PRAMEF2

Summary

PRAMEF2 (PRAME family member 2, HGNC:28841) is a protein-coding gene on chromosome 1p36.21, encoding PRAME family member 2 (O60811).

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 65122 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 68 total
• MANE Select transcript: NM_023014

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28841
Approved symbol	PRAMEF2
Name	PRAME family member 2
Location	1p36.21
Locus type	gene with protein product
Status	Approved
Aliases	FLJ43580
Ensembl gene	ENSG00000120952
Ensembl biotype	protein_coding
Entrez	65122

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000240189

RefSeq mRNA: 1 — MANE Select: NM_023014 NM_023014

CCDS: CCDS149

Canonical transcript exons

ENST00000240189 — 4 exons

Exon	Start	End
ENSE00001680306	12857086	12857147
ENSE00001765410	12859693	12860271
ENSE00001780999	12861221	12861909
ENSE00001790912	12858985	12859296

Expression profiles

Bgee: expression breadth not_expressed, 0 present calls, max score 37.20.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	37.20	gold quality
sural nerve	UBERON:0015488	36.49	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	34.92	gold quality
muscle tissue	UBERON:0002385	32.19	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
urinary bladder	UBERON:0001255	28.98	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
leukocyte	CL:0000738	27.44	gold quality
monocyte	CL:0000576	27.42	gold quality
tonsil	UBERON:0002372	27.05	gold quality
blood	UBERON:0000178	26.62	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
ectocervix	UBERON:0012249	25.88	gold quality
placenta	UBERON:0001987	25.81	gold quality
uterine cervix	UBERON:0000002	25.38	gold quality
muscle of leg	UBERON:0001383	25.35	gold quality
primary visual cortex	UBERON:0002436	24.61	gold quality
pancreas	UBERON:0001264	24.58	gold quality
gastrocnemius	UBERON:0001388	24.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.17

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

19 targeting PRAMEF2, 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-3646	100.00	73.56	5283
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-122B-5P	99.46	70.81	1457
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-7850-5P	98.12	67.28	1111
HSA-MIR-500A-3P	97.60	67.48	595
HSA-MIR-1271-3P	97.56	64.85	865
HSA-MIR-550A-3-5P	97.56	65.35	823
HSA-MIR-550A-5P	97.56	65.35	823
HSA-MIR-411-5P	97.11	66.82	601
HSA-MIR-3116	97.07	65.78	1324
HSA-MIR-376A-2-5P	96.43	68.06	715

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), PRAMEF12 (ENSG00000116726), 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 2 — O60811 (reviewed: O60811)

All UniProt accessions (1): O60811

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the PRAME family.

RefSeq proteins (1): NP_075390* (*=MANE)

Domains & families (InterPro)

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

UniProt features (26 total): sequence variant 16, repeat 9, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O60811-F1	81.46	0.43

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 43 (showing top): GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, GOBP_PROTEIN_CATABOLIC_PROCESS, GOCC_TRANSFERASE_COMPLEX, GOBP_PROTEOLYSIS, GOCC_CULLIN_RING_UBIQUITIN_LIGASE_COMPLEX, GOCC_UBIQUITIN_LIGASE_COMPLEX, chr1p36, GOBP_POSITIVE_REGULATION_OF_CELL_POPULATION_PROLIFERATION, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOCC_CUL2_RING_UBIQUITIN_LIGASE_COMPLEX, GSE10240_CTRL_VS_IL17_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP, MIR3646, MIR126_5P

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

2297 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRAMEF2	KRTAP13-3	Q3SY46	772
PRAMEF2	KHDC1L	Q5JSQ8	717
PRAMEF2	TRIM43	Q96BQ3	694
PRAMEF2	LEUTX	A8MZ59	653
PRAMEF2	KHDC1	Q4VXA5	623
PRAMEF2	CASP14	P31944	523
PRAMEF2	DUX4L2	P0CJ85	515
PRAMEF2	RFPL2	O75678	506
PRAMEF2	GRM7	Q14831	480
PRAMEF2	RFPL1	O75677	476
PRAMEF2	TRIM49	P0CI25	474
PRAMEF2	ZSCAN4	Q8NAM6	444
PRAMEF2	MBD3L2	Q8NHZ7	435
PRAMEF2	CCER1	Q8TC90	412
PRAMEF2	OR2T8	A6NH00	407

IntAct

0 interactions, top by confidence:

BioGRID (20): KHSRP (Affinity Capture-MS), TCEB2 (Affinity Capture-MS), TCEB1 (Affinity Capture-MS), RBX1 (Affinity Capture-MS), CUL2 (Affinity Capture-MS), LATS1 (Affinity Capture-MS), WDR5 (Affinity Capture-MS), FBXO2 (Affinity Capture-MS), DNAJB1 (Affinity Capture-MS), YBX1 (Affinity Capture-MS), API5 (Affinity Capture-MS), DEK (Affinity Capture-MS), SMARCB1 (Affinity Capture-MS), ANXA1 (Affinity Capture-MS), CUL2 (Affinity Capture-Western)

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	51
Likely benign	15
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

995 predictions. Top by Δscore:

Variant	Effect	Δscore
1:12858984:GA:G	acceptor_gain	1.0000
1:12859256:G:GT	donor_gain	1.0000
1:12859293:CCAG:C	donor_loss	1.0000
1:12859294:CAG:C	donor_loss	1.0000
1:12859295:AG:A	donor_loss	1.0000
1:12859297:GTGAG:G	donor_loss	1.0000
1:12859912:G:GG	donor_gain	1.0000
1:12861219:A:AG	acceptor_gain	1.0000
1:12861219:A:G	acceptor_loss	1.0000
1:12861220:G:A	acceptor_loss	1.0000
1:12861220:G:GG	acceptor_gain	1.0000
1:12861220:GGT:G	acceptor_gain	1.0000
1:12858983:A:AG	acceptor_gain	0.9900
1:12858984:G:GG	acceptor_gain	0.9900
1:12858984:GAGA:G	acceptor_gain	0.9900
1:12858984:GAGAT:G	acceptor_gain	0.9900
1:12859297:G:GG	donor_gain	0.9900
1:12859787:GCCA:G	donor_gain	0.9900
1:12859794:G:GG	donor_gain	0.9900
1:12859874:G:GT	donor_gain	0.9900
1:12859875:A:T	donor_gain	0.9900
1:12859886:G:GT	donor_gain	0.9900
1:12859928:A:T	donor_gain	0.9900
1:12860267:ATCAG:A	donor_loss	0.9900
1:12860268:TCAGG:T	donor_loss	0.9900
1:12860269:CAG:C	donor_loss	0.9900
1:12860270:AG:A	donor_loss	0.9900
1:12860271:GGTGA:G	donor_loss	0.9900
1:12860272:G:T	donor_loss	0.9900
1:12860273:T:G	donor_loss	0.9900

AlphaMissense

3098 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:12861253:T:C	L300S	0.912
1:12861606:A:C	S418R	0.902
1:12861608:T:A	S418R	0.902
1:12861608:T:G	S418R	0.902
1:12859190:T:C	F61L	0.891
1:12859192:C:A	F61L	0.891
1:12859192:C:G	F61L	0.891
1:12861421:T:C	L356S	0.878
1:12861247:T:C	L298S	0.876
1:12861705:T:C	F451L	0.873
1:12861707:C:A	F451L	0.873
1:12861707:C:G	F451L	0.873
1:12861504:T:C	F384L	0.872
1:12861506:T:A	F384L	0.872
1:12861506:T:G	F384L	0.872
1:12861436:T:C	I361T	0.856
1:12861584:G:C	E410D	0.855
1:12861584:G:T	E410D	0.855
1:12859184:T:A	W59R	0.853
1:12859184:T:C	W59R	0.853
1:12859139:T:C	F44L	0.851
1:12859141:C:A	F44L	0.851
1:12859141:C:G	F44L	0.851
1:12861574:T:C	L407S	0.835
1:12861415:T:A	L354H	0.830
1:12860240:T:C	F279L	0.822
1:12860242:C:A	F279L	0.822
1:12860242:C:G	F279L	0.822
1:12859915:G:C	W170C	0.818
1:12859915:G:T	W170C	0.818

dbSNP variants (sampled 300 via entrez): RS1000756610 (1:12858174 G>A,C), RS1001228456 (1:12858806 T>C), RS1003344895 (1:12856052 C>T), RS1003416242 (1:12858091 G>A), RS1004676984 (1:12858779 A>T), RS1006430729 (1:12857604 G>C,T), RS1006807396 (1:12858356 A>C), RS1007782518 (1:12856226 C>G,T), RS1010612529 (1:12857812 C>T), RS1010991 (1:12861941 T>G), RS1012052586 (1:12855371 C>T), RS1013614765 (1:12861472 T>C,G), RS1015651853 (1:12860501 A>C,G), RS1015725522 (1:12860748 GT>G), RS1015985417 (1:12858519 T>C)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:600057

GenCC curated gene-disease

Mondo (1): bladder exstrophy-epispadias-cloacal exstrophy complex (MONDO:0700039)

Orphanet (1): Classic bladder exstrophy (Orphanet:93930)

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

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	increases reaction, affects binding	1
Aflatoxin B1	increases expression	1

Clinical trials (associated diseases)

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