Incidental Mutation 'R4580:Nphp1'
ID 343566
Institutional Source Beutler Lab
Gene Symbol Nphp1
Ensembl Gene ENSMUSG00000027378
Gene Name nephronophthisis 1 (juvenile) homolog (human)
Synonyms nephrocystin
MMRRC Submission 041599-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4580 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 127582652-127630817 bp(-) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) A to G at 127610089 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000105986 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028857] [ENSMUST00000110357]
AlphaFold no structure available at present
Predicted Effect probably null
Transcript: ENSMUST00000028857
SMART Domains Protein: ENSMUSP00000028857
Gene: ENSMUSG00000027378

DomainStartEndE-ValueType
low complexity region 118 143 N/A INTRINSIC
SH3 158 214 5.91e-19 SMART
low complexity region 220 246 N/A INTRINSIC
Blast:14_3_3 391 491 3e-55 BLAST
low complexity region 634 641 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000110357
SMART Domains Protein: ENSMUSP00000105986
Gene: ENSMUSG00000027378

DomainStartEndE-ValueType
low complexity region 118 143 N/A INTRINSIC
SH3 158 214 5.91e-19 SMART
low complexity region 220 246 N/A INTRINSIC
Blast:14_3_3 390 490 3e-55 BLAST
low complexity region 633 640 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with src homology domain 3 (SH3) patterns. This protein interacts with Crk-associated substrate, and it appears to function in the control of cell division, as well as in cell-cell and cell-matrix adhesion signaling, likely as part of a multifunctional complex localized in actin- and microtubule-based structures. Mutations in this gene cause familial juvenile nephronophthisis type 1, a kidney disorder involving both tubules and glomeruli. Defects in this gene are also associated with Senior-Loken syndrome type 1, also referred to as juvenile nephronophthisis with Leber amaurosis, which is characterized by kidney and eye disease, and with Joubert syndrome type 4, which is characterized by cerebellar ataxia, oculomotor apraxia, psychomotor delay and neonatal breathing abnormalities, sometimes including retinal dystrophy and renal disease. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit male infertility due to defects in sperm maturation. Mice homozygous for another knock-out allele exhibit absent photoreceptor outer segment and photoreceptor degeneration. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2810408A11Rik T C 11: 69,791,237 (GRCm39) Y114C probably damaging Het
Abcc2 T C 19: 43,799,558 (GRCm39) S556P probably damaging Het
Arl6ip1 AAAATAAATAAATAAATAAATAAATA AAAATAAATAAATAAATAAATAAATAAATA 7: 117,721,122 (GRCm39) probably benign Het
Atp6v1g1 A G 4: 63,468,269 (GRCm39) N91D probably benign Het
BC005537 G T 13: 24,987,394 (GRCm39) A11S probably benign Het
Bltp1 A T 3: 37,084,174 (GRCm39) T3864S probably benign Het
Bub1 A C 2: 127,671,596 (GRCm39) probably null Het
Ccdc162 T C 10: 41,437,136 (GRCm39) T1758A probably benign Het
Cdh15 T C 8: 123,591,897 (GRCm39) L594P probably damaging Het
Cobll1 C T 2: 64,981,417 (GRCm39) V90I probably benign Het
Cog2 T C 8: 125,271,875 (GRCm39) V463A probably benign Het
Cpeb4 T A 11: 31,877,757 (GRCm39) probably null Het
Creb5 G A 6: 53,581,519 (GRCm39) M172I possibly damaging Het
Cyp4a32 T C 4: 115,460,126 (GRCm39) silent Het
Dnah8 T A 17: 30,881,026 (GRCm39) S588T probably benign Het
Ecpas T C 4: 58,840,751 (GRCm39) Y669C probably damaging Het
Esd T C 14: 74,979,517 (GRCm39) V120A possibly damaging Het
Fbxo5 T C 10: 5,755,255 (GRCm39) probably null Het
Gm4922 T C 10: 18,659,432 (GRCm39) D430G probably benign Het
Golga4 C A 9: 118,386,327 (GRCm39) Q1150K probably benign Het
Grb14 T C 2: 64,783,947 (GRCm39) N60S probably benign Het
Grk4 A G 5: 34,818,325 (GRCm39) N2S probably damaging Het
Henmt1 T A 3: 108,850,081 (GRCm39) S21R probably benign Het
Ifngr2 A G 16: 91,354,906 (GRCm39) K113E probably benign Het
Ighv15-2 T A 12: 114,528,590 (GRCm39) T15S probably benign Het
Kif24 A G 4: 41,395,287 (GRCm39) S529P probably damaging Het
Large2 T C 2: 92,200,957 (GRCm39) N51S possibly damaging Het
Lmtk2 A G 5: 144,111,599 (GRCm39) E773G possibly damaging Het
Lrfn3 A T 7: 30,059,467 (GRCm39) C253S probably damaging Het
Maea T C 5: 33,517,832 (GRCm39) V130A possibly damaging Het
Marchf11 A T 15: 26,311,189 (GRCm39) I222F probably damaging Het
Mast4 A T 13: 102,873,766 (GRCm39) Y1699* probably null Het
Mavs G T 2: 131,082,370 (GRCm39) A85S probably damaging Het
Mpzl3 T A 9: 44,979,529 (GRCm39) V160E possibly damaging Het
Myh15 T C 16: 48,885,388 (GRCm39) S88P possibly damaging Het
Myl2 A T 5: 122,244,801 (GRCm39) H157L probably benign Het
Myo9b A G 8: 71,767,779 (GRCm39) N284S probably damaging Het
Nrcam T C 12: 44,609,323 (GRCm39) probably null Het
Nt5c3b G T 11: 100,323,885 (GRCm39) F134L probably damaging Het
Or4c120 T A 2: 89,001,544 (GRCm39) Q4L probably benign Het
Otog A G 7: 45,937,225 (GRCm39) R1645G possibly damaging Het
Pask T C 1: 93,249,830 (GRCm39) I523M probably benign Het
Pcdhb7 T A 18: 37,475,188 (GRCm39) L108Q probably damaging Het
Pdp2 C A 8: 105,321,576 (GRCm39) T475K probably damaging Het
Pgbd1 G C 13: 21,612,499 (GRCm39) P113A probably benign Het
Plk5 C T 10: 80,196,301 (GRCm39) H291Y possibly damaging Het
Pmpca G T 2: 26,283,347 (GRCm39) S382I probably damaging Het
Prl3b1 A G 13: 27,433,450 (GRCm39) T202A possibly damaging Het
Ptgs2 A T 1: 149,979,845 (GRCm39) T317S possibly damaging Het
Ptprc C T 1: 137,998,989 (GRCm39) M1020I probably benign Het
Rhbdl3 T C 11: 80,244,471 (GRCm39) Y393H probably damaging Het
Sema3e T C 5: 14,283,717 (GRCm39) L482P probably damaging Het
Setd2 C T 9: 110,403,311 (GRCm39) T1984I probably benign Het
Slc17a1 T C 13: 24,071,960 (GRCm39) Y393H probably damaging Het
Slc9a3 C T 13: 74,307,005 (GRCm39) R377* probably null Het
Slitrk3 A G 3: 72,958,539 (GRCm39) S78P probably damaging Het
Smim35 G T 9: 45,155,426 (GRCm39) probably null Het
Specc1 T A 11: 62,110,157 (GRCm39) V1054E probably damaging Het
Tbc1d4 T C 14: 101,696,219 (GRCm39) T847A probably benign Het
Tcf7l2 G A 19: 55,907,468 (GRCm39) G343R probably damaging Het
Tex36 A C 7: 133,189,111 (GRCm39) Y154D possibly damaging Het
Topaz1 T A 9: 122,576,580 (GRCm39) M57K probably null Het
Trav6-4 T C 14: 53,692,156 (GRCm39) Y85H probably damaging Het
Trim30d A G 7: 104,121,765 (GRCm39) Y327H possibly damaging Het
Ttn A G 2: 76,781,740 (GRCm39) V1056A probably benign Het
Usp32 C A 11: 84,949,953 (GRCm39) probably null Het
Vmn1r59 A T 7: 5,457,136 (GRCm39) M208K probably damaging Het
Vmn2r25 T C 6: 123,799,982 (GRCm39) T787A possibly damaging Het
Vps39 A T 2: 120,169,814 (GRCm39) I246N probably benign Het
Xab2 T C 8: 3,660,162 (GRCm39) D855G probably damaging Het
Xpc A G 6: 91,476,993 (GRCm39) S369P probably benign Het
Ythdc2 T A 18: 44,991,265 (GRCm39) C758S possibly damaging Het
Zfp62 A G 11: 49,107,099 (GRCm39) I397V possibly damaging Het
Zscan4d A G 7: 10,896,435 (GRCm39) S312P probably benign Het
Other mutations in Nphp1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00570:Nphp1 APN 2 127,605,805 (GRCm39) missense probably damaging 0.99
IGL00589:Nphp1 APN 2 127,605,769 (GRCm39) missense probably damaging 1.00
IGL01143:Nphp1 APN 2 127,622,056 (GRCm39) missense probably benign 0.06
IGL01893:Nphp1 APN 2 127,611,564 (GRCm39) missense probably damaging 1.00
IGL01922:Nphp1 APN 2 127,621,989 (GRCm39) missense possibly damaging 0.95
IGL02123:Nphp1 APN 2 127,595,969 (GRCm39) missense probably benign 0.03
IGL02340:Nphp1 APN 2 127,621,987 (GRCm39) nonsense probably null
IGL02836:Nphp1 APN 2 127,611,543 (GRCm39) missense probably benign 0.00
IGL03109:Nphp1 APN 2 127,610,089 (GRCm39) critical splice donor site probably benign
R1632:Nphp1 UTSW 2 127,612,312 (GRCm39) missense probably benign 0.32
R1857:Nphp1 UTSW 2 127,612,296 (GRCm39) missense probably benign 0.00
R4425:Nphp1 UTSW 2 127,630,719 (GRCm39) missense possibly damaging 0.82
R4514:Nphp1 UTSW 2 127,590,007 (GRCm39) missense probably benign 0.26
R4546:Nphp1 UTSW 2 127,607,939 (GRCm39) splice site probably null
R5634:Nphp1 UTSW 2 127,601,570 (GRCm39) missense possibly damaging 0.81
R7152:Nphp1 UTSW 2 127,595,899 (GRCm39) missense probably benign
R7326:Nphp1 UTSW 2 127,603,137 (GRCm39) missense possibly damaging 0.76
R7985:Nphp1 UTSW 2 127,587,829 (GRCm39) missense probably damaging 0.97
R8029:Nphp1 UTSW 2 127,583,036 (GRCm39) missense probably benign 0.00
R8715:Nphp1 UTSW 2 127,605,729 (GRCm39) missense possibly damaging 0.91
R8967:Nphp1 UTSW 2 127,582,897 (GRCm39) missense probably damaging 1.00
R8997:Nphp1 UTSW 2 127,595,982 (GRCm39) missense possibly damaging 0.88
R9328:Nphp1 UTSW 2 127,582,892 (GRCm39) missense possibly damaging 0.77
R9450:Nphp1 UTSW 2 127,616,008 (GRCm39) missense
R9755:Nphp1 UTSW 2 127,595,951 (GRCm39) nonsense probably null
X0022:Nphp1 UTSW 2 127,603,134 (GRCm39) missense probably damaging 1.00
X0025:Nphp1 UTSW 2 127,621,047 (GRCm39) missense probably benign 0.16
Predicted Primers PCR Primer
(F):5'- AGAAGCCATGTTTGTGCAAC -3'
(R):5'- GCCGTTGCAATAGTGTTGAAG -3'

Sequencing Primer
(F):5'- ATGTGAACTTCAGGACCTCAG -3'
(R):5'- CCGTTGCAATAGTGTTGAAGTACTAC -3'
Posted On 2015-09-24