PFDN4 (prefoldin subunit 4) - Rat Genome Database

Name: PFDN4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: PFDN4 (prefoldin subunit 4) Homo sapiens

Analyze

Symbol:

PFDN4

Name:

prefoldin subunit 4

RGD ID:

1347549

HGNC Page

HGNC:8868

Description:

Enables amyloid-beta binding activity and unfolded protein binding activity. Involved in negative regulation of amyloid fibril formation and protein folding. Located in mitochondrion and nucleus. Part of prefoldin complex.

Type:

protein-coding

RefSeq Status:

REVIEWED

Previously known as:

C1; PFD4; prefoldin 4; protein C-1

RGD Orthologs

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Mus musculus (house mouse):	Pfdn4 (prefoldin 4)	HGNC	EggNOG, Ensembl, HGNC, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Rattus norvegicus (Norway rat):	Pfdn4 (prefoldin subunit 4)	HGNC	EggNOG, Ensembl, HomoloGene, NCBI, OMA, OrthoDB, Panther
Chinchilla lanigera (long-tailed chinchilla):	Pfdn4 (prefoldin subunit 4)	NCBI	Ortholog
Pan paniscus (bonobo/pygmy chimpanzee):	PFDN4 (prefoldin subunit 4)	NCBI	Ortholog
Canis lupus familiaris (dog):	PFDN4 (prefoldin subunit 4)	HGNC	HomoloGene, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pfdn4 (prefoldin subunit 4)	NCBI	Ortholog
Sus scrofa (pig):	PFDN4 (prefoldin subunit 4)	HGNC	EggNOG, Inparanoid, NCBI, OMA, OrthoDB, Panther, Treefam
Chlorocebus sabaeus (green monkey):	PFDN4 (prefoldin subunit 4)	NCBI	Ortholog
Heterocephalus glaber (naked mole-rat):	Pfdn4 (prefoldin subunit 4)	NCBI	Ortholog
Other homologs ²
Canis lupus familiaris (dog):	LOC610170 (prefoldin subunit 4 pseudogene)	HGNC	EggNOG, OMA, Panther
Sus scrofa (pig):	LOC100157600 (prefoldin subunit 4 pseudogene)	HGNC	Ensembl
Alliance orthologs ³
Mus musculus (house mouse):	Pfdn4 (prefoldin 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Rattus norvegicus (Norway rat):	Pfdn4 (prefoldin subunit 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	pfdn4 (prefoldin subunit 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid\|ZFIN)
Saccharomyces cerevisiae (baker's yeast):	GIM3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Pfdn4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	pfd-4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus laevis (African clawed frog):	pfdn4.S	Alliance	DIOPT (Xenbase)
Xenopus laevis (African clawed frog):	pfdn4.L	Alliance	DIOPT (Xenbase)
Xenopus tropicalis (tropical clawed frog):	pfdn4	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)

Related Pseudogenes:

AC006028.1

Allele / Splice:

See ClinVar data

Latest Assembly:

GRCh38 - Human Genome Assembly GRCh38

Position:

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	20	54,208,087 - 54,219,961 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	20	54,208,087 - 54,228,052 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	20	52,824,626 - 52,836,500 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	20	52,257,909 - 52,269,899 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	20	52,257,908 - 52,269,898	NCBI
Celera	20	49,529,139 - 49,541,129 (+)	NCBI		Celera
Cytogenetic Map	20	q13.2	NCBI
HuRef	20	49,571,022 - 49,583,013 (+)	NCBI		HuRef
CHM1_1	20	52,727,643 - 52,739,633 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	20	55,982,176 - 55,994,287 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (IAGP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (ISO)

(1->4)-beta-D-glucan (ISO)

1H-pyrazole (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

3-isobutyl-1-methyl-7H-xanthine (EXP)

4,4'-sulfonyldiphenol (EXP)

4-hydroxyphenyl retinamide (ISO)

aflatoxin M1 (EXP)

all-trans-retinoic acid (EXP)

Aroclor 1254 (ISO)

arsenite(3-) (EXP)

avobenzone (EXP)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

Bisphenol B (EXP)

bisphenol F (EXP)

bortezomib (EXP)

carbon nanotube (ISO)

choline (ISO)

copper(II) sulfate (EXP)

crocidolite asbestos (ISO)

cyclosporin A (EXP)

dexamethasone (EXP)

dibutyl phthalate (ISO)

dicrotophos (EXP)

doxorubicin (EXP)

enzyme inhibitor (EXP)

ethanol (ISO)

fenthion (ISO)

folic acid (ISO)

FR900359 (EXP)

gentamycin (ISO)

hydrogen peroxide (EXP)

indometacin (EXP)

ivermectin (EXP)

L-methionine (ISO)

mercury atom (ISO)

mercury(0) (ISO)

ozone (EXP,ISO)

paracetamol (ISO)

pentachlorophenol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

pirinixic acid (ISO)

resveratrol (EXP)

sodium arsenite (EXP)

tetrachloromethane (ISO)

thimerosal (EXP)

thioacetamide (ISO)

titanium dioxide (ISO)

tungsten (ISO)

valproic acid (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

chaperone-mediated protein folding (NAS)

negative regulation of amyloid fibril formation (IDA)

protein folding (IBA,IDA,IEA,TAS)

Cellular Component

cytoplasm (IBA,IDA,IEA)

cytosol (NAS)

membrane (IEA)

mitochondrion (IDA,IEA)

nucleus (IDA,IEA)

prefoldin complex (IBA,IDA,IEA,NAS)

Molecular Function

amyloid-beta binding (IDA)

protein binding (IPI)

protein-folding chaperone binding (TAS)

unfolded protein binding (IBA,IDA,IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	GOAs Human GO annotations	GOA_HUMAN data from the GO Consortium
2.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:8744932	PMID:9630229	PMID:10209023	PMID:10542082	PMID:11381030	PMID:11780052	PMID:11884745	PMID:12456645	PMID:12477932	PMID:14615539	PMID:14634002	PMID:15489334
PMID:17936702	PMID:19615732	PMID:20360068	PMID:20552408	PMID:21873635	PMID:22863883	PMID:22939629	PMID:23042114	PMID:23251661	PMID:23349634	PMID:23602568	PMID:23614719
PMID:24981860	PMID:25332235	PMID:25416956	PMID:25515538	PMID:25900982	PMID:26186194	PMID:26344197	PMID:26496610	PMID:26638075	PMID:26777405	PMID:27432908	PMID:27609421
PMID:27705803	PMID:27880917	PMID:28514442	PMID:28675297	PMID:28718761	PMID:28883622	PMID:29531219	PMID:29568061	PMID:30209976	PMID:30561431	PMID:30890647	PMID:30955883
PMID:31536960	PMID:31980649	PMID:32296183	PMID:32699605	PMID:32707033	PMID:32743796	PMID:32877691	PMID:33137104	PMID:33306668	PMID:33961781	PMID:34709727	PMID:35140242
PMID:35271311	PMID:35384245	PMID:35831314	PMID:36215168	PMID:37589075	PMID:37689310

Genomics

Comparative Map Data

PFDN4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	20	54,208,087 - 54,219,961 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	20	54,208,087 - 54,228,052 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	20	52,824,626 - 52,836,500 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	20	52,257,909 - 52,269,899 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	20	52,257,908 - 52,269,898	NCBI
Celera	20	49,529,139 - 49,541,129 (+)	NCBI		Celera
Cytogenetic Map	20	q13.2	NCBI
HuRef	20	49,571,022 - 49,583,013 (+)	NCBI		HuRef
CHM1_1	20	52,727,643 - 52,739,633 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	20	55,982,176 - 55,994,287 (+)	NCBI		T2T-CHM13v2.0

Pfdn4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	170,338,348 - 170,360,987 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	170,338,348 - 170,361,043 (+)	Ensembl		GRCm39 Ensembl
GRCm38	2	170,496,428 - 170,519,070 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	170,496,428 - 170,519,123 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	170,321,928 - 170,344,567 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	170,187,633 - 170,210,272 (+)	NCBI		MGSCv36	mm8
Celera	2	176,450,878 - 176,475,133 (+)	NCBI		Celera
Cytogenetic Map	2	H3	NCBI
cM Map	2	91.91	NCBI

Pfdn4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	179,721,765 - 179,729,901 (+)	NCBI		GRCr8
mRatBN7.2	3	159,303,173 - 159,311,221 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	159,303,071 - 159,311,219 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	163,102,547 - 163,110,617 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	171,602,181 - 171,610,251 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	169,343,410 - 169,351,480 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	168,124,634 - 168,132,739 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	168,124,673 - 168,132,786 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	174,227,543 - 174,235,604 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	3	157,847,358 - 157,855,463 (+)	NCBI		Celera
Cytogenetic Map	3	q42	NCBI

Pfdn4
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955445	4,831,493 - 4,844,168 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955445	4,832,220 - 4,844,007 (-)	NCBI	ChiLan1.0	ChiLan1.0

PFDN4
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	21	59,960,517 - 59,972,191 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	20	59,953,663 - 59,965,781 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	20	50,554,477 - 50,566,496 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	20	51,776,590 - 51,788,389 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	20	51,775,932 - 51,788,389 (+)	Ensembl	panpan1.1		panPan2

PFDN4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	24	39,904,803 - 39,915,173 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	24	39,910,458 - 39,915,164 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	24	39,149,417 - 39,160,953 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	24	40,616,922 - 40,629,139 (+)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	24	39,852,414 - 39,864,964 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	24	39,987,742 - 39,999,577 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	24	40,570,359 - 40,582,785 (+)	NCBI		UU_Cfam_GSD_1.0

Pfdn4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024408640	185,985,115 - 185,994,421 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936514	1,438,523 - 1,448,189 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936514	1,438,742 - 1,448,008 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PFDN4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	17	55,155,772 - 55,168,024 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	17	55,155,772 - 55,168,024 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	17	61,937,884 - 61,950,193 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PFDN4
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	2	9,823,762 - 9,835,010 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	2	9,823,297 - 9,835,384 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666050	57,943,415 - 57,954,986 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Pfdn4
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624790	2,151,082 - 2,162,643 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624790	2,151,353 - 2,161,331 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in PFDN4
6 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 20q13.13-13.2(chr20:49947237-55875406)x3	copy number gain	See cases [RCV000053037]	Chr20:49947237..55875406 [GRCh38] Chr20:48563774..54450462 [GRCh37] Chr20:47997181..53883869 [NCBI36] Chr20:20q13.13-13.2	pathogenic
GRCh38/hg38 20q13.12-13.33(chr20:44787704-64277321)x3	copy number gain	See cases [RCV000053035]	Chr20:44787704..64277321 [GRCh38] Chr20:43416345..62908674 [GRCh37] Chr20:42849759..62379118 [NCBI36] Chr20:20q13.12-13.33	pathogenic
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3	copy number gain	See cases [RCV000135859]	Chr20:99557..64277321 [GRCh38] Chr20:80198..62908674 [GRCh37] Chr20:28198..62379118 [NCBI36] Chr20:20p13-q13.33	pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:53236165-64284202)x3	copy number gain	See cases [RCV000143584]	Chr20:53236165..64284202 [GRCh38] Chr20:51852704..62915555 [GRCh37] Chr20:51286111..62385999 [NCBI36] Chr20:20q13.2-13.33	likely pathogenic
GRCh37/hg19 20q13.2-13.33(chr20:51542616-62915555)x3	copy number gain	See cases [RCV000511980]	Chr20:51542616..62915555 [GRCh37] Chr20:20q13.2-13.33	likely pathogenic
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555)x3	copy number gain	See cases [RCV000510832]	Chr20:61569..62915555 [GRCh37] Chr20:20p13-q13.33	pathogenic
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555)	copy number gain	See cases [RCV000512450]	Chr20:61569..62915555 [GRCh37] Chr20:20p13-q13.33	pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62948788)x3	copy number gain	not provided [RCV000741058]	Chr20:63244..62948788 [GRCh37] Chr20:20p13-q13.33	pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62961294)x3	copy number gain	not provided [RCV000741059]	Chr20:63244..62961294 [GRCh37] Chr20:20p13-q13.33	pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62912463)x3	copy number gain	not provided [RCV000741057]	Chr20:63244..62912463 [GRCh37] Chr20:20p13-q13.33	pathogenic
NM_002623.4(PFDN4):c.337G>A (p.Ala113Thr)	single nucleotide variant	Inborn genetic diseases [RCV003249417]	Chr20:54219082 [GRCh38] Chr20:52835621 [GRCh37] Chr20:20q13.2	uncertain significance
GRCh37/hg19 20q13.2-13.33(chr20:51799648-62916626)x3	copy number gain	not provided [RCV001537917]	Chr20:51799648..62916626 [GRCh37] Chr20:20q13.2-13.33	pathogenic
GRCh37/hg19 20q13.2-13.31(chr20:52517925-55402822)x3	copy number gain	not provided [RCV002474915]	Chr20:52517925..55402822 [GRCh37] Chr20:20q13.2-13.31	uncertain significance
NM_002623.4(PFDN4):c.172A>C (p.Met58Leu)	single nucleotide variant	Inborn genetic diseases [RCV003263211]	Chr20:54215339 [GRCh38] Chr20:52831878 [GRCh37] Chr20:20q13.2	uncertain significance
GRCh37/hg19 20q13.2-13.33(chr20:52773668-62965020)x3	copy number gain	See cases [RCV003329549]	Chr20:52773668..62965020 [GRCh37] Chr20:20q13.2-13.33	uncertain significance
NM_002623.4(PFDN4):c.14T>C (p.Met5Thr)	single nucleotide variant	Inborn genetic diseases [RCV003351838]	Chr20:54208114 [GRCh38] Chr20:52824653 [GRCh37] Chr20:20q13.2	uncertain significance
NM_002623.4(PFDN4):c.329G>A (p.Arg110Gln)	single nucleotide variant	Inborn genetic diseases [RCV003363317]	Chr20:54219074 [GRCh38] Chr20:52835613 [GRCh37] Chr20:20q13.2	uncertain significance
NM_002623.4(PFDN4):c.83G>A (p.Arg28Gln)	single nucleotide variant	Inborn genetic diseases [RCV003363656]	Chr20:54214409 [GRCh38] Chr20:52830948 [GRCh37] Chr20:20q13.2	uncertain significance
GRCh37/hg19 20q13.2(chr20:51192560-53918272)x1	copy number loss	not provided [RCV003483364]	Chr20:51192560..53918272 [GRCh37] Chr20:20q13.2	uncertain significance

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	619
Count of miRNA genes:	384
Interacting mature miRNAs:	401
Transcripts:	ENST00000371419, ENST00000441080, ENST00000474326, ENST00000487129, ENST00000493356
Prediction methods:	Microtar, 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

RH47160

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	7	2,875,323 - 2,875,505	UniSTS	GRCh37
GRCh37	20	52,830,934 - 52,831,957	UniSTS	GRCh37
Build 36	7	2,841,849 - 2,842,031	RGD	NCBI36
Celera	20	49,535,571 - 49,536,594	UniSTS
Celera	7	2,843,895 - 2,844,077	RGD
Cytogenetic Map	7	p22.2	UniSTS
Cytogenetic Map	20	q13.2	UniSTS
HuRef	7	2,793,848 - 2,794,030	UniSTS
HuRef	20	49,577,455 - 49,578,478	UniSTS
CRA_TCAGchr7v2	7	2,923,196 - 2,923,378	UniSTS
GeneMap99-GB4 RH Map	7	21.47	UniSTS

SHGC-2608

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	7	2,875,336 - 2,875,493	UniSTS	GRCh37
GRCh37	20	52,830,947 - 52,831,945	UniSTS	GRCh37
Build 36	7	2,841,862 - 2,842,019	RGD	NCBI36
Celera	20	49,535,584 - 49,536,582	UniSTS
Celera	7	2,843,908 - 2,844,065	RGD
Cytogenetic Map	20	q13.2	UniSTS
Cytogenetic Map	7	p22.2	UniSTS
HuRef	20	49,577,468 - 49,578,466	UniSTS
HuRef	7	2,793,861 - 2,794,018	UniSTS
CRA_TCAGchr7v2	7	2,923,209 - 2,923,366	UniSTS
TNG Radiation Hybrid Map	7	1565.0	UniSTS
GeneMap99-G3 RH Map	7	157.0	UniSTS

RH47163

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	20	52,830,934 - 52,831,901	UniSTS	GRCh37
Celera	20	49,535,571 - 49,536,538	UniSTS
Cytogenetic Map	20	q13.2	UniSTS
HuRef	20	49,577,455 - 49,578,422	UniSTS
GeneMap99-GB4 RH Map	7	33.22	UniSTS

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

entire extraembryonic component

pharyngeal arch

High

Medium

1698

1438

844

178

917

138

2653

1099

2847

311

1339

1018

1004

1590

Low

738

1052

881

445

537

326

1703

1095

878

107

113

592

119

200

1198

Below cutoff

483

481

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_002623	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017027879	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_047440198	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_047440199	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_054323507	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_054323508	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_054323509	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AK312059	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AL133335	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC010953	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH471077	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CN482830	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068258	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U41816	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENST00000371419 ⟹ ENSP00000360473

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	20	54,208,087 - 54,219,961 (+)	Ensembl

RefSeq Acc Id:

ENST00000441080 ⟹ ENSP00000432441

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	20	54,208,095 - 54,228,052 (+)	Ensembl

RefSeq Acc Id:

ENST00000474326

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	20	54,208,428 - 54,214,410 (+)	Ensembl

RefSeq Acc Id:

ENST00000487129

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	20	54,208,312 - 54,219,203 (+)	Ensembl

RefSeq Acc Id:

ENST00000493356

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	20	54,208,300 - 54,219,285 (+)	Ensembl

RefSeq Acc Id:

NM_002623 ⟹ NP_002614

RefSeq Status:

REVIEWED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	20	54,208,087 - 54,219,961 (+)	NCBI
GRCh37	20	52,824,502 - 52,836,492 (+)	RGD
Build 36	20	52,257,909 - 52,269,899 (+)	NCBI Archive
Celera	20	49,529,139 - 49,541,129 (+)	RGD
HuRef	20	49,571,022 - 49,583,013 (+)	RGD
CHM1_1	20	52,727,643 - 52,739,633 (+)	NCBI
T2T-CHM13v2.0	20	55,982,413 - 55,994,287 (+)	NCBI

Sequence:

show sequence

AGTCCAGTCCCAAGATGGCGGCCACCATGAAGAAGGCGGCTGCAGAAGATGTCAATGTTACTTT
CGAAGATCAACAAAAGATAAACAAATTTGCACGGAATACAAGTAGAATCACAGAGCTGAAGGAA
GAAATAGAAGTAAAAAAGAAACAACTCCAAAACCTAGAAGATGCTTGTGATGACATCATGCTTG
CAGATGATGATTGCTTAATGATACCTTATCAAATTGGTGATGTCTTCATTAGCCATTCTCAAGA
AGAAACGCAAGAAATGTTAGAAGAAGCAAAGAAAAATTTGCAAGAAGAAATTGACGCCTTAGAA
TCCAGAGTGGAATCAATTCAGCGAGTGTTAGCAGATTTGAAAGTTCAGTTGTATGCAAAATTCG
GGAGCAACATAAACCTTGAAGCTGATGAAAGTTAAACATTTTATAATACTTTTTTTATTTGTTT
AATAAACTTGAATATTGTTTAAAATGATAATTTTCCTTCTTCAAATGACATGGAAAGCAAAACT
TTCTTTTTTAAAAATTTTCATTTATTTAATGGAAACTTGCCCATTTTCACATGTCTGCTTATTT
ATTTTATATTTTTAAAAGAAGACAGTATTCACCTATGTATTTTGCATAACGATTATATCAAGTC
TAGGGGCTTCATGTCATGTTATTAAAATCAGTTAAGCAATCTTTTATGTTTCTATATTATTTAG
AATATTTGTTGTTGCAATTTTCACATAAGAAAATTTAACAGTTGTGTCATGTTGTTTCTGTCTG
ATTTTAATTGCTGTCTAATGACGGGGAAAGCACGATGAAAAGATGTACAATCCTGCATCCTTGC
TTATTTCACAACTAAAGCTTTGTCATAGACTTCAAAATATATATGTATATATTTTATTTAAATA
TATGTTACATATTATATTTAAACATACATATTTAACATTTTTTACATATCTATCAATATCAGAG
ATTTGGGTAAAAGAATGGGTAATGTTTAAACATGTGGAGGCATGTGGAGCTTTATACAAACAGG
GCAGAACCACAGAAGAACGTTTTAGAAACCAAGAGATGTGCAGAAAGAAATGTTTAGTGTTTTT
TCGTTTTAAATTTTAGATTTTATTTTAGTGCTTTGTAATTAATTGGGGTTTATATTGATAAAGA
TGTGGAAGTTAAACAGCTATGTATGTAAAAGTAAGGCTTATTTCTTAAATAAAGGATGCATTTC
TTCCCACTCCCCCA

hide sequence

RefSeq Acc Id:

XM_017027879 ⟹ XP_016883368

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	20	54,208,402 - 54,219,961 (+)	NCBI

Sequence:

show sequence

TGTGGTTGGCCTTGACTCGGGCGTTGCACCGGCATGATCGCATTAGCCTCACTGGTTATGGGTA
GCTGCTGCTGGGAGCGTGGTTACGGGTGAGGAAACTGAGGCCCAGAGATGGGGAGTCACCTGCC
CGAGGTTACGCAGCTCATAACGGGGACAGCAGGTTCCTGCATCCCCAGATTAGCAGGCCCCAGA
GACCCTGTGTCCAACCTGGAGCTGCCCATTTCCACGCTTGATGCCCCTGAGTCCTTCAGGCTAA
AACCAGTATTTATTGAGAATGGAAGATGTGCCGGGCCCAGCAGCCGGCCGTTTATCTGTTATCC
TCCCCGCAACTCAGCAAGTGCAATGGGTTCCTCTCCACTTTGCAGGTAGAGAAACTTAGACACA
GAGCAGTTAGAGGCCCTAAAGTGACTCAGCTAGTAAGAAGCAGAGCTGGAGTTCAAACTCAGGC
TGCAGAAGATGTCAATGTTACTTTCGAAGATCAACAAAAGATAAACAAATTTGCACGGAATACA
AGTAGAATCACAGAGCTGAAGGAAGAAATAGAAGTAAAAAAGAAACAACTCCAAAACCTAGAAG
ATGCTTGTGATGACATCATGCTTGCAGATGATGATTGCTTAATGATACCTTATCAAATTGGTGA
TGTCTTCATTAGCCATTCTCAAGAAGAAACGCAAGAAATGTTAGAAGAAGCAAAGAAAAATTTG
CAAGAAGAAATTGACGCCTTAGAATCCAGAGTGGAATCAATTCAGCGAGTGTTAGCAGATTTGA
AAGTTCAGTTGTATGCAAAATTCGGGAGCAACATAAACCTTGAAGCTGATGAAAGTTAAACATT
TTATAATACTTTTTTTATTTGTTTAATAAACTTGAATATTGTTTAAAATGATAATTTTCCTTCT
TCAAATGACATGGAAAGCAAAACTTTCTTTTTTAAAAATTTTCATTTATTTAATGGAAACTTGC
CCATTTTCACATGTCTGCTTATTTATTTTATATTTTTAAAAGAAGACAGTATTCACCTATGTAT
TTTGCATAACGATTATATCAAGTCTAGGGGCTTCATGTCATGTTATTAAAATCAGTTAAGCAAT
CTTTTATGTTTCTATATTATTTAGAATATTTGTTGTTGCAATTTTCACATAAGAAAATTTAACA
GTTGTGTCATGTTGTTTCTGTCTGATTTTAATTGCTGTCTAATGACGGGGAAAGCACGATGAAA
AGATGTACAATCCTGCATCCTTGCTTATTTCACAACTAAAGCTTTGTCATAGACTTCAAAATAT
ATATGTATATATTTTATTTAAATATATGTTACATATTATATTTAAACATA

hide sequence

RefSeq Acc Id:

XM_047440198 ⟹ XP_047296154

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	20	54,208,087 - 54,219,961 (+)	NCBI

RefSeq Acc Id:

XM_047440199 ⟹ XP_047296155

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	20	54,208,087 - 54,215,407 (+)	NCBI

RefSeq Acc Id:

XM_054323507 ⟹ XP_054179482

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
T2T-CHM13v2.0	20	55,982,182 - 55,994,287 (+)	NCBI

RefSeq Acc Id:

XM_054323508 ⟹ XP_054179483

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
T2T-CHM13v2.0	20	55,982,728 - 55,994,287 (+)	NCBI

RefSeq Acc Id:

XM_054323509 ⟹ XP_054179484

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
T2T-CHM13v2.0	20	55,982,176 - 55,989,766 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_002614	(Get FASTA)	NCBI Sequence Viewer
	XP_016883368	(Get FASTA)	NCBI Sequence Viewer
	XP_047296154	(Get FASTA)	NCBI Sequence Viewer
	XP_047296155	(Get FASTA)	NCBI Sequence Viewer
	XP_054179482	(Get FASTA)	NCBI Sequence Viewer
	XP_054179483	(Get FASTA)	NCBI Sequence Viewer
	XP_054179484	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB17063	(Get FASTA)	NCBI Sequence Viewer
	AAH10953	(Get FASTA)	NCBI Sequence Viewer
	BAG34995	(Get FASTA)	NCBI Sequence Viewer
	EAW75572	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSP00000360473
	ENSP00000360473.2
	ENSP00000432441.1
GenBank Protein	Q9NQP4	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_002614 ⟸ NM_002623
- UniProtKB:	Q5TD11 (UniProtKB/Swiss-Prot), Q92779 (UniProtKB/Swiss-Prot), Q9NQP4 (UniProtKB/Swiss-Prot), B2R548 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAATMKKAAAEDVNVTFEDQQKINKFARNTSRITELKEEIEVKKKQLQNLEDACDDIMLADDDC LMIPYQIGDVFISHSQEETQEMLEEAKKNLQEEIDALESRVESIQRVLADLKVQLYAKFGSNIN LEADES hide sequence

RefSeq Acc Id:	XP_016883368 ⟸ XM_017027879
- Peptide Label:	isoform X2
- Sequence:	show sequence MCRAQQPAVYLLSSPQLSKCNGFLSTLQVEKLRHRAVRGPKVTQLVRSRAGVQTQAAEDVNVTF EDQQKINKFARNTSRITELKEEIEVKKKQLQNLEDACDDIMLADDDCLMIPYQIGDVFISHSQE ETQEMLEEAKKNLQEEIDALESRVESIQRVLADLKVQLYAKFGSNINLEADES hide sequence

RefSeq Acc Id:

ENSP00000360473 ⟸ ENST00000371419

RefSeq Acc Id:

ENSP00000432441 ⟸ ENST00000441080

RefSeq Acc Id:	XP_047296154 ⟸ XM_047440198
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_047296155 ⟸ XM_047440199
- Peptide Label:	isoform X3

RefSeq Acc Id:	XP_054179484 ⟸ XM_054323509
- Peptide Label:	isoform X3

RefSeq Acc Id:	XP_054179482 ⟸ XM_054323507
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_054179483 ⟸ XM_054323508
- Peptide Label:	isoform X2

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q9NQP4-F1-model_v2	AlphaFold	Q9NQP4	1-134	view protein structure

Promoters

RGD ID:

6798892

Promoter ID:

HG_KWN:39886

Type:

CpG-Island

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

CD4+TCell, CD4+TCell_12Hour, CD4+TCell_2Hour, HeLa_S3, K562, Lymphoblastoid, NB4

Transcripts:

OTTHUMT00000079771, OTTHUMT00000079772, OTTHUMT00000079773, OTTHUMT00000079774, OTTHUMT00000259207

Position:

Human Assembly	Chr	Position (strand)	Source
Build 36	20	52,257,761 - 52,258,261 (+)	MPROMDB

RGD ID:

13602140

Promoter ID:

EPDNEW_H27254

Type:

initiation region

Name:

PFDN4_2

Description:

prefoldin subunit 4

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Alternative Promoters:

null; see alsoEPDNEW_H27255

Experiment Methods:

Single-end sequencing.; Paired-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	20	54,207,847 - 54,207,907	EPDNEW

RGD ID:

13602142

Promoter ID:

EPDNEW_H27255

Type:

multiple initiation site

Name:

PFDN4_1

Description:

prefoldin subunit 4

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Alternative Promoters:

null; see alsoEPDNEW_H27254

Experiment Methods:

Single-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	20	54,208,087 - 54,208,147	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	HGNC:8868	AgrOrtholog
COSMIC	PFDN4	COSMIC
Ensembl Genes	ENSG00000101132	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript	ENST00000371419	ENTREZGENE
	ENST00000371419.7	UniProtKB/Swiss-Prot
	ENST00000441080.2	UniProtKB/TrEMBL
Gene3D-CATH	1.10.287.370	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx	ENSG00000101132	GTEx
HGNC ID	HGNC:8868	ENTREZGENE
Human Proteome Map	PFDN4	Human Proteome Map
InterPro	PFD_beta-like	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PFDN4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Prefoldin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	hsa:5203	UniProtKB/Swiss-Prot
NCBI Gene	5203	ENTREZGENE
OMIM	604898	OMIM
PANTHER	PREFOLDIN SUBUNIT 4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PTHR21100	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Prefoldin_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB	PA33209	PharmGKB
PIRSF	Prefoldin_subunit_4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	Prefoldin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	B2R548	ENTREZGENE, UniProtKB/TrEMBL
	E9PQY2_HUMAN	UniProtKB/TrEMBL
	L8EC97_HUMAN	UniProtKB/TrEMBL
	PFD4_HUMAN	UniProtKB/Swiss-Prot
	Q5TD11	ENTREZGENE
	Q92779	ENTREZGENE
	Q9NQP4	ENTREZGENE
UniProt Secondary	Q5TD11	UniProtKB/Swiss-Prot
	Q92779	UniProtKB/Swiss-Prot

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - ClinVar