C12orf42

Summary

C12orf42 (chromosome 12 open reading frame 42, HGNC:24729) is a protein-coding gene on chromosome 12q23.2, encoding Uncharacterized protein C12orf42 (Q96LP6).

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 10 total
• MANE Select transcript: NM_198521

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24729
Approved symbol	C12orf42
Name	chromosome 12 open reading frame 42
Location	12q23.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25323
Ensembl gene	ENSG00000179088
Ensembl biotype	protein_coding
Entrez	374470

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 10 protein_coding_CDS_not_defined, 4 protein_coding, 2 nonsense_mediated_decay

ENST00000378113, ENST00000546526, ENST00000547347, ENST00000547470, ENST00000548048, ENST00000548196, ENST00000548789, ENST00000548883, ENST00000549927, ENST00000550497, ENST00000550650, ENST00000551134, ENST00000551303, ENST00000552372, ENST00000552578, ENST00000552977

RefSeq mRNA: 8 — MANE Select: NM_198521 NM_001099336, NM_001278419, NM_001278420, NM_001386868, NM_001386869, NM_001386871, NM_001386872, NM_198521

CCDS: CCDS44963, CCDS91744

Canonical transcript exons

ENST00000548883 — 6 exons

Exon	Start	End
ENSE00001215145	103495902	103495968
ENSE00003466964	103401607	103401675
ENSE00003477898	103368887	103368998
ENSE00003495872	103305974	103306345
ENSE00003642042	103478349	103478447
ENSE00003666962	103301955	103302559

Expression profiles

Bgee: expression breadth ubiquitous, 123 present calls, max score 93.61.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.6053 / max 117.0225, expressed in 168 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
132964	0.6569	91
132965	0.5299	96
132966	0.1438	68
132969	0.1209	20
132967	0.0941	53
132970	0.0596	19

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	93.61	gold quality
left testis	UBERON:0004533	89.91	gold quality
right testis	UBERON:0004534	89.54	gold quality
testis	UBERON:0000473	87.07	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.32	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.60	gold quality
spleen	UBERON:0002106	72.84	gold quality
lymph node	UBERON:0000029	71.03	gold quality
granulocyte	CL:0000094	70.19	gold quality
adult organism	UBERON:0007023	67.68	gold quality
pancreatic ductal cell	CL:0002079	67.32	silver quality
secondary oocyte	CL:0000655	67.27	gold quality
vermiform appendix	UBERON:0001154	66.64	gold quality
blood	UBERON:0000178	63.57	gold quality
bone marrow cell	CL:0002092	62.25	silver quality
caecum	UBERON:0001153	60.91	gold quality
endothelial cell	CL:0000115	60.75	silver quality
ileal mucosa	UBERON:0000331	58.84	silver quality
tonsil	UBERON:0002372	58.04	gold quality
epithelial cell of pancreas	CL:0000083	55.54	gold quality
skin of hip	UBERON:0001554	55.30	silver quality
small intestine Peyer’s patch	UBERON:0003454	55.09	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
sural nerve	UBERON:0015488	54.31	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
prefrontal cortex	UBERON:0000451	54.02	gold quality
epithelium of nasopharynx	UBERON:0001951	54.01	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
rectum	UBERON:0001052	53.08	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting C12orf42, 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-489-3P	99.80	66.46	839
HSA-MIR-4690-5P	99.65	66.24	813
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-7114-5P	98.51	67.87	1349
HSA-MIR-5008-5P	98.42	65.87	1019
HSA-MIR-4303	98.01	68.13	2304
HSA-MIR-4712-5P	97.24	67.79	775
HSA-MIR-770-5P	97.24	68.10	758
HSA-MIR-152-5P	96.42	66.59	960
HSA-MIR-1256	95.44	66.33	784
HSA-MIR-604	93.13	64.42	299

Literature-anchored findings (GeneRIF, showing 1)

• deletional rearrangement of the TCR delta gene disrupted the hypothetical gene C12orf42 and brought the Achaete-scute complex homolog 1 gene into proximity of the TRA enhancer, which is overexpressed in thyroid and lung cancers (PMID:20659153)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	1700113H08Rik	ENSMUSG00000047129
rattus_norvegicus	C7h12orf42	ENSRNOG00000038943

Protein

Protein identifiers

Uncharacterized protein C12orf42 — Q96LP6 (reviewed: Q96LP6)

All UniProt accessions (4): Q96LP6, F8VV63, F8VX61, F8W1Y6

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt ID	Names	Canonical?
Q96LP6-1	1	yes
Q96LP6-2	2
Q96LP6-3	3

RefSeq proteins (8): NP_001092806, NP_001265348, NP_001265349, NP_001373797, NP_001373798, NP_001373800, NP_001373801, NP_940923* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029288	DUF4607	Family

Pfam: PF15380

UniProt features (10 total): splice variant 3, compositionally biased region 2, sequence variant 2, chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96LP6-F1	44.43	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 54 (showing top): AREB6_03, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, EVI1_05, TGIF_01, TGACATY_UNKNOWN, IRF_Q6, TATA_C, ISRE_01, PAX2_02, chr12q23, GATA_C, CDC5_01, TGATTTRY_GFI1_01, E47_02, MEF2_01

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

186 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C12orf42	LRRC63	Q05C16	568
C12orf42	CCDC74B	Q96LY2	524
C12orf42	SPATA31A1	Q5TZJ5	506
C12orf42	ZNF577	Q9BSK1	505
C12orf42	ANKRD60	Q9BZ19	479
C12orf42	ZNF571	Q7Z3V5	475
C12orf42	TTLL8	A6PVC2	454
C12orf42	ZNF730	Q6ZMV8	447
C12orf42	Q6GMV1	Q6GMV1	445
C12orf42	FAM47C	Q5HY64	431
C12orf42	ZNF578	Q96N58	413
C12orf42	ZNF793	Q6ZN11	400
C12orf42	ZNF208	O43345	399
C12orf42	ZNF492	Q9P255	396
C12orf42	KLHL18	O94889	394

IntAct

0 interactions, top by confidence:

BioGRID (3): C12orf42 (Affinity Capture-MS), C12orf42 (Affinity Capture-MS), C12orf42 (Affinity Capture-Western)

ESM2 similar proteins: A0A1B0GTK4, A0A1B0GTK5, A0JNL8, A2RUT3, A4D250, B2KGE5, F1MQW7, F2Z3F1, F5HHT4, O93195, O95411, P04610, P05905, P0C733, P0C7M3, P0DP71, P16722, P17758, P47939, P47940, P57738, Q0VD86, Q1HVB5, Q1RN00, Q1X6Y7, Q1X6Z1, Q1X6Z2, Q3ZN08, Q5PR19, Q5PXH1, Q5TC04, Q5TEZ4, Q64902, Q66669, Q66HF0, Q67863, Q6DGF6, Q6UYE1, Q7L4S7, Q8AZJ3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1815 predictions. Top by Δscore:

Variant	Effect	Δscore
12:103478446:CC:C	acceptor_gain	1.0000
12:103478447:CC:C	acceptor_gain	1.0000
12:103302556:GAAC:G	acceptor_gain	0.9900
12:103302557:AAC:A	acceptor_gain	0.9900
12:103302557:AACC:A	acceptor_loss	0.9900
12:103302560:C:CC	acceptor_gain	0.9900
12:103302561:T:A	acceptor_loss	0.9900
12:103302568:C:CT	acceptor_gain	0.9900
12:103302569:A:T	acceptor_gain	0.9900
12:103353512:A:T	acceptor_gain	0.9900
12:103401601:ACT:A	donor_loss	0.9900
12:103401602:CTCA:C	donor_loss	0.9900
12:103401603:TCAC:T	donor_loss	0.9900
12:103401604:CAC:C	donor_loss	0.9900
12:103401605:ACCT:A	donor_loss	0.9900
12:103401606:C:CA	donor_loss	0.9900
12:103478343:CATTA:C	donor_loss	0.9900
12:103478344:ATTAC:A	donor_loss	0.9900
12:103478345:TTA:T	donor_loss	0.9900
12:103478346:TA:T	donor_loss	0.9900
12:103478347:A:AG	donor_loss	0.9900
12:103478348:CCT:C	donor_loss	0.9900
12:103478444:CTCC:C	acceptor_gain	0.9900
12:103478445:TCCC:T	acceptor_loss	0.9900
12:103478446:CCCTA:C	acceptor_loss	0.9900
12:103478448:C:CC	acceptor_gain	0.9900
12:103478448:CTATA:C	acceptor_loss	0.9900
12:103478449:T:A	acceptor_loss	0.9900
12:103495444:T:TA	donor_gain	0.9900
12:103495741:C:CT	donor_gain	0.9900

AlphaMissense

2363 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:103368954:G:C	F64L	0.984
12:103368954:G:T	F64L	0.984
12:103368956:A:G	F64L	0.984
12:103302165:G:C	F342L	0.976
12:103302165:G:T	F342L	0.976
12:103302167:A:G	F342L	0.976
12:103368955:A:G	F64S	0.969
12:103368933:G:C	F71L	0.967
12:103368933:G:T	F71L	0.967
12:103368935:A:G	F71L	0.967
12:103401631:C:A	W41C	0.926
12:103401631:C:G	W41C	0.926
12:103368942:C:A	M68I	0.924
12:103368942:C:G	M68I	0.924
12:103368942:C:T	M68I	0.924
12:103368945:G:C	H67Q	0.922
12:103368945:G:T	H67Q	0.922
12:103302211:A:G	L327S	0.917
12:103401633:A:G	W41R	0.917
12:103401633:A:T	W41R	0.917
12:103368955:A:C	F64C	0.915
12:103306040:C:G	G189R	0.914
12:103302153:A:C	C346W	0.912
12:103368965:A:G	C61R	0.912
12:103302155:A:G	C346R	0.900
12:103368963:G:C	C61W	0.889
12:103368934:A:G	F71S	0.886
12:103302123:A:C	N356K	0.880
12:103302123:A:T	N356K	0.880
12:103306121:A:G	W162R	0.879

dbSNP variants (sampled 300 via entrez): RS1000005490 (12:103562806 C>T), RS1000007804 (12:103134438 T>C), RS1000015637 (12:103385110 G>A), RS1000022735 (12:103312020 C>A,T), RS1000028034 (12:103488010 G>A), RS1000028295 (12:103073749 G>A,T), RS1000033208 (12:103398491 T>C), RS1000036773 (12:103363749 C>T), RS1000039563 (12:103294627 A>G,T), RS1000041166 (12:103425974 A>G,T), RS1000045033 (12:103480551 A>G), RS1000047755 (12:103150439 G>A), RS1000050049 (12:103109136 C>A), RS1000058544 (12:103103891 C>T), RS1000069312 (12:103302419 G>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

10 associations (top):

Study	Trait	p-value
GCST001214_1	Coronary restenosis	1.000000e-07
GCST002539_17	Schizophrenia	5.000000e-08
GCST002783_48	Body mass index	6.000000e-06
GCST003518_89	Daytime sleep phenotypes	6.000000e-06
GCST006803_56	Schizophrenia	3.000000e-07
GCST007201_421	Schizophrenia	2.000000e-08
GCST007932_9	Medication use (thyroid preparations)	2.000000e-12
GCST010571_57	Autoimmune thyroid disease	8.000000e-15
GCST010988_500	Adult body size	4.000000e-16
GCST010989_48	Body size at age 10	2.000000e-09

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0007828	daytime rest measurement
EFO:0009933	Thyroid preparation use measurement
EFO:0009819	comparative body size at age 10, self-reported

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
rs10778228	C12orf42		0.00	0

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol F	decreases expression	1
bisphenol A	affects cotreatment, increases methylation	1
arsenite	decreases methylation	1
2-palmitoylglycerol	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Fenfluramine	increases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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