PRAMEF4 (PRAME family member 4) - Rat Genome Database

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Gene: PRAMEF4 (PRAME family member 4) Homo sapiens
Analyze
Symbol: PRAMEF4
Name: PRAME family member 4
RGD ID: 1606074
HGNC Page HGNC:31971
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 located in acrosomal vesicle. Predicted to be active in cytoplasm.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: RP5-845O24.6
RGD Orthologs
Mouse
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
GRCh38112,879,212 - 12,886,201 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl112,879,212 - 12,886,201 (-)EnsemblGRCh38hg38GRCh38
GRCh37112,939,033 - 12,946,025 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36112,861,632 - 12,868,612 (-)NCBINCBI36Build 36hg18NCBI36
Celera111,997,439 - 12,004,238 (-)NCBICelera
Cytogenetic Map1p36.21NCBI
HuRef112,037,903 - 12,044,703 (-)NCBIHuRef
CHM1_1112,927,268 - 12,934,257 (-)NCBICHM1_1
T2T-CHM13v2.0112,423,168 - 12,430,160 (-)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
acrosomal vesicle  (ISO)
cytoplasm  (IBA,IEA)

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16710414   PMID:21873635   PMID:26186194   PMID:27240091   PMID:28514442   PMID:33961781  


Genomics

Comparative Map Data
PRAMEF4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38112,879,212 - 12,886,201 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl112,879,212 - 12,886,201 (-)EnsemblGRCh38hg38GRCh38
GRCh37112,939,033 - 12,946,025 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36112,861,632 - 12,868,612 (-)NCBINCBI36Build 36hg18NCBI36
Celera111,997,439 - 12,004,238 (-)NCBICelera
Cytogenetic Map1p36.21NCBI
HuRef112,037,903 - 12,044,703 (-)NCBIHuRef
CHM1_1112,927,268 - 12,934,257 (-)NCBICHM1_1
T2T-CHM13v2.0112,423,168 - 12,430,160 (-)NCBIT2T-CHM13v2.0
Pramel1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394143,120,889 - 143,126,730 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4143,120,998 - 143,126,730 (+)EnsemblGRCm39 Ensembl
GRCm384143,394,441 - 143,399,819 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4143,394,428 - 143,400,160 (+)EnsemblGRCm38mm10GRCm38
MGSCv374142,984,344 - 142,989,722 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364142,661,115 - 142,666,847 (+)NCBIMGSCv36mm8
Celera4145,219,413 - 145,222,802 (+)NCBICelera
Cytogenetic Map4E1NCBI
cM Map477.64NCBI

Variants

.
Variants in PRAMEF4
61 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 1p36.22-36.21(chr1:12149586-13111056)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051796]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051796]|See cases [RCV000051796] Chr1:12149586..13111056 [GRCh38]
Chr1:12209643..13178528 [GRCh37]
Chr1:12132230..13101115 [NCBI36]
Chr1:1p36.22-36.21		 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 1p36.32-36.21(chr1:4898439-13111056)x1 copy number loss See cases [RCV000053724] Chr1:4898439..13111056 [GRCh38]
Chr1:4958499..13178528 [GRCh37]
Chr1:4858359..13101115 [NCBI36]
Chr1:1p36.32-36.21		 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 1p36.23-36.21(chr1:7165036-13111056)x1 copy number loss See cases [RCV000053755] Chr1:7165036..13111056 [GRCh38]
Chr1:7225096..13178528 [GRCh37]
Chr1:7147683..13101115 [NCBI36]
Chr1:1p36.23-36.21		 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
NM_001009611.4(PRAMEF4):c.970C>G (p.Gln324Glu) single nucleotide variant Malignant melanoma [RCV000064091] Chr1:12880011 [GRCh38]
Chr1:12939832 [GRCh37]
Chr1:12862419 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.655G>A (p.Val219Ile) single nucleotide variant Malignant melanoma [RCV000064092] Chr1:12882074 [GRCh38]
Chr1:12941895 [GRCh37]
Chr1:12864482 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.651G>T (p.Lys217Asn) single nucleotide variant Malignant melanoma [RCV000064093] Chr1:12882078 [GRCh38]
Chr1:12941899 [GRCh37]
Chr1:12864486 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.624T>A (p.Cys208Ter) single nucleotide variant Malignant melanoma [RCV000064094] Chr1:12882105 [GRCh38]
Chr1:12941926 [GRCh37]
Chr1:12864513 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.457G>A (p.Val153Ile) single nucleotide variant Malignant melanoma [RCV000064095] Chr1:12882272 [GRCh38]
Chr1:12942093 [GRCh37]
Chr1:12864680 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.442C>T (p.Pro148Ser) single nucleotide variant Malignant melanoma [RCV000064096] Chr1:12882287 [GRCh38]
Chr1:12942108 [GRCh37]
Chr1:12864695 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.426G>C (p.Arg142Ser) single nucleotide variant Malignant melanoma [RCV000064097] Chr1:12882303 [GRCh38]
Chr1:12942124 [GRCh37]
Chr1:12864711 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.408A>G (p.Pro136=) single nucleotide variant Malignant melanoma [RCV000064098] Chr1:12882321 [GRCh38]
Chr1:12942142 [GRCh37]
Chr1:12864729 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.407C>T (p.Pro136Leu) single nucleotide variant Malignant melanoma [RCV000064099] Chr1:12882322 [GRCh38]
Chr1:12942143 [GRCh37]
Chr1:12864730 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.406C>T (p.Pro136Ser) single nucleotide variant Malignant melanoma [RCV000064100] Chr1:12882323 [GRCh38]
Chr1:12942144 [GRCh37]
Chr1:12864731 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.401A>G (p.Lys134Arg) single nucleotide variant Malignant melanoma [RCV000064101] Chr1:12882328 [GRCh38]
Chr1:12942149 [GRCh37]
Chr1:12864736 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.392A>T (p.Lys131Met) single nucleotide variant Malignant melanoma [RCV000064102] Chr1:12882337 [GRCh38]
Chr1:12942158 [GRCh37]
Chr1:12864745 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.374G>A (p.Gly125Glu) single nucleotide variant Malignant melanoma [RCV000064103] Chr1:12882355 [GRCh38]
Chr1:12942176 [GRCh37]
Chr1:12864763 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.363T>C (p.Ala121=) single nucleotide variant Malignant melanoma [RCV000064104] Chr1:12882366 [GRCh38]
Chr1:12942187 [GRCh37]
Chr1:12864774 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.324G>A (p.Gln108=) single nucleotide variant Malignant melanoma [RCV000064105] Chr1:12882405 [GRCh38]
Chr1:12942226 [GRCh37]
Chr1:12864813 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.253G>A (p.Asp85Asn) single nucleotide variant Malignant melanoma [RCV000064106] Chr1:12883142 [GRCh38]
Chr1:12942963 [GRCh37]
Chr1:12865550 [NCBI36]
Chr1:1p36.21		 not provided
NM_001009611.4(PRAMEF4):c.124T>C (p.Phe42Leu) single nucleotide variant Malignant melanoma [RCV000064107] Chr1:12883271 [GRCh38]
Chr1:12943092 [GRCh37]
Chr1:12865679 [NCBI36]
Chr1:1p36.21		 not provided
GRCh38/hg38 1p36.21(chr1:12852720-13330100)x1 copy number loss See cases [RCV000139263] Chr1:12852720..13330100 [GRCh38]
Chr1:12912573..13448340 [GRCh37]
Chr1:12835160..13320927 [NCBI36]
Chr1:1p36.21		 likely benign
GRCh38/hg38 1p36.22-36.21(chr1:12293275-13111197)x3 copy number gain See cases [RCV000135466] Chr1:12293275..13111197 [GRCh38]
Chr1:12353332..13178669 [GRCh37]
Chr1:12275919..13101256 [NCBI36]
Chr1:1p36.22-36.21		 benign
GRCh38/hg38 1p36.21(chr1:12779298-13075120)x1 copy number loss See cases [RCV000136259] Chr1:12779298..13075120 [GRCh38]
Chr1:12839441..13142569 [GRCh37]
Chr1:12762028..13065156 [NCBI36]
Chr1:1p36.21		 benign
GRCh38/hg38 1p36.21(chr1:12666714-13181499)x3 copy number gain See cases [RCV000136288] Chr1:12666714..13181499 [GRCh38]
Chr1:12726725..13385572 [GRCh37]
Chr1:12649312..13258159 [NCBI36]
Chr1:1p36.21		 benign
GRCh38/hg38 1p36.32-36.21(chr1:4898439-12911913)x1 copy number loss See cases [RCV000137461] Chr1:4898439..12911913 [GRCh38]
Chr1:4958499..12971757 [GRCh37]
Chr1:4858359..12894344 [NCBI36]
Chr1:1p36.32-36.21		 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 1p36.22-36.21(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(chr1:12264268-13119398)x3 copy number gain See cases [RCV000141874] Chr1:12264268..13119398 [GRCh38]
Chr1:12324325..13186871 [GRCh37]
Chr1:12246912..13109458 [NCBI36]
Chr1:1p36.22-36.21		 uncertain significance
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
Single allele complex Breast ductal adenocarcinoma [RCV000207058] Chr1:909238..24706269 [GRCh37]
Chr1:1p36.33-36.11		 uncertain significance
chr1:909238-16736132 complex variant complex Breast ductal adenocarcinoma [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 1p36.22-36.21(chr1:12357424-13187457)x3 copy number gain See cases [RCV000447930] Chr1:12357424..13187457 [GRCh37]
Chr1:1p36.22-36.21		 likely benign
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_001009611.4(PRAMEF4):c.788C>A (p.Thr263Asn) single nucleotide variant Inborn genetic diseases [RCV003300068] Chr1:12881941 [GRCh38]
Chr1:12941762 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.743G>C (p.Arg248Pro) single nucleotide variant Inborn genetic diseases [RCV003285354] Chr1:12881986 [GRCh38]
Chr1:12941807 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.625A>G (p.Ile209Val) single nucleotide variant Inborn genetic diseases [RCV003277504] Chr1:12882104 [GRCh38]
Chr1:12941925 [GRCh37]
Chr1:1p36.21		 uncertain significance
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(chr1:12785494-12998343)x1 copy number loss not provided [RCV000736410] Chr1:12785494..12998343 [GRCh37]
Chr1:1p36.21		 benign
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 1p36.21(chr1:12837728-13052586)x1 copy number loss not provided [RCV000748902] Chr1:12837728..13052586 [GRCh37]
Chr1:1p36.21		 benign
GRCh37/hg19 1p36.21(chr1:12890761-13326730)x1 copy number loss not provided [RCV000748903] Chr1:12890761..13326730 [GRCh37]
Chr1:1p36.21		 benign
NM_001009611.4(PRAMEF4):c.1A>G (p.Met1Val) single nucleotide variant not provided [RCV001573789] Chr1:12883394 [GRCh38]
Chr1:12943215 [GRCh37]
Chr1:1p36.21		 likely benign
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
NM_001009611.4(PRAMEF4):c.83C>G (p.Ser28Cys) single nucleotide variant Inborn genetic diseases [RCV003241854] Chr1:12883312 [GRCh38]
Chr1:12943133 [GRCh37]
Chr1:1p36.21		 uncertain significance
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_001009611.4(PRAMEF4):c.1273G>A (p.Asp425Asn) single nucleotide variant Inborn genetic diseases [RCV002837356] Chr1:12879708 [GRCh38]
Chr1:12939529 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.53G>A (p.Ser18Asn) single nucleotide variant Inborn genetic diseases [RCV002752904] Chr1:12883342 [GRCh38]
Chr1:12943163 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.1133G>A (p.Arg378His) single nucleotide variant Inborn genetic diseases [RCV002749721] Chr1:12879848 [GRCh38]
Chr1:12939669 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.209C>T (p.Pro70Leu) single nucleotide variant Inborn genetic diseases [RCV002860267] Chr1:12883186 [GRCh38]
Chr1:12943007 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.67C>G (p.Gln23Glu) single nucleotide variant Inborn genetic diseases [RCV002992452] Chr1:12883328 [GRCh38]
Chr1:12943149 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.118C>G (p.Pro40Ala) single nucleotide variant Inborn genetic diseases [RCV002992124] Chr1:12883277 [GRCh38]
Chr1:12943098 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.212T>C (p.Leu71Pro) single nucleotide variant Inborn genetic diseases [RCV002864923] Chr1:12883183 [GRCh38]
Chr1:12943004 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.1140T>G (p.Phe380Leu) single nucleotide variant Inborn genetic diseases [RCV002759815] Chr1:12879841 [GRCh38]
Chr1:12939662 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.1142A>C (p.Glu381Ala) single nucleotide variant Inborn genetic diseases [RCV002823480] Chr1:12879839 [GRCh38]
Chr1:12939660 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.170T>C (p.Met57Thr) single nucleotide variant Inborn genetic diseases [RCV002853897] Chr1:12883225 [GRCh38]
Chr1:12943046 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.1292G>A (p.Ser431Asn) single nucleotide variant Inborn genetic diseases [RCV002984637] Chr1:12879689 [GRCh38]
Chr1:12939510 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.148C>T (p.Arg50Cys) single nucleotide variant Inborn genetic diseases [RCV002698652] Chr1:12883247 [GRCh38]
Chr1:12943068 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.1346A>T (p.His449Leu) single nucleotide variant Inborn genetic diseases [RCV002698672] Chr1:12879635 [GRCh38]
Chr1:12939456 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.1144C>A (p.Leu382Ile) single nucleotide variant Inborn genetic diseases [RCV002893157] Chr1:12879837 [GRCh38]
Chr1:12939658 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.1069C>G (p.Leu357Val) single nucleotide variant Inborn genetic diseases [RCV002641107] Chr1:12879912 [GRCh38]
Chr1:12939733 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.772A>T (p.Ile258Phe) single nucleotide variant Inborn genetic diseases [RCV002955756] Chr1:12881957 [GRCh38]
Chr1:12941778 [GRCh37]
Chr1:1p36.21		 likely benign
NM_001009611.4(PRAMEF4):c.1295G>C (p.Arg432Thr) single nucleotide variant Inborn genetic diseases [RCV002955791] Chr1:12879686 [GRCh38]
Chr1:12939507 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.598A>C (p.Ile200Leu) single nucleotide variant Inborn genetic diseases [RCV002855487] Chr1:12882131 [GRCh38]
Chr1:12941952 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.526A>T (p.Arg176Trp) single nucleotide variant Inborn genetic diseases [RCV002672798] Chr1:12882203 [GRCh38]
Chr1:12942024 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.287G>A (p.Arg96His) single nucleotide variant Inborn genetic diseases [RCV003184868] Chr1:12883108 [GRCh38]
Chr1:12942929 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.919G>A (p.Val307Met) single nucleotide variant Inborn genetic diseases [RCV003181020] Chr1:12880062 [GRCh38]
Chr1:12939883 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.583C>T (p.Arg195Cys) single nucleotide variant Inborn genetic diseases [RCV003178897] Chr1:12882146 [GRCh38]
Chr1:12941967 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.1108A>T (p.Asn370Tyr) single nucleotide variant Inborn genetic diseases [RCV003207759] Chr1:12879873 [GRCh38]
Chr1:12939694 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.530A>G (p.Lys177Arg) single nucleotide variant Inborn genetic diseases [RCV003173905] Chr1:12882199 [GRCh38]
Chr1:12942020 [GRCh37]
Chr1:1p36.21		 uncertain significance
NC_000001.10:g.4481271_20530242del deletion Chromosome 1p36 deletion syndrome [RCV003159574] Chr1:4481271..20530242 [GRCh37]
Chr1:1p36.32-36.12		 pathogenic
NM_001009611.4(PRAMEF4):c.319T>G (p.Leu107Val) single nucleotide variant Inborn genetic diseases [RCV003369502] Chr1:12882410 [GRCh38]
Chr1:12942231 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.116C>A (p.Pro39His) single nucleotide variant Inborn genetic diseases [RCV003386577] Chr1:12883279 [GRCh38]
Chr1:12943100 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.1014C>T (p.Tyr338=) single nucleotide variant not provided [RCV003422615] Chr1:12879967 [GRCh38]
Chr1:12939788 [GRCh37]
Chr1:1p36.21		 likely benign
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
NM_001009611.4(PRAMEF4):c.1289G>C (p.Trp430Ser) single nucleotide variant not provided [RCV003422614] Chr1:12879692 [GRCh38]
Chr1:12939513 [GRCh37]
Chr1:1p36.21		 likely benign
NM_001009611.4(PRAMEF4):c.128T>C (p.Met43Thr) single nucleotide variant not provided [RCV003422620] Chr1:12883267 [GRCh38]
Chr1:12943088 [GRCh37]
Chr1:1p36.21		 likely benign
NM_001009611.4(PRAMEF4):c.584G>A (p.Arg195His) single nucleotide variant not provided [RCV003422617] Chr1:12882145 [GRCh38]
Chr1:12941966 [GRCh37]
Chr1:1p36.21		 likely benign
NM_001009611.4(PRAMEF4):c.456C>T (p.Phe152=) single nucleotide variant not provided [RCV003422618] Chr1:12882273 [GRCh38]
Chr1:12942094 [GRCh37]
Chr1:1p36.21		 likely benign
NM_001009611.4(PRAMEF4):c.293+7T>C single nucleotide variant not provided [RCV003422619] Chr1:12883095 [GRCh38]
Chr1:12942916 [GRCh37]
Chr1:1p36.21		 likely benign
NM_001009611.4(PRAMEF4):c.609G>C (p.Met203Ile) single nucleotide variant not provided [RCV003422616] Chr1:12882120 [GRCh38]
Chr1:12941941 [GRCh37]
Chr1:1p36.21		 likely benign
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
GRCh37/hg19 1p36.32-36.21(chr1:4558588-13187457)x1 copy number loss See cases [RCV000446359] Chr1:4558588..13187457 [GRCh37]
Chr1:1p36.32-36.21		 pathogenic
GRCh37/hg19 1p36.22-36.21(chr1:11143298-13709344)x3 copy number gain See cases [RCV000510407] Chr1:11143298..13709344 [GRCh37]
Chr1:1p36.22-36.21		 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
NM_001009611.4(PRAMEF4):c.349G>T (p.Val117Phe) single nucleotide variant Inborn genetic diseases [RCV002750016] Chr1:12882380 [GRCh38]
Chr1:12942201 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.838G>A (p.Val280Ile) single nucleotide variant Inborn genetic diseases [RCV002744338] Chr1:12881891 [GRCh38]
Chr1:12941712 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.650A>C (p.Lys217Thr) single nucleotide variant Inborn genetic diseases [RCV002644843] Chr1:12882079 [GRCh38]
Chr1:12941900 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.1055C>T (p.Ala352Val) single nucleotide variant Inborn genetic diseases [RCV002960520] Chr1:12879926 [GRCh38]
Chr1:12939747 [GRCh37]
Chr1:1p36.21		 likely benign
NM_001009611.4(PRAMEF4):c.8T>C (p.Met3Thr) single nucleotide variant Inborn genetic diseases [RCV003345546] Chr1:12883387 [GRCh38]
Chr1:12943208 [GRCh37]
Chr1:1p36.21		 uncertain significance
NM_001009611.4(PRAMEF4):c.577C>T (p.Pro193Ser) single nucleotide variant Inborn genetic diseases [RCV003348433] Chr1:12882152 [GRCh38]
Chr1:12941973 [GRCh37]
Chr1:1p36.21		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:140
Count of miRNA genes:138
Interacting mature miRNAs:140
Transcripts:ENST00000235349
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.

Markers in Region
D1S3693  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map16q24.3UniSTS
Cytogenetic Map22q13.1UniSTS
Cytogenetic Map3p22UniSTS
Cytogenetic Map22q12.1UniSTS
Cytogenetic Map20q11.21UniSTS
Cytogenetic Map21q22.3UniSTS
Cytogenetic Map17q25.3UniSTS
Cytogenetic Map13q34UniSTS
Cytogenetic Map1q22-q23UniSTS
Cytogenetic Map1p36.21UniSTS
Cytogenetic Map19p13UniSTS
Cytogenetic Map8p21.3UniSTS
Cytogenetic Map20q13.33UniSTS
Cytogenetic Map11q13.2UniSTS
Cytogenetic Map12p13.3UniSTS
Cytogenetic Map15q14UniSTS
Cytogenetic Map6p25.2UniSTS
Cytogenetic MapXp22.33UniSTS
Cytogenetic MapYp11.32UniSTS
Cytogenetic Map10p15.3-p15.2UniSTS
Cytogenetic Map13q14.13UniSTS
Cytogenetic Map17p13.3UniSTS
Cytogenetic Map3p22.3UniSTS
Cytogenetic Map2q13UniSTS
Cytogenetic Map1q32.3-q41UniSTS
Cytogenetic Map1p13.3UniSTS
Cytogenetic Map11q13.5UniSTS
Cytogenetic Map9q34.11UniSTS
Cytogenetic Map1p36.32UniSTS
Cytogenetic Map19q13.42UniSTS
Cytogenetic Map11q13UniSTS
Cytogenetic Map1q32.1UniSTS
Cytogenetic Map22q13.2UniSTS
Cytogenetic Map19p13.3UniSTS
Cytogenetic Map17q12UniSTS


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 9 9 1 9
Low 2 37 37 3 37 3 2 3 1 7 1 1
Below cutoff 99 110 148 114 64 111 113 78 64 6 231 39 3 26 79

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000235349   ⟹   ENSP00000235349
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl112,879,212 - 12,886,201 (-)Ensembl
RefSeq Acc Id: NM_001009611   ⟹   NP_001009611
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38112,879,212 - 12,886,201 (-)NCBI
GRCh37112,939,033 - 12,946,025 (-)RGD
Build 36112,861,632 - 12,868,612 (-)NCBI Archive
CHM1_1112,927,268 - 12,934,257 (-)NCBI
T2T-CHM13v2.0112,423,168 - 12,430,160 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001009611 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAB41253 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000235349
  ENSP00000235349.5
  ENSP00000488161.1
GenBank Protein O60810 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001009611   ⟸   NM_001009611
- UniProtKB: Q5LJB5 (UniProtKB/Swiss-Prot),   O60810 (UniProtKB/Swiss-Prot),   B7ZW04 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000235349   ⟸   ENST00000235349

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O60810-F1-model_v2 AlphaFold O60810 1-478 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:31971 AgrOrtholog
COSMIC PRAMEF4 COSMIC
Ensembl Genes ENSG00000243073 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSG00000282584 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000235349 ENTREZGENE
  ENST00000235349.6 UniProtKB/Swiss-Prot
  ENST00000632563.2 UniProtKB/Swiss-Prot
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000243073 GTEx
  ENSG00000282584 GTEx
HGNC ID HGNC:31971 ENTREZGENE
Human Proteome Map PRAMEF4 Human Proteome Map
InterPro LRR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PRAME_family UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:400735 UniProtKB/Swiss-Prot
NCBI Gene 400735 ENTREZGENE
PANTHER PRAME FAMILY MEMBER 11-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SIMILAR TO PREFERENTIALLY EXPRESSED ANTIGEN IN MELANOMA-LIKE 3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA142671141 PharmGKB
PIRSF PRAME UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP RNI-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B7ZW04 ENTREZGENE, UniProtKB/TrEMBL
  O60810 ENTREZGENE, UniProtKB/Swiss-Prot
  Q5LJB5 ENTREZGENE
UniProt Secondary Q5LJB5 UniProtKB/Swiss-Prot