C2orf72

Summary

C2orf72 ( chromosome 2 open reading frame 72 , HGNC:27418) is a protein-coding gene on chromosome 2q37.1, encoding Uncharacterized protein C2orf72 (A6NCS6).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001144994

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27418
Approved symbol	C2orf72
Name	chromosome 2 open reading frame 72
Location	2q37.1
Locus type	gene with protein product
Status	Approved
Aliases	LOC257407
Ensembl gene	ENSG00000204128
Ensembl biotype	protein_coding
Entrez	257407

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000373640, ENST00000463834, ENST00000477463, ENST00000941869

RefSeq mRNA: 1 — MANE Select: NM_001144994 NM_001144994

CCDS: CCDS46539

Canonical transcript exons

ENST00000373640 — 3 exons

Exon	Start	End
ENSE00001461088	231037523	231038199
ENSE00001622626	231046882	231049719
ENSE00003464888	231041296	231041409

Expression profiles

Bgee: expression breadth ubiquitous, 190 present calls, max score 96.64.

FANTOM5 (CAGE): breadth broad, TPM avg 2.8044 / max 125.9027, expressed in 411 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
25857	1.9157	317
25858	0.2601	122
25854	0.2545	103
25856	0.2386	134
25855	0.1164	24
25859	0.0191	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	96.64	gold quality
liver	UBERON:0002107	94.40	gold quality
right frontal lobe	UBERON:0002810	93.11	gold quality
nucleus accumbens	UBERON:0001882	92.77	gold quality
ventricular zone	UBERON:0003053	92.64	gold quality
amygdala	UBERON:0001876	92.55	gold quality
putamen	UBERON:0001874	92.45	gold quality
caudate nucleus	UBERON:0001873	92.39	gold quality
Brodmann (1909) area 9	UBERON:0013540	91.72	gold quality
Ammon’s horn	UBERON:0001954	91.05	gold quality
cingulate cortex	UBERON:0003027	90.98	gold quality
anterior cingulate cortex	UBERON:0009835	90.75	gold quality
prefrontal cortex	UBERON:0000451	90.32	gold quality
hypothalamus	UBERON:0001898	90.32	gold quality
type B pancreatic cell	CL:0000169	90.11	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	90.08	gold quality
telencephalon	UBERON:0001893	90.05	gold quality
temporal lobe	UBERON:0001871	89.73	gold quality
olfactory bulb	UBERON:0002264	89.70	gold quality
neocortex	UBERON:0001950	89.64	gold quality
substantia nigra	UBERON:0002038	89.58	gold quality
frontal cortex	UBERON:0001870	89.54	gold quality
cerebral cortex	UBERON:0000956	89.39	gold quality
CA1 field of hippocampus	UBERON:0003881	89.33	gold quality
mucosa of transverse colon	UBERON:0004991	89.31	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	89.01	gold quality
primary visual cortex	UBERON:0002436	88.87	gold quality
midbrain	UBERON:0001891	88.79	gold quality
forebrain	UBERON:0001890	88.78	gold quality
rectum	UBERON:0001052	88.07	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

96 targeting C2orf72, 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-3120-5P	100.00	65.56	965
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-513A-5P	100.00	69.77	2465
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-150-5P	99.99	66.69	1976
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-4447	99.85	67.81	2900

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	2810459M11Rik	ENSMUSG00000026227
rattus_norvegicus	C9h2orf72	ENSRNOG00000017557

Protein

Protein identifiers

Uncharacterized protein C2orf72 — A6NCS6 (reviewed: A6NCS6)

All UniProt accessions (1): A6NCS6

RefSeq proteins (1): NP_001138466* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027868	C2orf72-like_C	Domain

Pfam: PF15443

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NCS6-F1	65.95	0.25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 61 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, SABATES_COLORECTAL_ADENOMA_SIZE_DN, XU_GH1_EXOGENOUS_TARGETS_UP, PILON_KLF1_TARGETS_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, RAPA_EARLY_UP.V1_UP, FOXN3_TARGET_GENES, PBXIP1_TARGET_GENES, ZNF322_TARGET_GENES, ZNF436_TARGET_GENES, ZNF92_TARGET_GENES, MIR607, MIR195_5P, MIR16_5P, MIR96_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

120 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C2orf72	CLBA1	Q96F83	583
C2orf72	ENTPD5	O75356	479
C2orf72	B3GNT7	Q8NFL0	377
C2orf72	RAB3B	P20337	335
C2orf72	SP140	Q13342	307
C2orf72	DIS3L2	Q8IYB7	302
C2orf72	PSMD1	Q99460	289
C2orf72	B3GAT1	Q9P2W7	286
C2orf72	CISD1	Q9NZ45	260
C2orf72	NTNG2	Q96CW9	259
C2orf72	ATP7B	P35670	231
C2orf72	PGBD1	Q96JS3	220
C2orf72	LAMB3	Q13751	220
C2orf72	HTR2B	P41595	211
C2orf72	B3GAT2	Q9NPZ5	198

IntAct

11 interactions, top by confidence:

A	B	Type	Score
CD81	C2orf72	psi-mi:“MI:0914”(association)	0.530
SLC31A1	C2orf72	psi-mi:“MI:0914”(association)	0.530
CD81	STX3	psi-mi:“MI:0914”(association)	0.350
CD81	PVR	psi-mi:“MI:0914”(association)	0.350
CD81	CD276	psi-mi:“MI:0914”(association)	0.350
SLC31A1	DENND11	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): C2orf72 (Affinity Capture-MS), C2orf72 (Proximity Label-MS), C2orf72 (Proximity Label-MS), C2orf72 (Negative Genetic), C2orf72 (Affinity Capture-RNA), C2orf72 (Affinity Capture-MS), C2orf72 (Affinity Capture-MS), C2orf72 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RQ45, A0A0U1RQS6, A0A286YF58, A0A2R8YCJ5, A0A7I2V3R4, A2A699, A2VDX9, A6NCS6, A6NGB7, A6NJG2, A6NKF7, A6NKL6, A6NLJ0, A8MVW0, B2RU40, B7Z1M9, B8ZZ34, C9JH25, C9JVW0, D4A9R4, J3QNX5, M0QZC1, P03971, P0CG09, P0DPE3, Q0PHV7, Q0VD38, Q14761, Q29RK8, Q29RM6, Q2KJ18, Q2M3G4, Q2M3V2, Q5T442, Q64697, Q69YZ2, Q6F5E0, Q6NY19, Q6UXK2, Q80XF7

Diamond homologs: A6NCS6, Q9CYS6

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	4
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

530 predictions. Top by Δscore:

Variant	Effect	Δscore
2:231041294:A:AG	acceptor_gain	1.0000
2:231041295:G:GG	acceptor_gain	1.0000
2:231041408:GG:G	donor_gain	1.0000
2:231041409:GG:G	donor_gain	1.0000
2:231046857:A:AG	acceptor_gain	1.0000
2:231046858:G:GG	acceptor_gain	1.0000
2:231038197:CAGG:C	donor_loss	0.9900
2:231038198:AGGTG:A	donor_loss	0.9900
2:231038199:GGT:G	donor_loss	0.9900
2:231038200:G:C	donor_loss	0.9900
2:231038201:T:A	donor_loss	0.9900
2:231041294:AGT:A	acceptor_gain	0.9900
2:231041295:GT:G	acceptor_gain	0.9900
2:231041295:GTG:G	acceptor_gain	0.9900
2:231042592:G:GT	donor_gain	0.9900
2:231046857:AGT:A	acceptor_gain	0.9900
2:231046858:GT:G	acceptor_gain	0.9900
2:231046858:GTG:G	acceptor_gain	0.9900
2:231046874:T:TA	acceptor_gain	0.9900
2:231046880:A:AG	acceptor_gain	0.9900
2:231046881:G:GG	acceptor_gain	0.9900
2:231046881:GAA:G	acceptor_gain	0.9900
2:231038200:G:GG	donor_gain	0.9800
2:231041291:CCTA:C	acceptor_loss	0.9800
2:231041293:TA:T	acceptor_loss	0.9800
2:231041294:AGTG:A	acceptor_gain	0.9800
2:231041294:AGTGG:A	acceptor_gain	0.9800
2:231041295:GTGG:G	acceptor_gain	0.9800
2:231041409:GGTGA:G	donor_loss	0.9800
2:231041410:G:GA	donor_loss	0.9800

AlphaMissense

1821 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:231037888:T:C	F108S	0.994
2:231038076:T:C	F171L	0.994
2:231038078:C:A	F171L	0.994
2:231038078:C:G	F171L	0.994
2:231037720:T:C	F52S	0.992
2:231038149:T:A	V195D	0.988
2:231037719:T:C	F52L	0.987
2:231037721:C:A	F52L	0.987
2:231037721:C:G	F52L	0.987
2:231038076:T:A	F171I	0.985
2:231038161:C:A	A199D	0.985
2:231037720:T:G	F52C	0.984
2:231038115:T:G	Y184D	0.984
2:231037995:G:A	G144R	0.983
2:231037995:G:C	G144R	0.983
2:231037996:G:A	G144E	0.982
2:231037674:G:C	G37R	0.981
2:231037735:T:C	F57S	0.981
2:231037995:G:T	G144W	0.981
2:231037678:A:T	E38V	0.976
2:231037675:G:A	G37D	0.975
2:231037677:G:A	E38K	0.975
2:231038065:T:C	L167S	0.975
2:231038077:T:C	F171S	0.975
2:231038115:T:A	Y184N	0.975
2:231037896:T:C	C111R	0.974
2:231037698:A:C	S45R	0.973
2:231037700:C:A	S45R	0.973
2:231037700:C:G	S45R	0.973
2:231037669:T:A	L35Q	0.972

dbSNP variants (sampled 300 via entrez): RS1000142095 (2:231039130 A>C), RS1000723470 (2:231047301 T>C), RS1000753555 (2:231047043 C>G,T), RS1000862534 (2:231041204 C>A,G,T), RS1000893883 (2:231041473 G>A), RS1001026970 (2:231047665 G>A), RS1001030030 (2:231041042 C>T), RS1002110002 (2:231041671 GA>G), RS1002313470 (2:231041564 A>G,T), RS1002316401 (2:231047385 G>A,T), RS1002569485 (2:231036155 G>T), RS1002771165 (2:231043224 T>G), RS1002967847 (2:231037351 G>C), RS1003284397 (2:231049155 A>G), RS1003492644 (2:231037112 C>A,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
GCST010917_4	Proportion of activated microglia (midfrontal cortex)	6.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases methylation	4
bisphenol A	increases methylation, affects expression, increases expression	3
Acetaminophen	decreases expression	2
Nickel	decreases expression	2
Cyclosporine	decreases expression	2
aristolochic acid I	decreases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
perfluorooctanoic acid	increases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases reaction, increases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
perfluorohexanesulfonic acid	increases expression	1
abrine	decreases expression	1
jinfukang	increases expression	1
Sunitinib	increases expression	1
Caffeine	decreases phosphorylation	1
Estradiol	affects cotreatment, increases expression	1
Lipopolysaccharides	decreases reaction, increases expression	1
Quercetin	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	affects expression	1
Aflatoxin B1	decreases expression	1
Antirheumatic Agents	decreases expression	1
Okadaic Acid	decreases expression	1
beta-Naphthoflavone	decreases expression	1

Clinical trials (associated diseases)

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