Incidental Mutation 'R0650:Npdc1'
ID 62181
Institutional Source Beutler Lab
Gene Symbol Npdc1
Ensembl Gene ENSMUSG00000015094
Gene Name neural proliferation, differentiation and control 1
Synonyms NPDC-1
MMRRC Submission 038835-MU
Accession Numbers
Is this an essential gene? Non essential (E-score: 0.000) question?
Stock # R0650 (G1)
Quality Score 191
Status Validated
Chromosome 2
Chromosomal Location 25399351-25409494 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) C to T at 25408009 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 199 (T199I)
Ref Sequence ENSEMBL: ENSMUSP00000049602 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000055921] [ENSMUST00000071442] [ENSMUST00000133409] [ENSMUST00000141567] [ENSMUST00000154809]
AlphaFold Q64322
Predicted Effect probably benign
Transcript: ENSMUST00000055921
AA Change: T199I

PolyPhen 2 Score 0.159 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000049602
Gene: ENSMUSG00000015094
AA Change: T199I

DomainStartEndE-ValueType
Pfam:NPDC1 1 341 9.1e-234 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000071442
AA Change: T190I

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000071387
Gene: ENSMUSG00000015094
AA Change: T190I

DomainStartEndE-ValueType
Pfam:NPDC1 1 332 7.2e-217 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124277
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128144
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131185
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132287
Predicted Effect probably benign
Transcript: ENSMUST00000133409
AA Change: T122I

PolyPhen 2 Score 0.069 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000117773
Gene: ENSMUSG00000015094
AA Change: T122I

DomainStartEndE-ValueType
Pfam:NPDC1 1 274 3.4e-163 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000136138
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138651
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141106
Predicted Effect probably benign
Transcript: ENSMUST00000141567
AA Change: T189I

PolyPhen 2 Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000116275
Gene: ENSMUSG00000015094
AA Change: T189I

DomainStartEndE-ValueType
Pfam:NPDC1 1 231 7.8e-141 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144413
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156824
Predicted Effect probably benign
Transcript: ENSMUST00000154809
SMART Domains Protein: ENSMUSP00000123386
Gene: ENSMUSG00000015094

DomainStartEndE-ValueType
Pfam:NPDC1 1 142 1.8e-88 PFAM
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.5%
  • 3x: 99.0%
  • 10x: 97.8%
  • 20x: 96.0%
Validation Efficiency 99% (77/78)
MGI Phenotype PHENOTYPE: Homozygous null mice display no obvious abnormalities in viability, fertility, behavior, or brain morphology. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700020N15Rik A G X: 69,945,785 S96G unknown Het
4930447C04Rik T C 12: 72,910,056 D120G probably damaging Het
4930548H24Rik T C 5: 31,485,968 probably benign Het
Adgrg5 T A 8: 94,934,157 probably null Het
Afg3l2 G T 18: 67,415,557 H534Q possibly damaging Het
Ankar G A 1: 72,656,221 probably benign Het
Arid2 T A 15: 96,402,049 F1814L possibly damaging Het
Asb15 C T 6: 24,566,164 A372V probably damaging Het
Atg16l1 A T 1: 87,781,699 D403V possibly damaging Het
BC024978 A T 7: 27,202,647 H233L probably damaging Het
Bnc2 T C 4: 84,293,196 D407G probably benign Het
Cdan1 A G 2: 120,726,045 V633A probably benign Het
Cfap46 T C 7: 139,605,655 Y2482C unknown Het
Chd8 T C 14: 52,202,304 E964G probably benign Het
Cyp2s1 A G 7: 25,809,258 V253A probably damaging Het
Depdc1b A G 13: 108,323,909 N18D probably damaging Het
Fis1 T A 5: 136,962,194 V4E probably damaging Het
Gba2 T A 4: 43,570,424 probably null Het
Gm2381 C T 7: 42,820,080 G207R probably damaging Het
Gpr89 T A 3: 96,897,324 probably benign Het
Gtf2i A G 5: 134,261,837 probably benign Het
Herc2 T G 7: 56,113,210 S896A probably damaging Het
Huwe1 T C X: 151,876,313 S921P probably damaging Het
Iqgap1 T A 7: 80,736,395 K936I probably damaging Het
Kcna4 T A 2: 107,295,582 Y220* probably null Het
Krt18 A G 15: 102,029,485 D139G possibly damaging Het
Krt83 T C 15: 101,487,040 N392D probably damaging Het
L3mbtl4 G A 17: 68,774,291 C558Y probably damaging Het
Lamc2 T A 1: 153,143,876 I440F possibly damaging Het
Lrrc28 T C 7: 67,618,085 N98S probably damaging Het
Lrrk1 G A 7: 66,292,336 A718V probably damaging Het
Mrgprx2 T C 7: 48,482,918 I51V probably damaging Het
Myt1 A T 2: 181,782,615 R25* probably null Het
Nup98 T A 7: 102,152,453 Y755F probably damaging Het
Olfr494 T A 7: 108,367,789 C100S probably damaging Het
Olfr502 G T 7: 108,523,082 N289K probably damaging Het
Olfr638 A G 7: 104,003,239 probably null Het
Olfr936 T A 9: 39,046,700 M240L probably benign Het
Osgin1 A T 8: 119,445,472 Y335F probably damaging Het
Pde10a A T 17: 8,942,965 I493F probably damaging Het
Pdgfrb A G 18: 61,079,708 I895V probably benign Het
Peg10 T TCCCCANNANNNN 6: 4,756,475 probably benign Het
Pidd1 A T 7: 141,440,813 L457* probably null Het
Pik3c2a A G 7: 116,346,247 probably benign Het
Pkd1l3 C G 8: 109,623,649 D375E possibly damaging Het
Plcg1 C T 2: 160,753,363 probably benign Het
Prr13 A C 15: 102,462,215 *138C probably null Het
Prrc2b T C 2: 32,229,255 probably benign Het
Psph T C 5: 129,791,570 probably benign Het
Ripor1 A G 8: 105,618,114 probably benign Het
Scg3 A G 9: 75,669,335 S253P probably damaging Het
Sema6a G A 18: 47,290,045 probably null Het
Sgk1 A G 10: 21,882,657 N7D probably damaging Het
Skor2 T C 18: 76,876,560 F940L probably benign Het
Slbp T C 5: 33,645,489 probably benign Het
Snrnp40 C G 4: 130,378,043 probably null Het
Susd5 A T 9: 114,082,535 H171L possibly damaging Het
Sybu T C 15: 44,673,268 E354G probably benign Het
Synpo T C 18: 60,602,340 N845D possibly damaging Het
Tdrd6 A T 17: 43,628,159 I666N probably damaging Het
Tm9sf4 T C 2: 153,187,365 I111T probably benign Het
Tnc T C 4: 64,008,734 T852A probably benign Het
Tnfrsf10b T A 14: 69,776,176 I185K probably damaging Het
Tnks1bp1 A G 2: 85,062,630 E305G possibly damaging Het
Tnrc6b T C 15: 80,784,758 V22A probably benign Het
Ttn A T 2: 76,768,612 F19319Y probably damaging Het
Ubr5 T C 15: 38,030,807 probably benign Het
Ugt2b5 T A 5: 87,139,768 Q191L probably benign Het
Urod T C 4: 116,991,276 T300A probably benign Het
Vmn1r213 A G 13: 23,011,394 probably benign Het
Znfx1 G A 2: 167,047,654 Q723* probably null Het
Other mutations in Npdc1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01654:Npdc1 APN 2 25407637 missense possibly damaging 0.61
IGL02023:Npdc1 APN 2 25408020 unclassified probably benign
IGL02894:Npdc1 APN 2 25407995 missense probably benign 0.04
danke UTSW 2 25406245 missense probably damaging 1.00
R1136:Npdc1 UTSW 2 25407715 missense probably benign 0.09
R4008:Npdc1 UTSW 2 25408980 nonsense probably null
R4724:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R4725:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R4726:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R4728:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R4836:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R4843:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R4882:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R5108:Npdc1 UTSW 2 25408655 missense probably damaging 1.00
R5393:Npdc1 UTSW 2 25408670 missense probably damaging 1.00
R5572:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R5573:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R5574:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R5605:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R5630:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R5632:Npdc1 UTSW 2 25408945 missense probably damaging 1.00
R5655:Npdc1 UTSW 2 25407680 missense possibly damaging 0.71
R6823:Npdc1 UTSW 2 25409109 missense probably damaging 1.00
R7151:Npdc1 UTSW 2 25409108 missense probably damaging 0.98
R7400:Npdc1 UTSW 2 25406245 missense probably damaging 1.00
R8777:Npdc1 UTSW 2 25408117 missense probably damaging 0.98
R8777-TAIL:Npdc1 UTSW 2 25408117 missense probably damaging 0.98
R9233:Npdc1 UTSW 2 25406317 missense probably damaging 1.00
R9391:Npdc1 UTSW 2 25407967 missense possibly damaging 0.72
Predicted Primers PCR Primer
(F):5'- CAAAGGCCAAGTCCTGCTGACTAC -3'
(R):5'- ACTGGAGTCTGAAGCTCACCTACAC -3'

Sequencing Primer
(F):5'- TATATACCCGACTTTAGCAGCTAC -3'
(R):5'- TCACCTACACCAGCAGAGGG -3'
Posted On 2013-07-30