C12orf54

Summary

C12orf54 (chromosome 12 open reading frame 54, HGNC:28553) is a protein-coding gene on chromosome 12q13.11, encoding Uncharacterized protein C12orf54 (Q6X4T0).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 8 total
• MANE Select transcript: NM_152319

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28553
Approved symbol	C12orf54
Name	chromosome 12 open reading frame 54
Location	12q13.11
Locus type	gene with protein product
Status	Approved
Aliases	MGC35033
Ensembl gene	ENSG00000177627
Ensembl biotype	protein_coding
Entrez	121273

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 nonsense_mediated_decay, 1 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000380491, ENST00000548364, ENST00000548913, ENST00000549398, ENST00000551266

RefSeq mRNA: 1 — MANE Select: NM_152319 NM_152319

CCDS: CCDS8764

Canonical transcript exons

ENST00000548364 — 9 exons

Exon	Start	End
ENSE00001213585	48488924	48488956
ENSE00001213589	48486688	48486726
ENSE00001213594	48486178	48486208
ENSE00001213605	48483240	48483361
ENSE00002217583	48482498	48482576
ENSE00003530182	48490812	48490836
ENSE00003578864	48492947	48492995
ENSE00003692283	48494798	48494979
ENSE00003750295	48496181	48496524

Expression profiles

Bgee: expression breadth ubiquitous, 170 present calls, max score 97.10.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0328 / max 27.5162, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
125263	0.0328	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	97.10	gold quality
left testis	UBERON:0004533	95.33	gold quality
right testis	UBERON:0004534	95.19	gold quality
testis	UBERON:0000473	92.58	gold quality
pancreatic ductal cell	CL:0002079	85.00	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.96	gold quality
endothelial cell	CL:0000115	82.95	gold quality
cardiac muscle of right atrium	UBERON:0003379	82.50	gold quality
left ventricle myocardium	UBERON:0006566	82.49	gold quality
kidney epithelium	UBERON:0004819	80.18	gold quality
adult organism	UBERON:0007023	80.17	gold quality
lower esophagus mucosa	UBERON:0035834	78.67	gold quality
esophagus mucosa	UBERON:0002469	76.19	gold quality
myocardium	UBERON:0002349	72.63	gold quality
palpebral conjunctiva	UBERON:0001812	72.29	gold quality
vagina	UBERON:0000996	72.05	gold quality
esophagus squamous epithelium	UBERON:0006920	71.79	gold quality
gingival epithelium	UBERON:0001949	71.59	silver quality
buccal mucosa cell	CL:0002336	70.23	gold quality
nasal cavity epithelium	UBERON:0005384	70.13	gold quality
left ovary	UBERON:0002119	69.18	gold quality
tibialis anterior	UBERON:0001385	68.95	silver quality
tibial nerve	UBERON:0001323	68.90	gold quality
tendon of biceps brachii	UBERON:0008188	68.77	silver quality
upper arm skin	UBERON:0004263	68.56	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	68.42	gold quality
esophagus	UBERON:0001043	68.24	gold quality
oral cavity	UBERON:0000167	68.18	gold quality
right adrenal gland cortex	UBERON:0035827	67.56	gold quality
ectocervix	UBERON:0012249	67.48	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	31.90
E-ANND-3	no	3.02

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting C12orf54, 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-4729	99.69	72.18	4233
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-154-3P	99.50	70.05	831
HSA-MIR-487A-3P	99.50	69.95	840
HSA-MIR-548V	99.29	69.47	1157
HSA-MIR-502-5P	98.77	66.51	906
HSA-MIR-1-5P	98.70	68.66	1017
HSA-MIR-219B-5P	97.91	65.80	531
HSA-MIR-6793-3P	97.66	65.78	1084
HSA-MIR-890	97.47	68.67	982
HSA-MIR-3157-5P	97.41	67.61	998
HSA-MIR-4288	97.11	67.23	1636

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Uncharacterized protein C12orf54 — Q6X4T0 (reviewed: Q6X4T0)

All UniProt accessions (3): C9IYT5, H0YIT5, Q6X4T0

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 (2)

UniProt ID	Names	Canonical?
Q6X4T0-1	1	yes
Q6X4T0-2	2

RefSeq proteins (1): NP_689532* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031465	DUF4681	Family

Pfam: PF15732

UniProt features (9 total): compositionally biased region 3, region of interest 2, splice variant 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6X4T0-F1	68.06	0.22

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): FOXJ2_02, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, TAL1BETAITF2_01, RICKMAN_HEAD_AND_NECK_CANCER_E, KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES, MIR502_5P, BDP1_TARGET_GENES, GSE2706_UNSTIM_VS_2H_LPS_AND_R848_DC_DN, GSE2770_IL12_ACT_VS_ACT_CD4_TCELL_2H_UP, GSE1112_OT1_CD8AB_VS_HY_CD8AA_THYMOCYTE_RTOC_CULTURE_UP, ZHOU_INFLAMMATORY_RESPONSE_FIMA_UP, chr12q13, ZID_01, GSE30971_2H_VS_4H_LPS_STIM_MACROPHAGE_WBP7_HET_DN, AATGTGA_MIR23A_MIR23B

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

92 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C12orf54	PAGE3	Q5JUK9	662
C12orf54	MAGEB1	P43366	570
C12orf54	ANP32D	O95626	480
C12orf54	VCX	Q9H320	446
C12orf54	MDH1B	Q5I0G3	435
C12orf54	KXD1	Q9BQD3	418
C12orf54	PPDPF	Q9H3Y8	397
C12orf54	A0A0B4J2G0	A0A0B4J2G0	393
C12orf54	TTLL3	Q9Y4R7	392
C12orf54	SIPA1L2	Q9P2F8	370
C12orf54	A0A0A6YYG9	A0A0A6YYG9	370
C12orf54	MIPOL1	Q8TD10	369
C12orf54	ZNF208	O43345	336
C12orf54	PLAAT1	Q9HDD0	323
C12orf54	DUOXA1	Q1HG43	301

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0D9SF12, A2A8T7, A6H7E2, A6NF36, A6NFA0, A6NI87, E1C7U0, P03246, P03247, P0DO92, P14355, P14683, Q0VG49, Q1HVF6, Q32LN6, Q3KPU7, Q3KSS3, Q4V7D2, Q4ZG55, Q5DU28, Q5JX69, Q5JX71, Q5R7E2, Q5U4U4, Q642A3, Q6NRW0, Q6P1U0, Q6P4J6, Q6P9N1, Q6PEX7, Q6X4T0, Q7L3B6, Q7SYV9, Q7T346, Q80Y73, Q8BJS8, Q8CF25, Q8IWB6, Q8N6T0, Q8NCU1

Diamond homologs: Q3SZX7, Q6X4T0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1287 predictions. Top by Δscore:

Variant	Effect	Δscore
12:48492945:AG:A	acceptor_gain	0.9900
12:48492946:GG:G	acceptor_gain	0.9900
12:48492946:GGGAT:G	acceptor_gain	0.9900
12:48492994:GG:G	donor_gain	0.9900
12:48492995:GG:G	donor_gain	0.9900
12:48492996:G:GG	donor_gain	0.9900
12:48492996:GTA:G	donor_loss	0.9900
12:48492997:T:A	donor_loss	0.9900
12:48492998:A:AG	donor_loss	0.9900
12:48494790:T:A	acceptor_gain	0.9900
12:48494797:GAAGC:G	acceptor_gain	0.9900
12:48494953:G:GT	donor_gain	0.9900
12:48486686:A:AG	acceptor_gain	0.9800
12:48486687:G:GG	acceptor_gain	0.9800
12:48492940:A:AG	acceptor_gain	0.9800
12:48492941:CTTTA:C	acceptor_loss	0.9800
12:48492942:TTTAG:T	acceptor_loss	0.9800
12:48492943:TTA:T	acceptor_loss	0.9800
12:48492944:TA:T	acceptor_loss	0.9800
12:48492945:A:AG	acceptor_gain	0.9800
12:48492945:A:AT	acceptor_loss	0.9800
12:48492945:AGG:A	acceptor_gain	0.9800
12:48492946:G:GG	acceptor_gain	0.9800
12:48492946:GGG:G	acceptor_gain	0.9800
12:48494791:G:A	acceptor_gain	0.9800
12:48492999:AGTGT:A	donor_loss	0.9700
12:48494786:ATTTT:A	acceptor_gain	0.9700
12:48494795:C:G	acceptor_gain	0.9700
12:48494796:A:AG	acceptor_gain	0.9700
12:48494797:G:GG	acceptor_gain	0.9700

AlphaMissense

833 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:48486720:G:C	W43C	0.981
12:48486720:G:T	W43C	0.981
12:48488936:T:C	F50L	0.981
12:48488938:T:A	F50L	0.981
12:48488938:T:G	F50L	0.981
12:48490813:T:C	L57P	0.980
12:48486718:T:A	W43R	0.976
12:48486718:T:C	W43R	0.976
12:48488937:T:C	F50S	0.967
12:48490821:G:C	D60H	0.960
12:48490824:G:C	A61P	0.958
12:48488950:A:C	Q54H	0.948
12:48488950:A:T	Q54H	0.948
12:48488928:T:C	L47P	0.947
12:48486719:G:C	W43S	0.946
12:48488925:T:A	V46E	0.942
12:48490822:A:T	D60V	0.936
12:48490822:A:C	D60A	0.935
12:48490834:G:C	R64P	0.927
12:48490825:C:A	A61D	0.925
12:48488949:A:C	Q54P	0.924
12:48490823:T:A	D60E	0.924
12:48490823:T:G	D60E	0.924
12:48488946:T:A	I53K	0.921
12:48486716:T:C	L42P	0.920
12:48488937:T:G	F50C	0.916
12:48490836:G:T	G65W	0.911
12:48488946:T:G	I53R	0.909
12:48486704:T:G	I38S	0.906
12:48490822:A:G	D60G	0.906

dbSNP variants (sampled 300 via entrez): RS1000005821 (12:48439869 C>A), RS1000069556 (12:48460015 A>C), RS1000079048 (12:48460274 A>G), RS1000110506 (12:48445367 A>G), RS1000153605 (12:48482458 A>C,G), RS1000198688 (12:48450939 A>C), RS1000199491 (12:48465953 A>G), RS1000228266 (12:48454352 G>T), RS1000270761 (12:48414250 T>C), RS1000289335 (12:48434469 G>A), RS1000296745 (12:48495486 T>C), RS1000315043 (12:48489716 C>T), RS1000355023 (12:48450648 A>G), RS1000412913 (12:48419235 G>A,T), RS1000484927 (12:48479071 A>G)

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
GCST010083_167	Hemoglobin levels	3.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004509	hemoglobin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
arsenite	decreases methylation	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Demecolcine	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Malathion	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Vincristine	increases expression	1

Clinical trials (associated diseases)

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