:C:A	M98I	0.894
2:208181218:C:G	M98I	0.894

dbSNP variants (sampled 300 via entrez): RS1000010684 (2:208171686 A>C,T), RS1000051543 (2:208166575 C>T), RS1000052503 (2:208187967 A>C), RS1000156505 (2:208172347 T>C), RS1000317000 (2:208176818 T>C), RS1000320978 (2:208181789 G>C,T), RS1000374746 (2:208182017 T>C), RS1000655531 (2:208180437 G>A), RS1000869118 (2:208189599 A>G), RS1000921503 (2:208189279 A>C,G), RS1001009237 (2:208186680 C>T), RS1001196464 (2:208172252 G>A), RS1001244985 (2:208166659 T>A), RS1001646606 (2:208182701 C>G), RS1001658899 (2:208188533 C>T)

Disease associations

OMIM: gene MIM:615536 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST006904_9	Cerebral amyloid deposition (PET imaging)	5.000000e-06
GCST011004_3	Adult diffuse glioma (IDH mutation)	7.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007707	cerebral amyloid deposition measurement

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
rs7579275	C2orf80		0.00	0

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, affects cotreatment	4
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
methylmercuric chloride	increases expression	1
trichostatin A	decreases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression, increases expression	1
Ivermectin	decreases expression	1
Lead	affects expression	1
Thiram	increases expression	1

Clinical trials (associated diseases)

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