PRAMEF12

Summary

PRAMEF12 (PRAME family member 12, HGNC:22125) is a protein-coding gene on chromosome 1p36.21, encoding PRAME family member 12 (O95522).

Predicted to enable ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be part of Cul2-RING ubiquitin ligase complex. Predicted to be active in cytoplasm.

Source: NCBI Gene 390999 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 84 total
• MANE Select transcript: NM_001080830

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22125
Approved symbol	PRAMEF12
Name	PRAME family member 12
Location	1p36.21
Locus type	gene with protein product
Status	Approved
Aliases	OTTHUMG00000001927
Ensembl gene	ENSG00000116726
Ensembl biotype	protein_coding
Entrez	390999

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000357726

RefSeq mRNA: 1 — MANE Select: NM_001080830 NM_001080830

CCDS: CCDS41254

Canonical transcript exons

ENST00000357726 — 3 exons

Exon	Start	End
ENSE00001402229	12777011	12777906
ENSE00001469725	12773738	12775154
ENSE00001726997	12775543	12776118

Expression profiles

Bgee: expression breadth tissue_specific, 1 present calls, max score 83.50.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
type B pancreatic cell	CL:0000169	83.50	gold quality
olfactory bulb	UBERON:0002264	83.39	gold quality
endometrium epithelium	UBERON:0004811	79.81	gold quality
diaphragm	UBERON:0001103	77.34	gold quality
frontal pole	UBERON:0002795	77.10	gold quality
paraflocculus	UBERON:0005351	76.54	gold quality
middle frontal gyrus	UBERON:0002702	75.78	gold quality
Brodmann (1909) area 10	UBERON:0013541	73.74	gold quality
vastus lateralis	UBERON:0001379	72.41	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	72.15	silver quality
quadriceps femoris	UBERON:0001377	71.75	gold quality
upper arm skin	UBERON:0004263	71.47	gold quality
mucosa of urinary bladder	UBERON:0001259	71.38	gold quality
triceps brachii	UBERON:0001509	71.06	gold quality
gluteal muscle	UBERON:0002000	71.06	gold quality
epithelial cell of pancreas	CL:0000083	71.01	gold quality
cervix epithelium	UBERON:0004801	70.91	gold quality
cerebellar vermis	UBERON:0004720	70.22	gold quality
thymus	UBERON:0002370	69.64	gold quality
myocardium	UBERON:0002349	69.51	gold quality
cervix squamous epithelium	UBERON:0006922	68.87	gold quality
metanephric glomerulus	UBERON:0004736	68.61	gold quality
cardiac muscle of right atrium	UBERON:0003379	67.74	gold quality
left ventricle myocardium	UBERON:0006566	67.73	gold quality
nasal cavity epithelium	UBERON:0005384	67.12	gold quality
layer of synovial tissue	UBERON:0007616	66.44	gold quality
kidney epithelium	UBERON:0004819	66.38	gold quality
dorsal plus ventral thalamus	UBERON:0001897	65.74	gold quality
lateral globus pallidus	UBERON:0002476	65.61	gold quality
superficial temporal artery	UBERON:0001614	65.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-3929	yes	944.02
E-ANND-3	no	1.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting PRAMEF12, 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-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-4690-5P	99.65	66.24	813
HSA-MIR-6758-3P	99.57	67.55	1078
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-330-5P	98.73	67.63	1788
HSA-MIR-326	98.25	66.44	1565
HSA-MIR-6501-5P	97.41	68.24	712
HSA-MIR-7106-3P	97.33	65.33	644
HSA-MIR-671-3P	92.07	62.01	40

Literature-anchored findings (GeneRIF, showing 1)

• PRAMEF12, a novel cancer/testis gene, regulates proliferation and apoptosis to promote progression of glioma. (PMID:38913622)

Cross-species orthologs

125 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch73-174h16.4	ENSDARG00000036493
mus_musculus	Pramel6	ENSMUSG00000025838
mus_musculus	Pramel7	ENSMUSG00000025839
mus_musculus	Pramel13	ENSMUSG00000028591
mus_musculus	Pramel27	ENSMUSG00000029451
mus_musculus	Pramel17	ENSMUSG00000035201
mus_musculus	Pramel5	ENSMUSG00000036749
mus_musculus	Pramel18	ENSMUSG00000037028
mus_musculus	Pramel32	ENSMUSG00000038330
mus_musculus	Pramel1	ENSMUSG00000041805
mus_musculus	C130073F10Rik	ENSMUSG00000046133
mus_musculus	Pramel29	ENSMUSG00000046262
mus_musculus	Pramel24	ENSMUSG00000046435
mus_musculus	Pramel12	ENSMUSG00000046862
mus_musculus	Oog4	ENSMUSG00000047799
mus_musculus	Oog3	ENSMUSG00000050810
mus_musculus	Pramel26	ENSMUSG00000059218
mus_musculus	Pramel51	ENSMUSG00000066027
mus_musculus	Oog2	ENSMUSG00000066030
mus_musculus	Pramel25	ENSMUSG00000066031
mus_musculus	Pramel21	ENSMUSG00000066688
mus_musculus	Gm13040	ENSMUSG00000070616
mus_musculus	Pramel23	ENSMUSG00000070617
mus_musculus	Pramel20	ENSMUSG00000070618
mus_musculus	Pramel31	ENSMUSG00000070619
mus_musculus	Pramel48	ENSMUSG00000070677
mus_musculus	Pramel34	ENSMUSG00000070686
mus_musculus	Pramel19	ENSMUSG00000070890
mus_musculus	Pramel55	ENSMUSG00000072813
mus_musculus	Pramel54	ENSMUSG00000072814
mus_musculus	Pramel53	ENSMUSG00000072821
mus_musculus	Pramel37	ENSMUSG00000072822
mus_musculus	Pramel15	ENSMUSG00000073721
mus_musculus	Pramel61	ENSMUSG00000073723
mus_musculus	Pramel4	ENSMUSG00000073724
mus_musculus	Pramel41	ENSMUSG00000074011
		ENSMUSG00000074720
mus_musculus	Pramel30	ENSMUSG00000078508
mus_musculus	Pramel14	ENSMUSG00000078509
mus_musculus	Pramel28	ENSMUSG00000078510
mus_musculus	Pramel16	ENSMUSG00000078511
mus_musculus	Pramel11	ENSMUSG00000078512
mus_musculus	Pramel22	ENSMUSG00000078513
mus_musculus	Prame62	ENSMUSG00000078625
mus_musculus	Gm12790	ENSMUSG00000078626
mus_musculus	Pramel57	ENSMUSG00000079423
mus_musculus	Pramel47	ENSMUSG00000079424
		ENSMUSG00000091585
mus_musculus	Pramel45	ENSMUSG00000092166
mus_musculus	Pramel49	ENSMUSG00000094043
		ENSMUSG00000094172
mus_musculus	Pramel44	ENSMUSG00000094195
		ENSMUSG00000094303
		ENSMUSG00000094337
		ENSMUSG00000094383
		ENSMUSG00000094474
		ENSMUSG00000094722
		ENSMUSG00000094741
		ENSMUSG00000094791
		ENSMUSG00000094836
		ENSMUSG00000094855
		ENSMUSG00000094887
mus_musculus	Pramel42	ENSMUSG00000095074
mus_musculus	Gm13043	ENSMUSG00000095409
		ENSMUSG00000095475
mus_musculus	Pramel43	ENSMUSG00000095503
		ENSMUSG00000095505
		ENSMUSG00000095523
		ENSMUSG00000095570
		ENSMUSG00000095666
mus_musculus	Pramel40	ENSMUSG00000095718
		ENSMUSG00000095763
mus_musculus	Pramel56	ENSMUSG00000095954
mus_musculus	Pramel60	ENSMUSG00000095996
mus_musculus	Pramel33	ENSMUSG00000096044
mus_musculus	Pramel46	ENSMUSG00000096066
mus_musculus	Pramel50	ENSMUSG00000096139
mus_musculus	Gm13057	ENSMUSG00000096154
mus_musculus	Pramel36	ENSMUSG00000096230
		ENSMUSG00000096236
mus_musculus	Pramel38	ENSMUSG00000096259
mus_musculus	Gm2042	ENSMUSG00000096276
		ENSMUSG00000096550
mus_musculus	Oog1	ENSMUSG00000096576
		ENSMUSG00000096680
		ENSMUSG00000096728
		ENSMUSG00000096756
mus_musculus	Pramel35	ENSMUSG00000107392
rattus_norvegicus	Pramel6	ENSRNOG00000021920
rattus_norvegicus	Pramel7	ENSRNOG00000021949
rattus_norvegicus	Pramef25	ENSRNOG00000027000
rattus_norvegicus	Oog3	ENSRNOG00000027142
rattus_norvegicus	Pramef8	ENSRNOG00000027278
rattus_norvegicus	Pramef27	ENSRNOG00000027328
rattus_norvegicus	Oog1	ENSRNOG00000033000
rattus_norvegicus	Pramef12	ENSRNOG00000037035
rattus_norvegicus	Oog3l1	ENSRNOG00000037039
rattus_norvegicus	Pramef17	ENSRNOG00000042820
rattus_norvegicus	Pramel36	ENSRNOG00000043130
rattus_norvegicus	Oog3l2	ENSRNOG00000045614
rattus_norvegicus	Pramel36l1	ENSRNOG00000046931
rattus_norvegicus	LOC120103107	ENSRNOG00000047341
rattus_norvegicus	Pramef20	ENSRNOG00000053942
rattus_norvegicus	LOC134481896	ENSRNOG00000062749
rattus_norvegicus	Pramel53l1	ENSRNOG00000063444
rattus_norvegicus	LOC120096511	ENSRNOG00000063633
rattus_norvegicus	Pramel36l1	ENSRNOG00000064574
rattus_norvegicus	Pramef20l1	ENSRNOG00000065680
rattus_norvegicus		ENSRNOG00000065869
rattus_norvegicus	LOC134481897	ENSRNOG00000067003
rattus_norvegicus	Pramef8l2	ENSRNOG00000067042
rattus_norvegicus	Pramel34	ENSRNOG00000067111
rattus_norvegicus	Pramef5	ENSRNOG00000067307
rattus_norvegicus	Pramef20-ps1	ENSRNOG00000067899
rattus_norvegicus		ENSRNOG00000071611
rattus_norvegicus		ENSRNOG00000072535
rattus_norvegicus		ENSRNOG00000073402
rattus_norvegicus		ENSRNOG00000073978
rattus_norvegicus		ENSRNOG00000075698
rattus_norvegicus		ENSRNOG00000077508
rattus_norvegicus		ENSRNOG00000083237
rattus_norvegicus		ENSRNOG00000084642
rattus_norvegicus		ENSRNOG00000086814
rattus_norvegicus		ENSRNOG00000088869
rattus_norvegicus		ENSRNOG00000089019

Paralogs (24): PRAMEF1 (ENSG00000116721), PRAMEF2 (ENSG00000120952), LRRC14 (ENSG00000160959), PRAMEF8 (ENSG00000182330), LRRC14B (ENSG00000185028), PRAME (ENSG00000185686), PRAMEF10 (ENSG00000187545), PRAMEF20 (ENSG00000204478), PRAMEF17 (ENSG00000204479), PRAMEF19 (ENSG00000204480), PRAMEF14 (ENSG00000204481), PRAMEF15 (ENSG00000204501), PRAMEF9 (ENSG00000204505), PRAMEF7 (ENSG00000204510), PRAMEF25 (ENSG00000229571), PRAMEF6 (ENSG00000232423), PRAMEF33 (ENSG00000237700), PRAMEF11 (ENSG00000239810), PRAMEF4 (ENSG00000243073), PRAMEF5 (ENSG00000270601), PRAMEF27 (ENSG00000274764), PRAMEF13 (ENSG00000279169), PRAMEF18 (ENSG00000279804), PRAMEF26 (ENSG00000280267)

Protein

Protein identifiers

PRAME family member 12 — O95522 (reviewed: O95522)

All UniProt accessions (1): O95522

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the PRAME family.

RefSeq proteins (1): NP_001074299* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026271	PRAME	Family
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR050694	LRRC14/PRAME	Family

UniProt features (12 total): repeat 9, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95522-F1	86.22	0.62

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 53 (showing top): GOBP_MACROMOLECULE_CATABOLIC_PROCESS, INGRAM_SHH_TARGETS_UP, GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, YAMAZAKI_TCEB3_TARGETS_DN, GOBP_PROTEIN_CATABOLIC_PROCESS, GOCC_TRANSFERASE_COMPLEX, GOBP_PROTEOLYSIS, GOCC_CULLIN_RING_UBIQUITIN_LIGASE_COMPLEX, GOCC_UBIQUITIN_LIGASE_COMPLEX, chr1p36, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MARTENS_TRETINOIN_RESPONSE_UP, GOBP_POSITIVE_REGULATION_OF_CELL_POPULATION_PROLIFERATION, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS

GO Biological Process (5): positive regulation of cell population proliferation (GO:0008284), negative regulation of apoptotic process (GO:0043066), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), negative regulation of cell differentiation (GO:0045596), negative regulation of DNA-templated transcription (GO:0045892)

GO Molecular Function (1): ubiquitin-like ligase-substrate adaptor activity (GO:1990756)

GO Cellular Component (2): cytoplasm (GO:0005737), Cul2-RING ubiquitin ligase complex (GO:0031462)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell population proliferation	1
regulation of cell population proliferation	1
positive regulation of cellular process	1
apoptotic process	1
regulation of apoptotic process	1
negative regulation of programmed cell death	1
ubiquitin-dependent protein catabolic process	1
proteasomal protein catabolic process	1
cell differentiation	1
regulation of cell differentiation	1
negative regulation of cellular process	1
negative regulation of developmental process	1
DNA-templated transcription	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
enzyme-substrate adaptor activity	1
intracellular anatomical structure	1
cellular anatomical structure	1
cullin-RING ubiquitin ligase complex	1

Protein interactions and networks

STRING

2343 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRAMEF12	RFPL1	O75677	557
PRAMEF12	RFPL2	O75678	502
PRAMEF12	TRIM43	Q96BQ3	471
PRAMEF12	MBD3L2	Q8NHZ7	448
PRAMEF12	ZSCAN4	Q8NAM6	437
PRAMEF12	RFPL3	O75679	434
PRAMEF12	IQCF3	P0C7M6	431
PRAMEF12	FAM170B	A6NMN3	420
PRAMEF12	DUX4L2	P0CJ85	375
PRAMEF12	CWF19L2	Q2TBE0	374
PRAMEF12	RFPL4B	Q6ZWI9	371
PRAMEF12	HEATR5A	Q86XA9	349
PRAMEF12	TEX29	Q8N6K0	348
PRAMEF12	KHDC1L	Q5JSQ8	339
PRAMEF12	FAM186A	A6NE01	325

IntAct

2 interactions, top by confidence:

A	B	Type	Score
PRAMEF12	HSPA8	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A0A0G2JMD5, A1Z198, A3QJZ6, A3QJZ7, A6NGN4, D9I2F9, D9I2G1, D9I2G3, D9I2G4, D9I2H0, E9Q5G7, H0Y7S4, O60809, O60810, O60811, O60813, O95521, O95522, P0DUQ1, P0DUQ2, P78395, Q0GKD5, Q288C4, Q2LKU9, Q2LKV5, Q2LKW6, Q3TKR3, Q3UWY1, Q5SWL7, Q5SWL8, Q5TYX0, Q5VT98, Q5VTA0, Q5VWM3, Q5VWM4, Q5VWM6, Q5VXH4, Q5VXH5, Q66X05, Q66X19

Diamond homologs: A0A0G2JMD5, A3QJZ6, A3QJZ7, A6NGN4, E9Q5G7, H0Y7S4, O60809, O60810, O60811, O60813, O95521, O95522, P0DUQ1, P0DUQ2, P78395, Q3UWY1, Q5SWL7, Q5SWL8, Q5TYX0, Q5VT98, Q5VTA0, Q5VWM3, Q5VWM4, Q5VWM6, Q5VXH4, Q5VXH5, Q7TPX8, Q810Y8, Q99MW3, Q3UJB3, A5PJJ5, Q15048, Q569B5, A6NHZ5, Q640Z9, P59047, Q7TSF4, Q8NAA5, Q8VC16

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	76
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

503 predictions. Top by Δscore:

Variant	Effect	Δscore
1:12775152:CAGG:C	donor_loss	1.0000
1:12775153:AG:A	donor_loss	1.0000
1:12775154:GGTGA:G	donor_loss	1.0000
1:12775874:G:GT	donor_gain	1.0000
1:12775878:TGG:T	donor_gain	1.0000
1:12776120:T:A	donor_loss	1.0000
1:12776124:G:GT	donor_gain	1.0000
1:12777009:A:AG	acceptor_gain	1.0000
1:12777009:AG:A	acceptor_gain	1.0000
1:12777009:AGGT:A	acceptor_gain	1.0000
1:12777010:G:A	acceptor_gain	1.0000
1:12777010:G:GA	acceptor_gain	1.0000
1:12777010:GGT:G	acceptor_gain	1.0000
1:12777010:GGTG:G	acceptor_gain	1.0000
1:12777010:GGTGT:G	acceptor_gain	1.0000
1:12774966:G:GT	donor_gain	0.9900
1:12775538:CACA:C	acceptor_loss	0.9900
1:12775540:CAGG:C	acceptor_loss	0.9900
1:12775541:A:T	acceptor_loss	0.9900
1:12775541:AGGC:A	acceptor_gain	0.9900
1:12775542:GGC:G	acceptor_gain	0.9900
1:12775542:GGCG:G	acceptor_gain	0.9900
1:12775631:GCCC:G	donor_gain	0.9900
1:12775879:GGA:G	donor_gain	0.9900
1:12775880:G:GT	donor_gain	0.9900
1:12776127:GTATG:G	donor_gain	0.9900
1:12775535:A:AG	acceptor_gain	0.9800
1:12775541:A:AG	acceptor_gain	0.9800
1:12775541:AGGCG:A	acceptor_gain	0.9800
1:12775542:G:GG	acceptor_gain	0.9800

AlphaMissense

3143 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:12775048:T:C	F61L	0.945
1:12775050:C:A	F61L	0.945
1:12775050:C:G	F61L	0.945
1:12775042:T:A	W59R	0.943
1:12775042:T:C	W59R	0.943
1:12777396:A:C	S417R	0.939
1:12777398:T:A	S417R	0.939
1:12777398:T:G	S417R	0.939
1:12777211:T:C	L355S	0.913
1:12776087:T:C	F278L	0.909
1:12776089:C:A	F278L	0.909
1:12776089:C:G	F278L	0.909
1:12777305:C:A	N386K	0.905
1:12777305:C:G	N386K	0.905
1:12775589:T:C	F112L	0.896
1:12775591:C:A	F112L	0.896
1:12775591:C:G	F112L	0.896
1:12774973:T:C	F36L	0.893
1:12774975:T:A	F36L	0.893
1:12774975:T:G	F36L	0.893
1:12777432:T:C	F429L	0.893
1:12777434:T:A	F429L	0.893
1:12777434:T:G	F429L	0.893
1:12777498:T:C	F451L	0.892
1:12777500:C:A	F451L	0.892
1:12777500:C:G	F451L	0.892
1:12777374:G:C	E409D	0.890
1:12777374:G:T	E409D	0.890
1:12775919:T:C	F222L	0.885
1:12775921:C:A	F222L	0.885

dbSNP variants (sampled 300 via entrez): RS1000221329 (1:12776131 G>A,C), RS1000507971 (1:12775216 T>G), RS1003168079 (1:12774144 T>G), RS1003256734 (1:12775117 G>A), RS1003522059 (1:12774428 C>T), RS1003616628 (1:12778289 C>A), RS1003911431 (1:12772805 C>T), RS1004280870 (1:12773179 C>A), RS1004355116 (1:12776731 G>A,T), RS1004442545 (1:12772891 C>T), RS1004668645 (1:12778099 G>C), RS1004669473 (1:12777097 G>C), RS1006460419 (1:12773858 A>G), RS1006895532 (1:12776822 T>A), RS1007627265 (1:12773302 T>C)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	increases expression	1
sodium arsenite	affects methylation	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Copper	affects cotreatment, decreases expression	1
Cyclosporine	increases methylation	1

Clinical trials (associated diseases)

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