PRAMEF20

Summary

PRAMEF20 (PRAME family member 20, HGNC:25224) is a protein-coding gene on chromosome 1p36.21, encoding PRAME family member 20 (Q5VT98).

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 645425 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 18 total
• MANE Select transcript: NM_001099852

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25224
Approved symbol	PRAMEF20
Name	PRAME family member 20
Location	1p36.21
Locus type	gene with protein product
Status	Approved
Aliases	OTTHUMG00000007911, OTTHUMT00000008157
Ensembl gene	ENSG00000204478
Ensembl biotype	protein_coding
Entrez	645425

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000602960

RefSeq mRNA: 1 — MANE Select: NM_001099852 NM_001099852

CCDS: CCDS41265

Canonical transcript exons

ENST00000602960 — 4 exons

Exon	Start	End
ENSE00001664409	13416351	13416641
ENSE00001757194	13418122	13418700
ENSE00001762385	13420697	13421328
ENSE00003970019	13410450	13410544

Expression profiles

Bgee: expression breadth tissue_specific, 1 present calls, max score 41.18.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	41.18	gold quality
colonic epithelium	UBERON:0000397	37.20	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
hindlimb stylopod muscle	UBERON:0004252	35.74	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	35.06	gold quality
muscle tissue	UBERON:0002385	32.29	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
monocyte	CL:0000576	30.50	gold quality
lymph node	UBERON:0000029	30.31	gold quality
leukocyte	CL:0000738	30.24	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.21	gold quality
urinary bladder	UBERON:0001255	28.86	gold quality
liver	UBERON:0002107	28.65	gold quality
duodenum	UBERON:0002114	28.14	gold quality
right adrenal gland cortex	UBERON:0035827	28.07	gold quality
muscle of leg	UBERON:0001383	27.99	gold quality
adrenal tissue	UBERON:0018303	27.23	gold quality
ectocervix	UBERON:0012249	26.86	silver quality
blood	UBERON:0000178	26.77	gold quality
gastrocnemius	UBERON:0001388	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
placenta	UBERON:0001987	25.81	gold quality
pancreas	UBERON:0001264	25.12	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.47

Regulation

Is transcription factor: no

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), PRAMEF2 (ENSG00000120952), LRRC14 (ENSG00000160959), PRAMEF8 (ENSG00000182330), LRRC14B (ENSG00000185028), PRAME (ENSG00000185686), PRAMEF10 (ENSG00000187545), 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 20 — Q5VT98 (reviewed: Q5VT98)

All UniProt accessions (1): Q5VT98

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the PRAME family.

RefSeq proteins (1): NP_001093322* (*=MANE)

Domains & families (InterPro)

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

UniProt features (10 total): repeat 9, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VT98-F1	85.13	0.54

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 25 (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, GOMF_MOLECULAR_ADAPTOR_ACTIVITY, GOCC_INTRACELLULAR_PROTEIN_CONTAINING_COMPLEX, GOBP_PROTEOLYSIS_INVOLVED_IN_PROTEIN_CATABOLIC_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

2153 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRAMEF20	NANOGNB	Q7Z5D8	555
PRAMEF20	OR51A2	Q8NGJ7	545
PRAMEF20	SAAL1	Q96ER3	519
PRAMEF20	TANGO6	Q9C0B7	488
PRAMEF20	ISOC1	Q96CN7	440
PRAMEF20	FASTKD1	Q53R41	440
PRAMEF20	ZER1	Q7Z7L7	407
PRAMEF20	SCAPER	Q9BY12	399
PRAMEF20	WFIKKN2	Q8TEU8	381
PRAMEF20	PLEKHM3	Q6ZWE6	381
PRAMEF20	POLR1F	Q3B726	375
PRAMEF20	MCTP2	Q6DN12	372
PRAMEF20	MICU3	Q86XE3	369
PRAMEF20	HTRA4	P83105	363
PRAMEF20	DET1	Q7L5Y6	323

IntAct

3 interactions, top by confidence:

A	B	Type	Score
K8.1	EXOC5	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): PRAMEF20 (Affinity Capture-MS), PRAMEF20 (Affinity Capture-MS)

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, Q1L8H0, Q640Z9, Q8VC16, P59047, Q7TSF4, Q8NAA5

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	14
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

543 predictions. Top by Δscore:

Variant	Effect	Δscore
1:13418697:TCAG:T	donor_loss	1.0000
1:13418698:CAG:C	donor_loss	1.0000
1:13418698:CAGG:C	donor_loss	1.0000
1:13418699:AG:A	donor_loss	1.0000
1:13418699:AGG:A	donor_loss	1.0000
1:13418700:GGTG:G	donor_loss	1.0000
1:13418701:G:GA	donor_loss	1.0000
1:13420695:A:AG	acceptor_gain	1.0000
1:13420696:G:GG	acceptor_gain	1.0000
1:13420696:GCT:G	acceptor_gain	1.0000
1:13410528:G:GG	donor_gain	0.9900
1:13416342:CAGAT:C	acceptor_loss	0.9900
1:13416343:A:AG	acceptor_gain	0.9900
1:13416344:G:A	acceptor_loss	0.9900
1:13416344:G:GG	acceptor_gain	0.9900
1:13416500:G:GG	donor_gain	0.9900
1:13416637:CTCAG:C	donor_loss	0.9900
1:13416638:TCAG:T	donor_loss	0.9900
1:13416641:GG:G	donor_loss	0.9900
1:13416642:GTG:G	donor_loss	0.9900
1:13416643:T:A	donor_loss	0.9900
1:13418118:TCAG:T	acceptor_loss	0.9900
1:13418119:CAG:C	acceptor_loss	0.9900
1:13418120:A:AC	acceptor_loss	0.9900
1:13418120:A:C	acceptor_loss	0.9900
1:13418120:AG:A	acceptor_gain	0.9900
1:13418120:AGGAG:A	acceptor_gain	0.9900
1:13418121:G:GT	acceptor_loss	0.9900
1:13418121:G:T	acceptor_loss	0.9900
1:13418121:GG:G	acceptor_gain	0.9900

AlphaMissense

3120 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:13416535:T:C	F61L	0.927
1:13416537:C:A	F61L	0.927
1:13416537:C:G	F61L	0.927
1:13416529:T:A	W59R	0.898
1:13416529:T:C	W59R	0.898
1:13418168:T:C	F112L	0.880
1:13418170:C:A	F112L	0.880
1:13418170:C:G	F112L	0.880
1:13416460:T:C	F36L	0.877
1:13416462:T:A	F36L	0.877
1:13416462:T:G	F36L	0.877
1:13420991:T:A	N387K	0.876
1:13420991:T:G	N387K	0.876
1:13418504:T:C	F224L	0.873
1:13418506:T:A	F224L	0.873
1:13418506:T:G	F224L	0.873
1:13421082:A:C	S418R	0.864
1:13421084:T:A	S418R	0.864
1:13421084:T:G	S418R	0.864
1:13416484:T:C	F44L	0.860
1:13416486:C:A	F44L	0.860
1:13416486:C:G	F44L	0.860
1:13421184:T:C	F452L	0.850
1:13421186:C:A	F452L	0.850
1:13421186:C:G	F452L	0.850
1:13418669:T:C	F279L	0.843
1:13418671:C:A	F279L	0.843
1:13418671:C:G	F279L	0.843
1:13421060:G:C	E410D	0.833
1:13421060:G:T	E410D	0.833

dbSNP variants (sampled 300 via entrez): RS1000340460 (1:13412419 C>T), RS1000359063 (1:13412724 G>A,C), RS1000414338 (1:13418406 T>C), RS1000705380 (1:13411196 G>A,C,T), RS1000818659 (1:13417196 G>A), RS1001513216 (1:13412266 C>T), RS1001591995 (1:13417021 C>T), RS1001640993 (1:13417904 G>C), RS1001672294 (1:13417638 G>A), RS1001880997 (1:13410831 C>A), RS1001943974 (1:13412052 A>T), RS1002200057 (1:13421626 G>A), RS1002248279 (1:13411026 T>G), RS1002571646 (1:13420361 C>A,T), RS1002593389 (1:13413039 A>G,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

1 associations (top):

Study	Trait	p-value
GCST002938_8	Copper levels	7.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	1
Arsenic	affects methylation	1
Plant Extracts	decreases expression, affects cotreatment	1

Clinical trials (associated diseases)

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