Incidental Mutation 'R1585:Nptn'
ID 177445
Institutional Source Beutler Lab
Gene Symbol Nptn
Ensembl Gene ENSMUSG00000032336
Gene Name neuroplastin
Synonyms Sdfr1
MMRRC Submission 039622-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1585 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 58489504-58560162 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 58548073 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 159 (N159K)
Ref Sequence ENSEMBL: ENSMUSP00000109756 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000085651] [ENSMUST00000114121] [ENSMUST00000175945] [ENSMUST00000176250] [ENSMUST00000176557] [ENSMUST00000177292] [ENSMUST00000177064] [ENSMUST00000176916] [ENSMUST00000177380]
AlphaFold P97300
Predicted Effect probably benign
Transcript: ENSMUST00000085651
AA Change: N159K

PolyPhen 2 Score 0.079 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000082793
Gene: ENSMUSG00000032336
AA Change: N159K

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
IG 38 118 1.1e-3 SMART
IGc2 133 206 9.3e-7 SMART
transmembrane domain 221 243 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000114121
AA Change: N159K

PolyPhen 2 Score 0.167 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000109756
Gene: ENSMUSG00000032336
AA Change: N159K

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
IG 38 118 2.56e-1 SMART
IGc2 133 206 2.34e-4 SMART
transmembrane domain 221 243 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000175945
SMART Domains Protein: ENSMUSP00000135576
Gene: ENSMUSG00000032336

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176126
Predicted Effect probably benign
Transcript: ENSMUST00000176250
AA Change: N49K

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000135250
Gene: ENSMUSG00000032336
AA Change: N49K

DomainStartEndE-ValueType
IGc2 23 96 2.34e-4 SMART
transmembrane domain 111 133 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000176557
AA Change: N159K

PolyPhen 2 Score 0.138 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000135541
Gene: ENSMUSG00000032336
AA Change: N159K

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
IG 38 118 2.56e-1 SMART
IGc2 133 206 2.34e-4 SMART
transmembrane domain 221 243 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000177292
AA Change: N275K

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000135199
Gene: ENSMUSG00000032336
AA Change: N275K

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
IGc2 43 123 4.09e-9 SMART
IG 154 234 2.56e-1 SMART
IGc2 249 322 2.34e-4 SMART
transmembrane domain 337 359 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000177064
AA Change: N71K

PolyPhen 2 Score 0.103 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000135316
Gene: ENSMUSG00000032336
AA Change: N71K

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
IGc2 45 118 2.34e-4 SMART
transmembrane domain 133 155 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000176896
AA Change: N157K
SMART Domains Protein: ENSMUSP00000134761
Gene: ENSMUSG00000032336
AA Change: N157K

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
IG 37 117 2.56e-1 SMART
IGc2 132 205 2.34e-4 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000176916
AA Change: N49K

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000134977
Gene: ENSMUSG00000032336
AA Change: N49K

DomainStartEndE-ValueType
IGc2 23 96 2.34e-4 SMART
transmembrane domain 111 133 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000177380
SMART Domains Protein: ENSMUSP00000135886
Gene: ENSMUSG00000032336

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
IG 38 118 2.56e-1 SMART
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.1%
  • 10x: 95.7%
  • 20x: 91.2%
Validation Efficiency 95% (81/85)
MGI Phenotype PHENOTYPE: Mice homozygous for a knock-out allele exhibit abnormal dendritic spine morphology, decreased CNS synapse formation, abnormal CNS synaptic transmission and impaired hearing. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310057J18Rik T A 10: 28,858,518 (GRCm39) I50F possibly damaging Het
4930505A04Rik T C 11: 30,377,175 (GRCm39) probably benign Het
Aadat A T 8: 60,979,714 (GRCm39) D192V possibly damaging Het
Akap12 A G 10: 4,303,640 (GRCm39) D150G probably benign Het
Amigo3 A T 9: 107,931,231 (GRCm39) N218I probably damaging Het
Ankmy1 A G 1: 92,827,373 (GRCm39) S60P probably benign Het
Apol7e G A 15: 77,602,029 (GRCm39) S209N probably damaging Het
AW551984 A T 9: 39,510,632 (GRCm39) Y234* probably null Het
Bcam A T 7: 19,494,111 (GRCm39) D393E probably damaging Het
Card9 A G 2: 26,244,398 (GRCm39) L444P probably benign Het
Ccar1 T C 10: 62,586,780 (GRCm39) E886G unknown Het
Ccnb2 A T 9: 70,317,559 (GRCm39) probably null Het
Cd276 T C 9: 58,442,838 (GRCm39) S206G probably damaging Het
Cds1 T A 5: 101,965,828 (GRCm39) probably benign Het
Cfap96 G A 8: 46,409,515 (GRCm39) S268L probably benign Het
Chuk T C 19: 44,065,812 (GRCm39) S661G possibly damaging Het
Col17a1 T C 19: 47,639,276 (GRCm39) N1090D probably benign Het
Col3a1 A T 1: 45,367,026 (GRCm39) probably null Het
Crispld1 G T 1: 17,821,024 (GRCm39) V355F possibly damaging Het
Cspg4 A T 9: 56,806,151 (GRCm39) R2321W probably damaging Het
Dner T C 1: 84,563,177 (GRCm39) T61A probably benign Het
Dnmt3a A T 12: 3,951,660 (GRCm39) Y679F probably damaging Het
Dzip3 A T 16: 48,798,241 (GRCm39) probably benign Het
Eif3l T C 15: 78,968,381 (GRCm39) S217P possibly damaging Het
Fbxo42 T A 4: 140,925,417 (GRCm39) probably benign Het
Fhod1 A T 8: 106,063,957 (GRCm39) probably benign Het
Fzd1 T A 5: 4,806,278 (GRCm39) I435F probably damaging Het
Gapvd1 C T 2: 34,602,207 (GRCm39) V647I possibly damaging Het
Gm14496 T C 2: 181,638,002 (GRCm39) S359P possibly damaging Het
Gm5218 C A 15: 81,383,741 (GRCm39) noncoding transcript Het
Hnrnph3 A G 10: 62,851,579 (GRCm39) probably null Het
Hsd17b12 G T 2: 93,864,321 (GRCm39) T262K probably damaging Het
Igsf10 G C 3: 59,237,838 (GRCm39) P781R probably damaging Het
Il11ra1 T A 4: 41,768,207 (GRCm39) S373T probably damaging Het
Kdm3b A G 18: 34,942,345 (GRCm39) D612G probably damaging Het
Ldb1 T C 19: 46,022,903 (GRCm39) T261A probably damaging Het
Lep C A 6: 29,069,089 (GRCm39) H47N possibly damaging Het
Lrrtm2 A T 18: 35,346,428 (GRCm39) S291R possibly damaging Het
Ncor2 T C 5: 125,162,062 (GRCm39) Q404R unknown Het
Nlrp4d T C 7: 10,116,437 (GRCm39) H148R probably benign Het
Nlrp9a T A 7: 26,258,093 (GRCm39) D570E probably benign Het
Nphp3 G A 9: 103,886,413 (GRCm39) V202I probably damaging Het
Or4a69 T A 2: 89,313,315 (GRCm39) T55S probably benign Het
Or4a72 A T 2: 89,405,746 (GRCm39) V108D possibly damaging Het
Or51f2 G A 7: 102,526,980 (GRCm39) V218I probably benign Het
Or52a24 A T 7: 103,381,585 (GRCm39) T151S possibly damaging Het
Or8b53 A T 9: 38,667,716 (GRCm39) H244L probably damaging Het
Pcolce T A 5: 137,608,769 (GRCm39) R13* probably null Het
Pdgfra A G 5: 75,353,264 (GRCm39) Y1018C probably damaging Het
Prima1 A G 12: 103,201,854 (GRCm39) S74P probably damaging Het
Prl7c1 A G 13: 27,962,838 (GRCm39) L55P probably damaging Het
Rasef A G 4: 73,658,574 (GRCm39) V513A probably damaging Het
Rgs1 T C 1: 144,121,227 (GRCm39) probably null Het
Rlf T C 4: 121,005,488 (GRCm39) E1164G probably benign Het
Rnf213 A T 11: 119,354,171 (GRCm39) N4016I probably damaging Het
Sae1 C T 7: 16,064,537 (GRCm39) probably null Het
Serping1 A T 2: 84,601,848 (GRCm39) D207E probably benign Het
Setd2 T A 9: 110,380,464 (GRCm39) D33E unknown Het
Simc1 T C 13: 54,673,071 (GRCm39) M473T probably benign Het
Slc30a6 T A 17: 74,725,610 (GRCm39) probably benign Het
Slc4a5 T C 6: 83,242,669 (GRCm39) L346P probably damaging Het
Spef2 T A 15: 9,596,660 (GRCm39) Q1473L probably damaging Het
St3gal3 G T 4: 117,817,204 (GRCm39) A44D possibly damaging Het
Sv2b G T 7: 74,797,425 (GRCm39) T323K probably damaging Het
Sycp2 T A 2: 177,993,461 (GRCm39) N1228I possibly damaging Het
Thbs2 T A 17: 14,910,030 (GRCm39) M190L probably benign Het
Tnrc6a G A 7: 122,776,098 (GRCm39) V1190I probably benign Het
Utrn A T 10: 12,312,029 (GRCm39) I673K possibly damaging Het
Vmn2r114 C T 17: 23,510,675 (GRCm39) V602M probably damaging Het
Wdr7 A T 18: 64,057,989 (GRCm39) I1273L probably benign Het
Zfp618 T C 4: 63,051,175 (GRCm39) L652P probably damaging Het
Zfp804a G A 2: 81,884,095 (GRCm39) probably benign Het
Other mutations in Nptn
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00493:Nptn APN 9 58,550,922 (GRCm39) missense probably damaging 1.00
IGL02043:Nptn APN 9 58,548,012 (GRCm39) missense possibly damaging 0.56
kinda_slow UTSW 9 58,531,035 (GRCm39) missense probably damaging 1.00
R0212:Nptn UTSW 9 58,535,164 (GRCm39) missense probably benign 0.03
R1673:Nptn UTSW 9 58,531,015 (GRCm39) missense probably benign 0.12
R2484:Nptn UTSW 9 58,550,956 (GRCm39) missense possibly damaging 0.85
R4151:Nptn UTSW 9 58,550,825 (GRCm39) missense probably benign 0.14
R4389:Nptn UTSW 9 58,551,055 (GRCm39) missense probably damaging 1.00
R4721:Nptn UTSW 9 58,548,059 (GRCm39) missense probably damaging 1.00
R5166:Nptn UTSW 9 58,526,263 (GRCm39) nonsense probably null
R5346:Nptn UTSW 9 58,531,070 (GRCm39) nonsense probably null
R6494:Nptn UTSW 9 58,531,035 (GRCm39) missense probably damaging 1.00
R6520:Nptn UTSW 9 58,551,017 (GRCm39) missense probably damaging 1.00
R7506:Nptn UTSW 9 58,526,156 (GRCm39) missense probably damaging 1.00
R8762:Nptn UTSW 9 58,525,905 (GRCm39) intron probably benign
R8867:Nptn UTSW 9 58,526,264 (GRCm39) missense probably damaging 1.00
R9124:Nptn UTSW 9 58,558,498 (GRCm39) unclassified probably benign
Predicted Primers PCR Primer
(F):5'- CAGGACTCTGAGCCAGTAGGTAAGAC -3'
(R):5'- GCTCTGTATTCAACTGTGAAAGCAAGC -3'

Sequencing Primer
(F):5'- CTGAGCCAGTAGGTAAGACCTTTG -3'
(R):5'- CTTGTACACAGTCAATGCTGG -3'
Posted On 2014-04-24