C2orf42

Summary

C2orf42 (chromosome 2 open reading frame 42, HGNC:26056) is a protein-coding gene on chromosome 2p13.3, encoding Uncharacterized protein C2orf42 (Q9NWW7).

Located in nucleoplasm.

Source: NCBI Gene 54980 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 18 total
• MANE Select transcript: NM_017880

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26056
Approved symbol	C2orf42
Name	chromosome 2 open reading frame 42
Location	2p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20558
Ensembl gene	ENSG00000115998
Ensembl biotype	protein_coding
Entrez	54980

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 14 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000264434, ENST00000417203, ENST00000417865, ENST00000419381, ENST00000420306, ENST00000425268, ENST00000428010, ENST00000428751, ENST00000447804, ENST00000457952, ENST00000464505, ENST00000470096, ENST00000487560, ENST00000495353, ENST00000884989, ENST00000884990, ENST00000923678, ENST00000967691

RefSeq mRNA: 8 — MANE Select: NM_017880 NM_001348758, NM_001348759, NM_001348760, NM_001348761, NM_001348762, NM_001348763, NM_001348764, NM_017880

CCDS: CCDS1899

Canonical transcript exons

ENST00000264434 — 10 exons

Exon	Start	End
ENSE00000759560	70175673	70175777
ENSE00000759574	70169557	70169661
ENSE00000759598	70165528	70165635
ENSE00000846491	70179532	70179642
ENSE00000846492	70181163	70181997
ENSE00000963062	70165092	70165192
ENSE00000963063	70160625	70160787
ENSE00000963064	70149885	70150564
ENSE00001164252	70182667	70182935
ENSE00001164257	70190973	70191019

Expression profiles

Bgee: expression breadth ubiquitous, 265 present calls, max score 97.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.9131 / max 57.4145, expressed in 1617 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
29020	36.5786	1822
29013	2.3389	1328
29011	1.1751	697
29012	0.3991	186

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	97.36	gold quality
male germ cell	CL:0000015	95.53	gold quality
left testis	UBERON:0004533	92.34	gold quality
right testis	UBERON:0004534	92.16	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.64	gold quality
testis	UBERON:0000473	91.03	gold quality
adult organism	UBERON:0007023	87.10	gold quality
granulocyte	CL:0000094	85.37	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.60	gold quality
right lobe of liver	UBERON:0001114	82.68	gold quality
islet of Langerhans	UBERON:0000006	81.33	gold quality
right uterine tube	UBERON:0001302	81.32	gold quality
prefrontal cortex	UBERON:0000451	81.06	gold quality
ventricular zone	UBERON:0003053	81.06	gold quality
cerebellar hemisphere	UBERON:0002245	81.04	gold quality
cerebellar cortex	UBERON:0002129	81.03	gold quality
colonic epithelium	UBERON:0000397	80.99	gold quality
lymph node	UBERON:0000029	80.60	gold quality
cerebellum	UBERON:0002037	80.24	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.13	gold quality
right adrenal gland	UBERON:0001233	79.84	gold quality
hindlimb stylopod muscle	UBERON:0004252	79.72	gold quality
calcaneal tendon	UBERON:0003701	79.31	gold quality
right adrenal gland cortex	UBERON:0035827	79.30	gold quality
secondary oocyte	CL:0000655	79.29	gold quality
descending thoracic aorta	UBERON:0002345	79.27	gold quality
gall bladder	UBERON:0002110	79.16	gold quality
leukocyte	CL:0000738	78.98	gold quality
liver	UBERON:0002107	78.87	gold quality
body of uterus	UBERON:0009853	78.78	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

50 targeting C2orf42, 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-1252-5P	100.00	69.80	2774
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-497-5P	99.92	71.83	2674
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-6838-5P	99.89	71.94	2690
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-609	99.82	64.26	505
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	C5H2orf42	ENSDARG00000059636
mus_musculus	C87436	ENSMUSG00000046679
rattus_norvegicus	C4h2orf42	ENSRNOG00000017380
drosophila_melanogaster	CG2321	FBGN0039663

Protein

Protein identifiers

Uncharacterized protein C2orf42 — Q9NWW7 (reviewed: Q9NWW7)

All UniProt accessions (9): Q9NWW7, C9J4L7, C9J5U1, C9JJF4, C9JK51, C9JKD5, C9JS43, C9JV10, C9JZF3

RefSeq proteins (8): NP_001335687, NP_001335688, NP_001335689, NP_001335690, NP_001335691, NP_001335692, NP_001335693, NP_060350* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026049	C2orf42	Family
IPR029269	Zf-tcix	Domain

Pfam: PF14952

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NWW7-F1	74.37	0.39

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 107 (showing top): RNGTGGGC_UNKNOWN, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, NERF_Q2, TTTGCAC_MIR19A_MIR19B, CHEN_HOXA5_TARGETS_9HR_UP, SCGGAAGY_ELK1_02, CAGTGTT_MIR141_MIR200A, chr2p13, PHONG_TNF_RESPONSE_VIA_P38_COMPLETE, KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES, ATF6_TARGET_GENES, BRF1_TARGET_GENES, DYRK1A_TARGET_GENES, F10_TARGET_GENES, FOXN3_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

376 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C2orf42	GOLGA6C	A6NDK9	720
C2orf42	RSBN1L	Q6PCB5	666
C2orf42	ANKRD20A2P	Q5SQ80	579
C2orf42	APPL2	Q8NEU8	510
C2orf42	MYBBP1A	Q9BQG0	492
C2orf42	ZNF557	Q8N988	449
C2orf42	TFPI2	P48307	440
C2orf42	ADAMTS10	Q9H324	431
C2orf42	SMAP2	Q8WU79	428
C2orf42	POLR3H	Q9Y535	425
C2orf42	CALCR	P30988	407
C2orf42	GPR50	Q13585	377
C2orf42	TNIP1	Q15025	367
C2orf42	MIA3	Q5JRA6	364
C2orf42	PITPNA	Q00169	362

IntAct

18 interactions, top by confidence:

A	B	Type	Score
ALAS1	C2orf42	psi-mi:“MI:0915”(physical association)	0.560
PRKAB2	C2orf42	psi-mi:“MI:0915”(physical association)	0.560
PPP1R13B	C2orf42	psi-mi:“MI:0915”(physical association)	0.560
TLX3	C2orf42	psi-mi:“MI:0915”(physical association)	0.560
	C2orf42	psi-mi:“MI:0915”(physical association)	0.560
C2orf42		psi-mi:“MI:0915”(physical association)	0.000
C2orf42	PPP1R13B	psi-mi:“MI:0915”(physical association)	0.000
TLX3	C2orf42	psi-mi:“MI:0915”(physical association)	0.000
	C2orf42	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (9): C2orf42 (Two-hybrid), C2orf42 (Two-hybrid), PRKAB2 (Two-hybrid), TLX3 (Two-hybrid), HOMEZ (Two-hybrid), C2orf42 (Affinity Capture-RNA), C2orf42 (Affinity Capture-RNA), C2orf42 (Two-hybrid), C2orf42 (Two-hybrid)

ESM2 similar proteins: A2QRA0, A4IIA7, A6NHR9, B4XT64, B9F4I8, F4JSE7, P03273, P0CY36, P21784, P38899, P40434, P40889, P48752, P78746, Q03099, Q07888, Q0WL81, Q12789, Q3E7X8, Q3E7Y5, Q4R683, Q4R907, Q4WVM1, Q53NI2, Q5E9N5, Q5RAX4, Q60649, Q651A1, Q66J91, Q6P5D8, Q86UB2, Q8BLI4, Q8BMD5, Q8CBX9, Q8IPH9, Q8NG08, Q8VZF6, Q91YE9, Q93ZS1, Q96P26

Diamond homologs: Q3SYX3, Q4R907, Q8R3C1, Q9NWW7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4462 predictions. Top by Δscore:

Variant	Effect	Δscore
2:70150560:GTTGC:G	acceptor_gain	1.0000
2:70150561:TTGC:T	acceptor_gain	1.0000
2:70150562:TGC:T	acceptor_gain	1.0000
2:70150565:C:CC	acceptor_gain	1.0000
2:70160624:CCAA:C	donor_gain	1.0000
2:70160796:C:CT	acceptor_gain	1.0000
2:70160797:A:T	acceptor_gain	1.0000
2:70160803:A:C	acceptor_gain	1.0000
2:70160807:C:CT	acceptor_gain	1.0000
2:70160807:C:T	acceptor_gain	1.0000
2:70160808:A:T	acceptor_gain	1.0000
2:70165196:CAACG:C	acceptor_gain	1.0000
2:70165199:CG:C	acceptor_gain	1.0000
2:70165200:G:GC	acceptor_gain	1.0000
2:70165562:T:TA	donor_gain	1.0000
2:70165633:TGCC:T	acceptor_loss	1.0000
2:70165634:GCC:G	acceptor_loss	1.0000
2:70165635:CCTA:C	acceptor_loss	1.0000
2:70165636:C:CG	acceptor_loss	1.0000
2:70165637:T:A	acceptor_loss	1.0000
2:70169551:ACTT:A	donor_loss	1.0000
2:70169552:CTTA:C	donor_loss	1.0000
2:70169553:TTACC:T	donor_loss	1.0000
2:70169555:A:AC	donor_gain	1.0000
2:70169555:AC:A	donor_gain	1.0000
2:70169555:ACCAT:A	donor_gain	1.0000
2:70169556:C:CT	donor_gain	1.0000
2:70169556:CC:C	donor_gain	1.0000
2:70169556:CCA:C	donor_gain	1.0000
2:70169556:CCAT:C	donor_gain	1.0000

AlphaMissense

3734 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:70150471:A:T	I537N	1.000
2:70150474:C:G	R536P	1.000
2:70150477:A:G	L535P	1.000
2:70150483:C:A	G533V	1.000
2:70150483:C:T	G533D	1.000
2:70150484:C:A	G533C	1.000
2:70150484:C:G	G533R	1.000
2:70150501:A:G	L527P	1.000
2:70150515:C:A	W522C	1.000
2:70150515:C:G	W522C	1.000
2:70150516:C:G	W522S	1.000
2:70150517:A:G	W522R	1.000
2:70150517:A:T	W522R	1.000
2:70150522:A:T	I520N	1.000
2:70150528:A:G	F518S	1.000
2:70160627:A:T	V505D	1.000
2:70160633:A:G	L503P	1.000
2:70160633:A:T	L503H	1.000
2:70160762:A:G	F460S	1.000
2:70165117:A:T	V443D	1.000
2:70165140:C:A	W435C	1.000
2:70165140:C:G	W435C	1.000
2:70165141:C:G	W435S	1.000
2:70165142:A:G	W435R	1.000
2:70165142:A:T	W435R	1.000
2:70165155:A:C	F430L	1.000
2:70165155:A:T	F430L	1.000
2:70165157:A:G	F430L	1.000
2:70165162:C:T	G428E	1.000
2:70165163:C:G	G428R	1.000

dbSNP variants (sampled 300 via entrez): RS1000048221 (2:70188686 CT>C), RS1000169294 (2:70162050 C>T), RS1000268509 (2:70168059 C>T), RS1000290168 (2:70156431 A>C), RS1000299578 (2:70163508 G>A), RS1000314656 (2:70167858 G>A), RS1000341972 (2:70156123 C>G), RS1000350250 (2:70156724 T>C), RS1000367589 (2:70157112 T>C), RS1000523866 (2:70161657 A>G), RS1000625959 (2:70157599 C>T), RS1000658252 (2:70169291 G>A), RS1000788348 (2:70163514 T>A,G), RS1000794574 (2:70174604 A>G), RS1000831732 (2:70192634 T>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

7 associations (top):

Study	Trait	p-value
GCST001762_544	Obesity-related traits	6.000000e-06
GCST002481_1	Acne (severe)	5.000000e-06
GCST006661_199	Male-pattern baldness	3.000000e-08
GCST90002397_807	Mean spheric corpuscular volume	4.000000e-28
GCST90002398_340	Neutrophil count	1.000000e-15
GCST90002403_110	Red blood cell count	9.000000e-11
GCST90002407_52	White blood cell count	2.000000e-19

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004833	neutrophil count
EFO:0004305	erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression	2
Particulate Matter	decreases expression, increases abundance	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
triphenyl phosphate	affects expression	1
mono-(2-ethylhexyl)phthalate	decreases methylation, increases abundance	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
ferrous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
abrine	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Air Pollutants, Occupational	decreases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Atrazine	decreases expression	1
Vehicle Emissions	decreases expression, increases abundance	1
Cannabidiol	increases expression	1
Copper	affects binding, decreases expression	1
Diethylhexyl Phthalate	decreases methylation, increases abundance	1
Disulfiram	affects binding, decreases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Nickel	decreases expression	1
Selenium	affects cotreatment, increases expression, decreases expression	1
Smoke	decreases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Vitamin E	affects cotreatment, increases expression, decreases expression	1
Zinc	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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