C12orf76

Summary

C12orf76 (chromosome 12 open reading frame 76, HGNC:33790) is a protein-coding gene on chromosome 12q24.11, encoding Uncharacterized protein C12orf76 (Q8N812). It is a selective cancer dependency (DepMap: 25.0% of cell lines).

Predicted to be located in membrane.

Source: NCBI Gene 400073 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 3 total
• Cancer dependency (DepMap): dependent in 25.0% of screened cell lines
• MANE Select transcript: NM_001389625

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33790
Approved symbol	C12orf76
Name	chromosome 12 open reading frame 76
Location	12q24.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40142
Ensembl gene	ENSG00000174456
Ensembl biotype	protein_coding
Entrez	400073

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding_CDS_not_defined, 2 protein_coding

ENST00000309050, ENST00000546627, ENST00000546651, ENST00000547573, ENST00000548936, ENST00000549724, ENST00000551185, ENST00000615315, ENST00000650705, ENST00000685920, ENST00000687036, ENST00000687999

RefSeq mRNA: 1 — MANE Select: NM_001389625 NM_001389625

CCDS: CCDS91748

Canonical transcript exons

ENST00000615315 — 2 exons

Exon	Start	End
ENSE00003721337	110041177	110042459
ENSE00003846984	110048363	110048522

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 97.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.7899 / max 217.0966, expressed in 1804 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
133215	13.8078	1800
133216	2.8794	1102
133220	0.1026	42

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	97.62	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.36	gold quality
prefrontal cortex	UBERON:0000451	97.32	gold quality
spinal cord	UBERON:0002240	96.97	gold quality
hypothalamus	UBERON:0001898	96.91	gold quality
corpus callosum	UBERON:0002336	96.77	gold quality
anterior cingulate cortex	UBERON:0009835	96.73	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	96.44	gold quality
right frontal lobe	UBERON:0002810	96.38	gold quality
substantia nigra	UBERON:0002038	96.33	gold quality
frontal cortex	UBERON:0001870	96.14	gold quality
amygdala	UBERON:0001876	96.00	gold quality
neocortex	UBERON:0001950	95.98	gold quality
midbrain	UBERON:0001891	95.89	gold quality
Ammon’s horn	UBERON:0001954	95.57	gold quality
inferior vagus X ganglion	UBERON:0005363	95.56	gold quality
cerebral cortex	UBERON:0000956	95.55	gold quality
cortical plate	UBERON:0005343	95.00	gold quality
Brodmann (1909) area 46	UBERON:0006483	95.00	gold quality
putamen	UBERON:0001874	94.92	gold quality
caudate nucleus	UBERON:0001873	94.88	gold quality
middle temporal gyrus	UBERON:0002771	94.84	gold quality
pons	UBERON:0000988	94.74	gold quality
nucleus accumbens	UBERON:0001882	94.61	gold quality
forebrain	UBERON:0001890	94.61	gold quality
brain	UBERON:0000955	94.42	gold quality
temporal lobe	UBERON:0001871	94.14	gold quality
monocyte	CL:0000576	93.82	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.80	gold quality
subthalamic nucleus	UBERON:0001906	93.67	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-7303	no	344.07
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting C12orf76, 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-4673	100.00	66.64	1490
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-498-5P	99.76	69.64	1807
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-7157-5P	99.66	69.33	1829
HSA-MIR-6132	99.60	65.83	1554

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 25.0% of screened cell lines.

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
rattus_norvegicus	C12h12orf76	ENSRNOG00000069648

Protein

Protein identifiers

Uncharacterized protein C12orf76 — Q8N812 (reviewed: Q8N812)

All UniProt accessions (2): A0A087WX00, A0A494C145

RefSeq proteins (1): NP_001376554* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR041240	DUF5541	Family

Pfam: PF17695

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N812-F1	41.86	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 106 (showing top): TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, CHUNG_BLISTER_CYTOTOXICITY_DN, MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP, chr12q24, ARNT2_TARGET_GENES, CEBPZ_TARGET_GENES, DIDO1_TARGET_GENES, DLX4_TARGET_GENES, E2F2_TARGET_GENES, ELF2_TARGET_GENES, FEV_TARGET_GENES, FOXN3_TARGET_GENES, GLI4_TARGET_GENES, HMG20B_TARGET_GENES, HOXB4_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

62 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C12orf76	SVIP	Q8NHG7	435
C12orf76	FRMD3	A2A2Y4	396
C12orf76	MTRFR	Q9H3J6	372
C12orf76	TCTN1	Q2MV58	367
C12orf76	COPG1	Q9Y678	366
C12orf76	COPZ1	P61923	350
C12orf76	SLCO3A1	Q9UIG8	328
C12orf76	PUF60	Q9UHX1	317
C12orf76	MRPL58	Q14197	288
C12orf76	ISCU	Q9H1K1	274
C12orf76	SF3A1	Q15459	273
C12orf76	PAK6	Q9NQU5	272
C12orf76	VPS29	Q9UBQ0	271
C12orf76	AP5S1	Q9NUS5	269
C12orf76	PGRMC1	O00264	258

IntAct

3 interactions, top by confidence:

A	B	Type	Score
FKBP5	C12orf76	psi-mi:“MI:0915”(physical association)	0.400
C12orf76	CDC37	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (2): C12orf76 (Affinity Capture-RNA), C12orf76 (Affinity Capture-RNA)

ESM2 similar proteins: A0A023PZC7, A4VGD5, A5WCZ0, F5HES7, G2TRS6, O10307, O28885, O30086, O33285, P05665, P05666, P07116, P09504, P0CL37, P10018, P11319, P11519, P18786, P18896, P19779, P20183, P22994, P28247, P36558, P36706, P36708, P55423, P55486, P55514, P55550, P55563, P65042, P86807, P9WL52, P9WL53, Q08842, Q124Q1, Q64766, Q64769, Q6B0Y6

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	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2888 predictions. Top by Δscore:

Variant	Effect	Δscore
12:110028485:T:TA	acceptor_gain	1.0000
12:110028640:G:GT	donor_gain	1.0000
12:110028640:GAA:G	donor_gain	1.0000
12:110028643:G:GG	donor_gain	1.0000
12:110029632:A:AG	donor_gain	1.0000
12:110029632:A:G	donor_gain	1.0000
12:110030643:A:AG	acceptor_gain	1.0000
12:110030644:G:GG	acceptor_gain	1.0000
12:110030644:GA:G	acceptor_gain	1.0000
12:110030644:GAA:G	acceptor_gain	1.0000
12:110033792:TTCAG:T	acceptor_loss	1.0000
12:110033793:TCAG:T	acceptor_loss	1.0000
12:110033794:CAGC:C	acceptor_loss	1.0000
12:110033795:A:AG	acceptor_gain	1.0000
12:110033796:G:GA	acceptor_gain	1.0000
12:110033796:GCTT:G	acceptor_gain	1.0000
12:110033796:GCTTC:G	acceptor_gain	1.0000
12:110033955:CAGG:C	donor_loss	1.0000
12:110033957:GG:G	donor_loss	1.0000
12:110033958:GT:G	donor_loss	1.0000
12:110033959:T:A	donor_loss	1.0000
12:110037352:A:AG	acceptor_gain	1.0000
12:110037353:A:G	acceptor_gain	1.0000
12:110037354:CCCA:C	acceptor_loss	1.0000
12:110037356:CAGG:C	acceptor_loss	1.0000
12:110037357:A:AG	acceptor_gain	1.0000
12:110037357:A:T	acceptor_loss	1.0000
12:110037357:AG:A	acceptor_gain	1.0000
12:110037358:G:GG	acceptor_gain	1.0000
12:110037358:GG:G	acceptor_gain	1.0000

AlphaMissense

895 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:110059122:A:C	F19L	0.964
12:110059122:A:T	F19L	0.964
12:110059124:A:G	F19L	0.964
12:110059110:A:C	F23L	0.954
12:110059110:A:T	F23L	0.954
12:110059112:A:G	F23L	0.954
12:110059065:C:A	W38C	0.926
12:110059065:C:G	W38C	0.926
12:110059023:G:C	F52L	0.913
12:110059023:G:T	F52L	0.913
12:110059025:A:G	F52L	0.913
12:110059067:A:G	W38R	0.908
12:110059067:A:T	W38R	0.908
12:110042441:A:C	F106L	0.891
12:110042441:A:T	F106L	0.891
12:110042443:A:G	F106L	0.891
12:110057272:A:C	F72L	0.889
12:110057272:A:T	F72L	0.889
12:110057274:A:G	F72L	0.889
12:110059123:A:G	F19S	0.863
12:110042406:A:G	I118T	0.856
12:110059152:A:C	F9L	0.841
12:110059152:A:T	F9L	0.841
12:110059154:A:G	F9L	0.841
12:110059111:A:G	F23S	0.829
12:110058990:C:A	W63C	0.827
12:110058990:C:G	W63C	0.827
12:110059117:A:T	I21K	0.806
12:110058992:A:G	W63R	0.797
12:110058992:A:T	W63R	0.797

dbSNP variants (sampled 300 via entrez): RS1000021183 (12:110065839 G>A), RS1000111177 (12:110052907 T>C), RS1000117147 (12:110054910 A>T), RS1000153304 (12:110043260 T>C,G), RS1000255668 (12:110048557 C>T), RS1000285946 (12:110067675 C>A,T), RS1000411563 (12:110055356 G>A), RS1000514684 (12:110049456 T>G), RS1000531381 (12:110054501 T>C), RS1000534356 (12:110050075 G>A), RS1000588367 (12:110049742 C>T), RS1000711198 (12:110044130 T>G), RS1000761381 (12:110055576 G>A,T), RS1000772844 (12:110042884 C>A), RS1000826762 (12:110072867 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

2 associations (top):

Study	Trait	p-value
GCST005316_461	Intelligence (MTAG)	1.000000e-08
GCST008103_145	Bipolar disorder	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases methylation	7
trichostatin A	affects cotreatment, decreases expression	2
entinostat	decreases expression, affects cotreatment	2
Smoke	decreases expression, increases abundance, increases expression	2
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Carbamazepine	affects expression	1
Cisplatin	increases expression	1
Doxorubicin	decreases expression	1
Estradiol	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Lead	increases expression	1
Methyl Methanesulfonate	increases expression	1
Mustard Gas	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
1-Methyl-4-phenylpyridinium	increases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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