Incidental Mutation 'IGL01922:Nphp1'
ID 180142
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Nphp1
Ensembl Gene ENSMUSG00000027378
Gene Name nephronophthisis 1 (juvenile) homolog (human)
Synonyms nephrocystin
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # IGL01922
Quality Score
Status
Chromosome 2
Chromosomal Location 127582652-127630817 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 127621989 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 46 (Y46C)
Ref Sequence ENSEMBL: ENSMUSP00000028857 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028857] [ENSMUST00000110357]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000028857
AA Change: Y46C

PolyPhen 2 Score 0.954 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000028857
Gene: ENSMUSG00000027378
AA Change: Y46C

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 possibly damaging
Transcript: ENSMUST00000110357
AA Change: Y46C

PolyPhen 2 Score 0.901 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000105986
Gene: ENSMUSG00000027378
AA Change: Y46C

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
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: 29 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam12 C A 7: 133,539,201 (GRCm39) G104* probably null Het
Adamtsl1 A G 4: 86,168,139 (GRCm39) K477R probably damaging Het
Arhgap35 A C 7: 16,298,180 (GRCm39) V295G possibly damaging Het
Cacna1c A T 6: 118,629,629 (GRCm39) I1234N probably damaging Het
Cntnap5c A G 17: 58,637,114 (GRCm39) E997G possibly damaging Het
Cog6 T C 3: 52,893,846 (GRCm39) N601S probably benign Het
Col28a1 G T 6: 8,158,133 (GRCm39) D308E probably damaging Het
Cplane1 A G 15: 8,300,305 (GRCm39) K3204R unknown Het
Cspg4 G A 9: 56,795,171 (GRCm39) D969N probably damaging Het
Dhx8 G A 11: 101,630,633 (GRCm39) V347I probably damaging Het
Dnah9 G T 11: 65,965,860 (GRCm39) probably benign Het
Erap1 T C 13: 74,810,506 (GRCm39) Y282H probably damaging Het
Gm21738 G A 14: 19,416,979 (GRCm38) S144L probably benign Het
H2-T3 A G 17: 36,497,992 (GRCm39) M307T possibly damaging Het
Ifi204 T C 1: 173,589,288 (GRCm39) I48V possibly damaging Het
Myh1 T C 11: 67,101,292 (GRCm39) probably null Het
Odad3 G T 9: 21,904,826 (GRCm39) probably benign Het
Or14j7 A T 17: 38,234,850 (GRCm39) H131L possibly damaging Het
Or2t46 G A 11: 58,471,899 (GRCm39) M76I probably benign Het
Piezo1 G T 8: 123,219,431 (GRCm39) S1066R probably benign Het
Plekhh1 T C 12: 79,126,353 (GRCm39) S1353P probably benign Het
Prl6a1 A T 13: 27,499,343 (GRCm39) D37V possibly damaging Het
Scn4a A G 11: 106,229,978 (GRCm39) probably null Het
Selenoo T C 15: 88,983,852 (GRCm39) V585A probably benign Het
Tmf1 T C 6: 97,153,891 (GRCm39) T61A probably benign Het
Tshz3 A G 7: 36,469,030 (GRCm39) T340A probably damaging Het
Unc50 A G 1: 37,476,284 (GRCm39) D148G probably benign Het
Vmn2r129 C T 4: 156,690,549 (GRCm39) noncoding transcript Het
Xpc C T 6: 91,482,407 (GRCm39) R192H probably damaging 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
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
R4580:Nphp1 UTSW 2 127,610,089 (GRCm39) critical splice donor 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
Posted On 2014-05-07