Incidental Mutation 'R5574:Npdc1'
ID 437084
Institutional Source Beutler Lab
Gene Symbol Npdc1
Ensembl Gene ENSMUSG00000015094
Gene Name neural proliferation, differentiation and control 1
Synonyms NPDC-1
MMRRC Submission 043129-MU
Accession Numbers
Is this an essential gene? Non essential (E-score: 0.000) question?
Stock # R5574 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 25399351-25409494 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) G to A at 25408945 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Asparagine at position 284 (D284N)
Ref Sequence ENSEMBL: ENSMUSP00000071387 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000055921] [ENSMUST00000071442] [ENSMUST00000133409] [ENSMUST00000141567] [ENSMUST00000154809]
AlphaFold Q64322
Predicted Effect probably damaging
Transcript: ENSMUST00000055921
AA Change: D293N

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000049602
Gene: ENSMUSG00000015094
AA Change: D293N

DomainStartEndE-ValueType
Pfam:NPDC1 1 341 9.1e-234 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000071442
AA Change: D284N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000071387
Gene: ENSMUSG00000015094
AA Change: D284N

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 possibly damaging
Transcript: ENSMUST00000133409
AA Change: D226N

PolyPhen 2 Score 0.953 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000117773
Gene: ENSMUSG00000015094
AA Change: D226N

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
SMART Domains Protein: ENSMUSP00000116275
Gene: ENSMUSG00000015094

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

DomainStartEndE-ValueType
Pfam:NPDC1 1 142 1.8e-88 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156824
Meta Mutation Damage Score 0.5505 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.7%
  • 20x: 96.6%
Validation Efficiency 99% (68/69)
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: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700129C05Rik T A 14: 59,142,756 N31I possibly damaging Het
3110002H16Rik CTGTGTGTT CTGTGTGTTGTGTGTT 18: 12,185,006 probably null Het
Acvr1b T A 15: 101,202,077 M304K probably benign Het
Adamts1 G T 16: 85,799,642 D106E probably damaging Het
Blm C A 7: 80,499,773 C696F probably damaging Het
Bnip3l-ps T A 12: 18,217,118 noncoding transcript Het
C87499 T G 4: 88,628,043 E354A probably benign Het
Ccdc171 A T 4: 83,693,753 N895I probably damaging Het
Cdhr4 A T 9: 107,993,328 probably benign Het
Cfap97 T C 8: 46,170,142 S190P probably damaging Het
Chrnb1 A C 11: 69,793,683 probably benign Het
Clns1a A G 7: 97,720,958 probably benign Het
Col8a2 G A 4: 126,311,268 probably benign Het
Cr2 T A 1: 195,141,236 E721V probably damaging Het
Csk A G 9: 57,629,301 V172A probably benign Het
Cyp2g1 G A 7: 26,820,740 V466M possibly damaging Het
Cyp4f13 A G 17: 32,929,205 Y349H probably benign Het
Dnm1l T C 16: 16,329,821 Y205C probably damaging Het
Dync1i2 A T 2: 71,233,650 T113S probably benign Het
Edem2 T C 2: 155,716,155 E186G probably damaging Het
Eya2 G A 2: 165,763,816 R380H probably damaging Het
Fam214a A T 9: 75,010,390 D757V probably damaging Het
Fam60a C T 6: 148,944,880 probably benign Het
Gldn A G 9: 54,312,922 T132A probably damaging Het
Gm13941 A T 2: 111,100,606 I74K unknown Het
Gm3898 C T 9: 43,830,042 noncoding transcript Het
Ighmbp2 C T 19: 3,271,536 V408I probably benign Het
Klhdc10 C T 6: 30,439,865 L127F possibly damaging Het
Letm1 G A 5: 33,769,386 T189M possibly damaging Het
Lrrc17 A T 5: 21,570,357 I306F possibly damaging Het
Lrrk2 T A 15: 91,787,016 V2000E probably damaging Het
Mettl9 A T 7: 121,047,870 E66D probably benign Het
Mroh1 T A 15: 76,433,931 V877D probably benign Het
Mycbp2 C T 14: 103,142,767 V3760M possibly damaging Het
Nos3 A G 5: 24,368,861 T208A possibly damaging Het
Obp2a A T 2: 25,700,830 T70S possibly damaging Het
Olfr1040 T C 2: 86,146,191 D181G probably damaging Het
Olfr1100 A G 2: 86,978,523 V91A probably benign Het
Olfr1245 C T 2: 89,574,977 V250I possibly damaging Het
Olfr145 A T 9: 37,897,581 Y59F probably damaging Het
Olfr69 T G 7: 103,768,116 I94L possibly damaging Het
Pate2 A G 9: 35,686,115 probably benign Het
Pdzph1 A G 17: 58,973,947 F447L probably benign Het
Pias1 A G 9: 62,920,493 C211R probably damaging Het
Plb1 A G 5: 32,329,947 S929G probably benign Het
Prc1 G A 7: 80,294,542 probably benign Het
Prex2 A G 1: 11,140,058 D574G probably damaging Het
Rapgef4 G A 2: 72,034,120 probably null Het
Rock2 T C 12: 16,961,641 M690T possibly damaging Het
Slc18a2 A G 19: 59,261,405 I25V probably benign Het
Slc9a5 T A 8: 105,364,691 I701K probably benign Het
Sorcs1 T A 19: 50,222,133 N765Y probably damaging Het
Ssh2 A T 11: 77,450,115 I698L probably benign Het
Stam A G 2: 14,115,864 D58G probably damaging Het
Thsd4 C A 9: 59,972,400 R1018L probably damaging Het
Tnxb A G 17: 34,711,024 T2911A probably benign Het
Trpm7 A C 2: 126,813,030 F1329L probably benign Het
Ttll9 A G 2: 152,984,248 E126G possibly damaging Het
Tubgcp5 G A 7: 55,805,329 V258M probably benign Het
Unc45a G A 7: 80,334,856 A232V probably damaging Het
Utp14b G A 1: 78,666,409 V675M probably damaging Het
Vmn2r67 T A 7: 85,151,891 H279L probably benign Het
Vmn2r75 G T 7: 86,166,302 A118E probably benign Het
Wdr36 A T 18: 32,865,959 Q886L probably damaging Het
Zfp433 T A 10: 81,719,291 Y27* probably null Het
Zfp715 A T 7: 43,311,039 S43T possibly damaging Het
Zfyve26 A G 12: 79,239,924 S2297P possibly damaging 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
R0650:Npdc1 UTSW 2 25408009 missense probably benign 0.16
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
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'- TGAAGTGGCCGCTTTTCTC -3'
(R):5'- TGGTCAAACAGTGGGTTGC -3'

Sequencing Primer
(F):5'- GTCCCTACCTGCTCGAAAC -3'
(R):5'- AAACAGTGGGTTGCGCACC -3'
Posted On 2016-10-26