PRAMEF20 (PRAME family member 20) - Rat Genome Database

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Gene: PRAMEF20 (PRAME family member 20) Homo sapiens
Analyze
Symbol: PRAMEF20
Name: PRAME family member 20
RGD ID: 1626252
HGNC Page HGNC:25224
Description: Predicted to be involved in several processes, including negative regulation of DNA-templated transcription; negative regulation of apoptotic process; and positive regulation of cell population proliferation. Predicted to be active in cytoplasm.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: PRAME family member 20/21; PRAME family member 21; PRAMEF21
RGD Orthologs
Mouse
Rat
Bonobo
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38113,410,450 - 13,421,328 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl113,410,450 - 13,421,328 (+)EnsemblGRCh38hg38GRCh38
GRCh37113,736,907 - 13,747,803 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36113,609,494 - 13,620,390 (+)NCBINCBI36Build 36hg18NCBI36
Celera112,219,063 - 12,229,938 (+)NCBICelera
Cytogenetic Map1p36.21NCBI
HuRef112,253,404 - 12,264,251 (+)NCBIHuRef
CHM1_1113,535,692 - 13,546,570 (+)NCBICHM1_1
T2T-CHM13v2.0112,851,719 - 12,862,598 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,IEA)

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16159394   PMID:16710414   PMID:21873635   PMID:25544563  


Genomics

Comparative Map Data
PRAMEF20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38113,410,450 - 13,421,328 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl113,410,450 - 13,421,328 (+)EnsemblGRCh38hg38GRCh38
GRCh37113,736,907 - 13,747,803 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36113,609,494 - 13,620,390 (+)NCBINCBI36Build 36hg18NCBI36
Celera112,219,063 - 12,229,938 (+)NCBICelera
Cytogenetic Map1p36.21NCBI
HuRef112,253,404 - 12,264,251 (+)NCBIHuRef
CHM1_1113,535,692 - 13,546,570 (+)NCBICHM1_1
T2T-CHM13v2.0112,851,719 - 12,862,598 (+)NCBIT2T-CHM13v2.0
Pramel15
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394144,099,330 - 144,104,503 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4144,099,330 - 144,104,530 (-)EnsemblGRCm39 Ensembl
GRCm384144,372,760 - 144,377,933 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4144,372,760 - 144,377,933 (-)EnsemblGRCm38mm10GRCm38
MGSCv374143,962,663 - 143,967,836 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364143,639,447 - 143,644,620 (-)NCBIMGSCv36mm8
MGSCv364141,694,228 - 141,699,541 (-)NCBIMGSCv36mm8
Celera4145,973,855 - 145,979,151 (-)NCBICelera
Cytogenetic Map4E1NCBI
cM Map477.98NCBI
Pramef20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85161,454,398 - 161,458,874 (-)NCBIGRCr8
mRatBN7.25156,171,125 - 156,175,601 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5156,171,125 - 156,175,601 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.05162,406,599 - 162,411,066 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5162,406,599 - 162,411,063 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05166,097,294 - 166,101,846 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45162,746,264 - 162,750,628 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5154,474,742 - 154,479,271 (-)NCBICelera
Cytogenetic Map5q36NCBI
PRAMEF20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21213,494,300 - 213,506,635 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11212,745,084 - 212,760,561 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0112,006,813 - 12,010,964 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1113,553,798 - 13,564,608 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl113,553,798 - 13,564,608 (+)Ensemblpanpan1.1panPan2

Variants

.
Variants in PRAMEF20
8 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p36.31-36.13(chr1:6853513-17326813)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051795]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051795]|See cases [RCV000051795] Chr1:6853513..17326813 [GRCh38]
Chr1:6913573..17685411 [GRCh37]
Chr1:6836160..17557998 [NCBI36]
Chr1:1p36.31-36.13
pathogenic
GRCh38/hg38 1p36.21-36.12(chr1:13110797-20670207)x3 copy number gain See cases [RCV000051797] Chr1:13110797..20670207 [GRCh38]
Chr1:13178269..20996700 [GRCh37]
Chr1:13100856..20869287 [NCBI36]
Chr1:1p36.21-36.12
pathogenic
GRCh38/hg38 1p36.32-36.13(chr1:3006193-17688934)x1 copy number loss See cases [RCV000053714] Chr1:3006193..17688934 [GRCh38]
Chr1:2922757..18015429 [GRCh37]
Chr1:2912617..17888016 [NCBI36]
Chr1:1p36.32-36.13
pathogenic
GRCh38/hg38 1p36.22-36.12(chr1:10556797-22557907)x1 copy number loss See cases [RCV000053760] Chr1:10556797..22557907 [GRCh38]
Chr1:10616854..22884400 [GRCh37]
Chr1:10539441..22756987 [NCBI36]
Chr1:1p36.22-36.12
pathogenic
GRCh38/hg38 1p36.22-36.13(chr1:10621776-16520709)x1 copy number loss See cases [RCV000053763] Chr1:10621776..16520709 [GRCh38]
Chr1:10681833..16847204 [GRCh37]
Chr1:10604420..16719791 [NCBI36]
Chr1:1p36.22-36.13
pathogenic
GRCh38/hg38 1p36.22-36.13(chr1:10809039-16422500)x1 copy number loss See cases [RCV000053765] Chr1:10809039..16422500 [GRCh38]
Chr1:10869096..16748995 [GRCh37]
Chr1:10791683..16621582 [NCBI36]
Chr1:1p36.22-36.13
pathogenic
GRCh38/hg38 1p36.22-36.13(chr1:11121625-16324498)x1 copy number loss See cases [RCV000053766] Chr1:11121625..16324498 [GRCh38]
Chr1:11181682..16650993 [GRCh37]
Chr1:11104269..16523580 [NCBI36]
Chr1:1p36.22-36.13
pathogenic
GRCh38/hg38 1p36.23-36.13(chr1:9034671-16441465)x1 copy number loss See cases [RCV000053756] Chr1:9034671..16441465 [GRCh38]
Chr1:9094730..16767960 [GRCh37]
Chr1:9017317..16640547 [NCBI36]
Chr1:1p36.23-36.13
pathogenic
GRCh38/hg38 1p36.21-36.13(chr1:12724785-16034788)x1 copy number loss See cases [RCV000137720] Chr1:12724785..16034788 [GRCh38]
Chr1:12784752..16361283 [GRCh37]
Chr1:12707339..16233870 [NCBI36]
Chr1:1p36.21-36.13
pathogenic
GRCh38/hg38 1p36.21(chr1:12627415-13993978)x3 copy number gain See cases [RCV000138029] Chr1:12627415..13993978 [GRCh38]
Chr1:12687421..14320473 [GRCh37]
Chr1:12610008..14193060 [NCBI36]
Chr1:1p36.21
likely pathogenic
GRCh38/hg38 1p36.31-36.21(chr1:6303641-15799093)x1 copy number loss See cases [RCV000137948] Chr1:6303641..15799093 [GRCh38]
Chr1:6363701..16125588 [GRCh37]
Chr1:6286288..15998175 [NCBI36]
Chr1:1p36.31-36.21
pathogenic|likely benign
GRCh38/hg38 1p36.21(chr1:13400935-15356944)x1 copy number loss See cases [RCV000138889] Chr1:13400935..15356944 [GRCh38]
Chr1:13727391..15683440 [GRCh37]
Chr1:13599978..15556027 [NCBI36]
Chr1:1p36.21
likely pathogenic
GRCh38/hg38 1p36.22-36.21(chr1:9428538-15815791)x1 copy number loss See cases [RCV000140873] Chr1:9428538..15815791 [GRCh38]
Chr1:9488597..16142286 [GRCh37]
Chr1:9411184..16014873 [NCBI36]
Chr1:1p36.22-36.21
pathogenic
GRCh38/hg38 1p36.22-36.21(chr1:11021751-15236671)x3 copy number gain See cases [RCV000141823] Chr1:11021751..15236671 [GRCh38]
Chr1:11081808..15563167 [GRCh37]
Chr1:11004395..15435754 [NCBI36]
Chr1:1p36.22-36.21
likely pathogenic
GRCh38/hg38 1p36.22-36.21(chr1:10264397-15780840)x1 copy number loss See cases [RCV000141438] Chr1:10264397..15780840 [GRCh38]
Chr1:10324455..16107335 [GRCh37]
Chr1:10247042..15979922 [NCBI36]
Chr1:1p36.22-36.21
pathogenic
GRCh38/hg38 1p36.31-36.13(chr1:6554885-16056011)x3 copy number gain See cases [RCV000142906] Chr1:6554885..16056011 [GRCh38]
Chr1:6614945..16382506 [GRCh37]
Chr1:6537532..16255093 [NCBI36]
Chr1:1p36.31-36.13
pathogenic
GRCh38/hg38 1p36.31-36.13(chr1:5363826-18360302)x1 copy number loss See cases [RCV000142771] Chr1:5363826..18360302 [GRCh38]
Chr1:5423886..18686796 [GRCh37]
Chr1:5323746..18559383 [NCBI36]
Chr1:1p36.31-36.13
pathogenic
Single allele complex Ductal breast carcinoma [RCV000207058] Chr1:909238..24706269 [GRCh37]
Chr1:1p36.33-36.11
uncertain significance
chr1:909238-16736132 complex variant complex Ductal breast carcinoma [RCV000207094] Chr1:909238..16736132 [GRCh37]
Chr1:1p36.33-36.13
uncertain significance
GRCh37/hg19 1p36.33-36.21(chr1:746608-15077159)x1 copy number loss See cases [RCV000240403] Chr1:746608..15077159 [GRCh37]
Chr1:1p36.33-36.21
pathogenic
GRCh37/hg19 1p36.32-36.12(chr1:2749920-22564787)x1 copy number loss See cases [RCV000446470] Chr1:2749920..22564787 [GRCh37]
Chr1:1p36.32-36.12
pathogenic
GRCh37/hg19 1p36.21-36.13(chr1:13178371-19961858)x1 copy number loss See cases [RCV000447987] Chr1:13178371..19961858 [GRCh37]
Chr1:1p36.21-36.13
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
NM_001099852.2(PRAMEF20):c.247G>A (p.Asp83Asn) single nucleotide variant Inborn genetic diseases [RCV003296532] Chr1:13416601 [GRCh38]
Chr1:13743058 [GRCh37]
Chr1:1p36.21
uncertain significance
GRCh37/hg19 1p36.22-36.21(chr1:10722725-14267773)x1 copy number loss See cases [RCV000512501] Chr1:10722725..14267773 [GRCh37]
Chr1:1p36.22-36.21
likely pathogenic
GRCh37/hg19 1p36.23-36.13(chr1:8850514-16272383)x1 copy number loss See cases [RCV000512226] Chr1:8850514..16272383 [GRCh37]
Chr1:1p36.23-36.13
likely pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.21(chr1:12741240-15768304)x1 copy number loss not provided [RCV000736409] Chr1:12741240..15768304 [GRCh37]
Chr1:1p36.21
uncertain significance
GRCh37/hg19 1p36.22-21.1(chr1:103343285-103455144)x3 copy number gain Global developmental delay [RCV000787285] Chr1:103343285..103455144 [GRCh37]
Chr1:1p36.22-21.1
uncertain significance
GRCh37/hg19 1p36.21(chr1:13709328-13948225)x3 copy number gain not provided [RCV001005069] Chr1:13709328..13948225 [GRCh37]
Chr1:1p36.21
likely benign
GRCh37/hg19 1p36.33-36.13(chr1:849466-17525065)x1 copy number loss not provided [RCV001832902] Chr1:849466..17525065 [GRCh37]
Chr1:1p36.33-36.13
pathogenic
NC_000001.11:g.10115497_16283149dup duplication not specified [RCV002286386] Chr1:10115497..16283149 [GRCh38]
Chr1:1p36.22-36.13
likely pathogenic
GRCh37/hg19 1p36.31-36.13(chr1:6758933-19287770)x1 copy number loss not provided [RCV002474779] Chr1:6758933..19287770 [GRCh37]
Chr1:1p36.31-36.13
pathogenic
NM_001099852.2(PRAMEF20):c.197T>C (p.Leu66Pro) single nucleotide variant Inborn genetic diseases [RCV002902228] Chr1:13416551 [GRCh38]
Chr1:13743008 [GRCh37]
Chr1:1p36.21
uncertain significance
NM_001099852.2(PRAMEF20):c.188G>A (p.Arg63His) single nucleotide variant Inborn genetic diseases [RCV002749715] Chr1:13416542 [GRCh38]
Chr1:13742999 [GRCh37]
Chr1:1p36.21
uncertain significance
NM_001099852.2(PRAMEF20):c.280C>T (p.Arg94Cys) single nucleotide variant Inborn genetic diseases [RCV002734429] Chr1:13416634 [GRCh38]
Chr1:13743091 [GRCh37]
Chr1:1p36.21
uncertain significance
NM_001099852.2(PRAMEF20):c.65C>T (p.Ala22Val) single nucleotide variant Inborn genetic diseases [RCV002779187] Chr1:13416419 [GRCh38]
Chr1:13742876 [GRCh37]
Chr1:1p36.21
uncertain significance
NM_001099852.2(PRAMEF20):c.199G>A (p.Gly67Arg) single nucleotide variant Inborn genetic diseases [RCV002707242] Chr1:13416553 [GRCh38]
Chr1:13743010 [GRCh37]
Chr1:1p36.21
uncertain significance
NM_001099852.2(PRAMEF20):c.83T>C (p.Leu28Pro) single nucleotide variant Inborn genetic diseases [RCV002763753] Chr1:13416437 [GRCh38]
Chr1:13742894 [GRCh37]
Chr1:1p36.21
uncertain significance
NM_001099852.2(PRAMEF20):c.136A>G (p.Arg46Gly) single nucleotide variant Inborn genetic diseases [RCV003209291] Chr1:13416490 [GRCh38]
Chr1:13742947 [GRCh37]
Chr1:1p36.21
likely benign
NC_000001.10:g.4481271_20530242del deletion Chromosome 1p36 deletion syndrome [RCV003159574] Chr1:4481271..20530242 [GRCh37]
Chr1:1p36.32-36.12
pathogenic
GRCh38/hg38 1p36.33-35.1(chr1:99125-34026935)x3 copy number gain Trisomy 12p [RCV003447845] Chr1:99125..34026935 [GRCh38]
Chr1:1p36.33-35.1
pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:229
Count of miRNA genes:111
Interacting mature miRNAs:115
Transcripts:ENST00000316412, ENST00000602960
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage
High
Medium 1
Low 6 4 4 6 6 19 3 2
Below cutoff 136 155 123 16 95 12 353 249 194 13 420 63 4 51 285

Sequence


RefSeq Acc Id: ENST00000316412   ⟹   ENSP00000346275
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl113,410,450 - 13,421,328 (+)Ensembl
RefSeq Acc Id: ENST00000602960   ⟹   ENSP00000473584
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl113,410,450 - 13,421,328 (+)Ensembl
RefSeq Acc Id: NM_001099852   ⟹   NP_001093322
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38113,410,450 - 13,421,328 (+)NCBI
GRCh37113,736,907 - 13,747,803 (+)RGD
Build 36113,609,494 - 13,620,390 (+)NCBI Archive
CHM1_1113,535,692 - 13,546,570 (+)NCBI
T2T-CHM13v2.0112,851,719 - 12,862,598 (+)NCBI
Sequence:
RefSeq Acc Id: XM_054338214   ⟹   XP_054194189
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0112,857,605 - 12,862,598 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001093322 (Get FASTA)   NCBI Sequence Viewer  
  XP_054194189 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000473584
  ENSP00000473584.1
GenBank Protein Q5VT98 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001093322   ⟸   NM_001099852
- UniProtKB: Q5VT98 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000473584   ⟸   ENST00000602960
RefSeq Acc Id: ENSP00000346275   ⟸   ENST00000316412
RefSeq Acc Id: XP_054194189   ⟸   XM_054338214
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5VT98-F1-model_v2 AlphaFold Q5VT98 1-475 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:25224 AgrOrtholog
COSMIC PRAMEF20 COSMIC
Ensembl Genes ENSG00000204478 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000602960 ENTREZGENE
  ENST00000602960.2 UniProtKB/Swiss-Prot
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot
GTEx ENSG00000204478 GTEx
HGNC ID HGNC:25224 ENTREZGENE
Human Proteome Map PRAMEF20 Human Proteome Map
InterPro LRR_dom_sf UniProtKB/Swiss-Prot
  PRAME_family UniProtKB/Swiss-Prot
KEGG Report hsa:645425 UniProtKB/Swiss-Prot
NCBI Gene 645425 ENTREZGENE
PANTHER PRAME FAMILY MEMBER 20 UniProtKB/Swiss-Prot
  SIMILAR TO PREFERENTIALLY EXPRESSED ANTIGEN IN MELANOMA-LIKE 3 UniProtKB/Swiss-Prot
PharmGKB PA145148198 PharmGKB
PIRSF PRAME UniProtKB/Swiss-Prot
Superfamily-SCOP RNI-like UniProtKB/Swiss-Prot
UniProt PRA20_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-22 PRAMEF20  PRAME family member 20  PRAMEF21  PRAME family member 21  Data merged from RGD:1604150 737654 PROVISIONAL