Nphs1 (NPHS1 adhesion molecule, nephrin) - Rat Genome Database
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Gene: Nphs1 (NPHS1 adhesion molecule, nephrin) Rattus norvegicus
Analyze
Symbol: Nphs1
Name: NPHS1 adhesion molecule, nephrin
RGD ID: 620460
Description: Exhibits alpha-actinin binding activity; protein domain specific binding activity; and spectrin binding activity. Predicted to be involved in several processes, including JNK cascade; myoblast fusion; and positive regulation of actin filament polymerization. Localizes to several cellular components, including membrane raft; plasma membrane; and slit diaphragm. Biomarker of end stage renal disease; kidney failure; membranous glomerulonephritis; and nephrotic syndrome. Human ortholog(s) of this gene implicated in nephrotic syndrome type 1. Orthologous to human NPHS1 (NPHS1 adhesion molecule, nephrin); INTERACTS WITH 5-hydroxymethylfurfural; mycophenolate mofetil; streptozocin.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: nephrin; nephrosis 1 homolog (human); nephrosis 1 homolog, nephrin; nephrosis 1 homolog, nephrin (human); nephrosis 1, congenital, Finnish type; nephrosis 1, congenital, Finnish type (nephrin); NPHS1 nephrin; renal glomerulus-specific cell adhesion receptor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2185,720,812 - 85,749,079 (+)NCBI
Rnor_6.0 Ensembl188,922,433 - 88,950,559 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0188,922,346 - 88,950,560 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0190,077,799 - 90,106,425 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4185,414,492 - 85,444,233 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1185,516,160 - 85,522,343 (+)NCBI
Celera180,092,938 - 80,121,035 (+)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Ahola H, etal., Am J Pathol 1999 Sep;155(3):907-13.
2. Babayeva S, etal., Am J Physiol Renal Physiol. 2011 Feb;300(2):F549-60. doi: 10.1152/ajprenal.00566.2009. Epub 2010 Jun 9.
3. Barletta GM, etal., J Biol Chem 2003 May 23;278(21):19266-71. Epub 2003 Mar 19.
4. Beltcheva O, etal., Hum Mutat 2001 May;17(5):368-73.
5. Bonnet F, etal., Clin Exp Hypertens 2002 Jul;24(5):371-81.
6. Devaraj S, etal., Arterioscler Thromb Vasc Biol. 2011 Aug;31(8):1796-804. doi: 10.1161/ATVBAHA.111.228924. Epub 2011 May 26.
7. Endlich N, etal., J Cell Mol Med. 2018 Nov;22(11):5265-5277. doi: 10.1111/jcmm.13762. Epub 2018 Aug 21.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. GOA data from the GO Consortium
10. Hamano Y, etal., J Biol Chem 2002 Aug 23;277(34):31154-62. Epub 2002 May 30.
11. He JC, etal., J Am Soc Nephrol. 2007 Jan;18(1):93-102. doi: 10.1681/ASN.2006070727. Epub 2006 Dec 20.
12. Hiramatsu N, etal., J Am Soc Nephrol. 2007 Feb;18(2):515-27. doi: 10.1681/ASN.2006030217. Epub 2007 Jan 17.
13. Ito N, etal., Lab Invest. 2011 Nov;91(11):1584-95. doi: 10.1038/labinvest.2011.135. Epub 2011 Aug 29.
14. Kajiho Y, etal., FEBS J. 2012 Sep;279(17):3010-21. doi: 10.1111/j.1742-4658.2012.08682.x. Epub 2012 Jul 23.
15. Kawachi H, etal., Kidney Int 2000 May;57(5):1949-61.
16. Kawachi H, etal., Nephrol Dial Transplant 2002;17 Suppl 9:20-2.
17. Kelly DJ, etal., Nephrol Dial Transplant 2002 Jul;17(7):1327-32.
18. Lehtonen S, etal., Am J Pathol. 2004 Sep;165(3):923-36.
19. Lehtonen S, etal., Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9814-9. Epub 2005 Jul 1.
20. Liu G, etal., J Clin Invest 2003 Jul;112(2):209-21.
21. Mallipattu SK, etal., J Biol Chem. 2012 Jun 1;287(23):19122-35. doi: 10.1074/jbc.M112.345983. Epub 2012 Apr 9.
22. MGD data from the GO Consortium
23. Müller-Krebs S, etal., Eur J Clin Invest. 2008 May;38(5):296-305. doi: 10.1111/j.1365-2362.2008.01945.x. Epub 2008 Mar 16.
24. Nakatsue T, etal., Kidney Int. 2005 Jun;67(6):2239-53.
25. Nakhoul F, etal., Am J Physiol Renal Physiol. 2005 Oct;289(4):F880-90. Epub 2005 Jun 7.
26. Navarro-Muñoz M, etal., Nephrol Dial Transplant. 2011 Dec;26(12):3914-23. doi: 10.1093/ndt/gfr128. Epub 2011 Mar 17.
27. NCBI rat LocusLink and RefSeq merged data July 26, 2002
28. Nugrahaningsih DA, etal., Hypertens Res. 2014 Mar;37(3):202-9. doi: 10.1038/hr.2013.143. Epub 2013 Oct 10.
29. OMIM Disease Annotation Pipeline
30. Putaala H, etal., J Am Soc Nephrol 2000 Jun;11(6):991-1001.
31. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. RGD automated import pipeline for gene-chemical interactions
33. Sakurai N, etal., Nephrol Dial Transplant. 2009 Aug;24(8):2378-83. doi: 10.1093/ndt/gfp012. Epub 2009 Feb 2.
34. Sato Y, etal., J Am Soc Nephrol. 2009 May;20(5):1041-52. doi: 10.1681/ASN.2007121328. Epub 2009 Apr 23.
35. Yang H, etal., Mol Metab. 2019 May;23:24-36. doi: 10.1016/j.molmet.2019.02.007. Epub 2019 Feb 26.
36. You H, etal., Am J Physiol Renal Physiol. 2013 Dec 15;305(12):F1719-27. doi: 10.1152/ajprenal.00141.2013. Epub 2013 Oct 30.
37. Yuan H, etal., Am J Physiol Renal Physiol 2002 Apr;282(4):F585-91.
38. Zhang Y, etal., Chin Med J (Engl). 2007 Jun 5;120(11):988-95.
39. Zhong Y, etal., PLoS One. 2011;6(11):e27945. doi: 10.1371/journal.pone.0027945. Epub 2011 Nov 18.
Additional References at PubMed
PMID:11136707   PMID:11562357   PMID:12544453   PMID:14633129   PMID:15385636   PMID:15465010   PMID:15545998   PMID:15579503   PMID:15924139   PMID:15979540   PMID:16934223   PMID:17429054  
PMID:17457371   PMID:17464107   PMID:17545045   PMID:17599973   PMID:17667985   PMID:17923684   PMID:18033240   PMID:18256598   PMID:18258597   PMID:19042927   PMID:19052472   PMID:19056867  
PMID:19179337   PMID:19443634   PMID:19470472   PMID:19948823   PMID:20045917   PMID:20629321   PMID:21306299   PMID:21402783   PMID:21565142   PMID:21858180   PMID:22094487   PMID:22809625  
PMID:23376485   PMID:25025298   PMID:25298195   PMID:25404734   PMID:26539476   PMID:27248136   PMID:27995418   PMID:29162887  


Genomics

Comparative Map Data
Nphs1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2185,720,812 - 85,749,079 (+)NCBI
Rnor_6.0 Ensembl188,922,433 - 88,950,559 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0188,922,346 - 88,950,560 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0190,077,799 - 90,106,425 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4185,414,492 - 85,444,233 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1185,516,160 - 85,522,343 (+)NCBI
Celera180,092,938 - 80,121,035 (+)NCBICelera
Cytogenetic Map1q21NCBI
NPHS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1935,825,964 - 35,869,287 (-)EnsemblGRCh38hg38GRCh38
GRCh381935,862,915 - 35,869,287 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371936,316,274 - 36,342,895 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361941,008,697 - 41,034,579 (-)NCBINCBI36hg18NCBI36
Build 341941,008,696 - 41,034,579NCBI
Celera1933,029,746 - 33,057,068 (-)NCBI
Cytogenetic Map19q13.12NCBI
HuRef1932,820,999 - 32,848,201 (-)NCBIHuRef
CHM1_11936,355,097 - 36,361,471 (-)NCBICHM1_1
Nphs1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39730,157,259 - 30,188,048 (+)NCBIGRCm39mm39
GRCm38730,458,207 - 30,488,623 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl730,458,315 - 30,487,223 (+)EnsemblGRCm38mm10GRCm38
MGSCv37731,245,077 - 31,273,628 (+)NCBIGRCm37mm9NCBIm37
MGSCv36730,168,976 - 30,195,476 (+)NCBImm8
MGSCv36722,737,759 - 22,764,662 (+)NCBImm8
Celera725,051,854 - 25,074,685 (+)NCBICelera
Cytogenetic Map7B1NCBI
Nphs1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554682,714,419 - 2,734,830 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554682,715,728 - 2,734,174 (+)NCBIChiLan1.0ChiLan1.0
NPHS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11941,492,126 - 41,518,587 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1941,492,444 - 41,518,471 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01932,742,802 - 32,770,600 (-)NCBIMhudiblu_PPA_v0panPan3
Nphs1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936570495,421 - 514,179 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NPHS1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1630,736,869 - 30,763,054 (-)NCBI
ChlSab1.1 Ensembl630,736,966 - 30,762,929 (-)Ensembl
Nphs1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479410,117,464 - 10,138,511 (-)NCBI

Position Markers
D1Wox80  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0188,949,186 - 88,949,355NCBIRnor6.0
Rnor_5.0190,105,051 - 90,105,220UniSTSRnor5.0
RGSC_v3.4185,442,859 - 85,443,028UniSTSRGSC3.4
Celera180,119,661 - 80,119,830UniSTS
Cytogenetic Map1q22UniSTS
PMC164293P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0188,926,319 - 88,926,496NCBIRnor6.0
Rnor_5.0190,081,710 - 90,081,887UniSTSRnor5.0
RGSC_v3.4185,418,379 - 85,418,556UniSTSRGSC3.4
Celera180,096,809 - 80,096,986UniSTS
Cytogenetic Map1q22UniSTS
PMC164293P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0188,926,343 - 88,926,496NCBIRnor6.0
Rnor_5.0190,081,734 - 90,081,887UniSTSRnor5.0
RGSC_v3.4185,418,403 - 85,418,556UniSTSRGSC3.4
Celera180,096,833 - 80,096,986UniSTS
Cytogenetic Map1q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13537750894364229Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14957857794578577Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15052271494225616Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157761301104391981Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)158209327103209327Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)164588516125875986Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)166113339122614963Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)16722768394201552Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)179134941113593716Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)179689548124689548Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)17968976594909507Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)183502376128502376Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)183656882126240667Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185779320130779320Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185917265130917265Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)186776571131776571Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)188634585106002500Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:503
Count of miRNA genes:198
Interacting mature miRNAs:242
Transcripts:ENSRNOT00000028358, ENSRNOT00000045212
Prediction methods:Microtar, Miranda, Targetscan
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 appendage
High
Medium 31 1
Low 2 13 19 1 1 32 2 11 11 1
Below cutoff 1 23 16 13 13 7 10 40 2 22 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000045212   ⟹   ENSRNOP00000049922
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl188,922,433 - 88,950,559 (+)Ensembl
RefSeq Acc Id: NM_022628   ⟹   NP_072150
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2185,720,812 - 85,749,079 (+)NCBI
Rnor_6.0188,922,433 - 88,950,560 (+)NCBI
Rnor_5.0190,077,799 - 90,106,425 (+)NCBI
RGSC_v3.4185,414,492 - 85,444,233 (+)RGD
Celera180,092,938 - 80,121,035 (+)RGD
Sequence:
RefSeq Acc Id: XM_008759186   ⟹   XP_008757408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0188,922,347 - 88,949,217 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008759187   ⟹   XP_008757409
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0188,922,346 - 88,949,217 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_072150   ⟸   NM_022628
- Peptide Label: precursor
- UniProtKB: Q9R044 (UniProtKB/Swiss-Prot),   A0A140TAG4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008757408   ⟸   XM_008759186
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008757409   ⟸   XM_008759187
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000049922   ⟸   ENSRNOT00000045212
Protein Domains
Fibronectin type-III   Ig-like   Ig-like C2-type

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 90078282 90078283 C T snv LH/MavRrrc (KNAW), F344/Jcl (KyushuU), LN/MavRrrc (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), GK/Ox (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), LEC/Tj (KyushuU), LL/MavRrrc (KNAW)


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 88922891 88922892 C T snv F344/NRrrc (MCW), WKY/N (MCW), F344/NCrl (RGD), GK/Ox (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), WKY/NHsd (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), LL/MavRrrc (RGD)
1 88926269 88926270 G A snv WKY/NHsd (RGD)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 85414950 85414951 C T snv SHR/OlaIpcv (ICL), F344/NHsd (ICAHN), F344/NRrrc (KNAW), LE/Stm (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), F344/NCrl (ICL), LE/Stm (ICL), GK/Ox (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), SHRSP/Gcrc (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620460 AgrOrtholog
Ensembl Genes ENSRNOG00000020873 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000049922 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000045212 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CD80_C2-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64563 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 64563 ENTREZGENE
Pfam C2-set_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  fn3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nphs1 PhenoGen
PROSITE FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140TAG4 ENTREZGENE, UniProtKB/TrEMBL
  NPHN_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9JIX2 UniProtKB/Swiss-Prot
  Q9QXX7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-04 Nphs1  NPHS1 adhesion molecule, nephrin  Nphs1  NPHS1 nephrin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-17 Nphs1  NPHS1 nephrin  Nphs1  nephrosis 1, congenital, Finnish type (nephrin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-05 Nphs1  nephrosis 1, congenital, Finnish type (nephrin)  Nphs1  nephrosis 1, congenital, Finnish type  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-07-06 Nphs1  nephrosis 1, congenital, Finnish type  Nphs1  nephrosis 1 homolog (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-11-06 Nphs1  nephrosis 1 homolog (human)  Nphs1  nephrosis 1 homolog, nephrin (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Nphs1  nephrosis 1 homolog, nephrin (human)    nephrin  Name updated 1299863 APPROVED
2002-08-07 Nphs1        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease human homolog is mutated in congenital nephrotic syndrome of the Finnish type 633453