Incidental Mutation 'ANU05:Npas3'
ID 262505
Institutional Source Beutler Lab
Gene Symbol Npas3
Ensembl Gene ENSMUSG00000021010
Gene Name neuronal PAS domain protein 3
Synonyms bHLHe12, 4930423H22Rik
Accession Numbers
Essential gene? Probably essential (E-score: 0.927) question?
Stock # ANU05
Quality Score 110
Status Not validated
Chromosome 12
Chromosomal Location 53294940-54118958 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 54114857 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 593 (E593G)
Ref Sequence ENSEMBL: ENSMUSP00000098975 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000101432] [ENSMUST00000223057] [ENSMUST00000223358]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000101432
AA Change: E593G

PolyPhen 2 Score 0.491 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000098975
Gene: ENSMUSG00000021010
AA Change: E593G

DomainStartEndE-ValueType
HLH 64 119 1.34e-6 SMART
PAS 154 220 8.69e-11 SMART
low complexity region 234 256 N/A INTRINSIC
PAS 326 392 7.4e-5 SMART
PAC 398 441 2.46e-1 SMART
low complexity region 461 477 N/A INTRINSIC
low complexity region 524 544 N/A INTRINSIC
low complexity region 598 627 N/A INTRINSIC
low complexity region 696 709 N/A INTRINSIC
low complexity region 739 754 N/A INTRINSIC
low complexity region 759 773 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000185390
Predicted Effect probably benign
Transcript: ENSMUST00000223057
AA Change: E575G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
Predicted Effect probably benign
Transcript: ENSMUST00000223358
AA Change: E562G

PolyPhen 2 Score 0.425 (Sensitivity: 0.89; Specificity: 0.90)
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.5%
  • 20x: 93.3%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the basic helix-loop-helix and PAS domain-containing family of transcription factors. The encoded protein is localized to the nucleus and may regulate genes involved in neurogenesis. Chromosomal abnormalities that affect the coding potential of this gene are associated with schizophrenia and mental retardation. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
PHENOTYPE: Mice homozygous for some knock-out alleles exhibit abnormal behavior and nervous system morphology. Mice homozygous for another knock-out allele exhibit defective lung branching morphogenesis and die shortly after birth. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110038F14Rik G A 15: 76,834,475 (GRCm39) V124I probably damaging Het
Acaca A G 11: 84,206,678 (GRCm39) K1513E probably damaging Het
Acacb T A 5: 114,363,931 (GRCm39) F1464Y probably benign Het
Adgrg6 G A 10: 14,286,274 (GRCm39) A1114V possibly damaging Het
Agl A G 3: 116,566,438 (GRCm39) I975T possibly damaging Het
Akap7 T C 10: 25,147,451 (GRCm39) H93R probably damaging Het
Arhgef11 T C 3: 87,640,481 (GRCm39) W1213R probably benign Het
Ccar1 T A 10: 62,592,428 (GRCm39) E708V probably damaging Het
Cfap206 C T 4: 34,721,562 (GRCm39) S162N probably damaging Het
Cilp T C 9: 65,186,265 (GRCm39) S787P possibly damaging Het
Col6a3 G A 1: 90,730,014 (GRCm39) T1157I probably damaging Het
D630003M21Rik T C 2: 158,038,308 (GRCm39) Y1046C probably benign Het
Dock3 A G 9: 106,772,862 (GRCm39) S464P probably benign Het
Dusp19 A G 2: 80,454,618 (GRCm39) T113A probably benign Het
Dync1h1 A C 12: 110,615,538 (GRCm39) Y2957S probably benign Het
Epdr1 T C 13: 19,778,814 (GRCm39) Y94C probably damaging Het
Fcho1 A T 8: 72,165,191 (GRCm39) L422Q probably benign Het
Gca T A 2: 62,520,787 (GRCm39) Y210* probably null Het
Gpnmb T C 6: 49,032,615 (GRCm39) V513A probably benign Het
Irx4 A G 13: 73,415,786 (GRCm39) T192A probably damaging Het
Isca1 T C 13: 59,906,785 (GRCm39) T54A probably benign Het
Kif12 GGGGC GGGGCCTCCACCCGGCGGGC 4: 63,089,660 (GRCm39) probably benign Het
L3mbtl1 T C 2: 162,812,100 (GRCm39) V715A probably benign Het
Lama1 G A 17: 68,045,865 (GRCm39) D257N probably damaging Het
Lgr5 T C 10: 115,314,439 (GRCm39) H166R probably damaging Het
M6pr A G 6: 122,289,218 (GRCm39) R9G probably benign Het
Nmt2 T G 2: 3,315,731 (GRCm39) S240R probably benign Het
Or8k30 G A 2: 86,339,513 (GRCm39) A237T possibly damaging Het
Pank4 T C 4: 155,059,103 (GRCm39) M412T probably damaging Het
Psd A G 19: 46,303,186 (GRCm39) V100A possibly damaging Het
Rab11fip3 T C 17: 26,235,087 (GRCm39) T28A probably damaging Het
Rnpepl1 A T 1: 92,847,468 (GRCm39) D685V probably benign Het
Rrad T C 8: 105,357,283 (GRCm39) E88G probably benign Het
Sdk2 T A 11: 113,733,906 (GRCm39) M846L probably benign Het
Sparcl1 A T 5: 104,242,581 (GRCm39) V36E possibly damaging Het
Spmip5 A T 19: 58,777,545 (GRCm39) H80Q probably damaging Het
Srrm4 C T 5: 116,605,628 (GRCm39) E210K unknown Het
Stk25 A T 1: 93,551,145 (GRCm39) probably null Het
Tacr3 A T 3: 134,635,810 (GRCm39) Y338F probably damaging Het
Tap2 A T 17: 34,428,184 (GRCm39) Q286L probably benign Het
Tedc1 C T 12: 113,126,808 (GRCm39) R357* probably null Het
Tubgcp5 C A 7: 55,458,277 (GRCm39) A396E possibly damaging Het
Ube2o T C 11: 116,430,960 (GRCm39) D980G probably damaging Het
Vmn1r86 T C 7: 12,836,433 (GRCm39) M98V probably benign Het
Vmn2r58 T A 7: 41,513,935 (GRCm39) H236L probably benign Het
Zfp521 T C 18: 13,950,303 (GRCm39) H1217R probably damaging Het
Zfyve1 A T 12: 83,601,779 (GRCm39) F110I probably benign Het
Other mutations in Npas3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01021:Npas3 APN 12 54,050,343 (GRCm39) missense probably damaging 1.00
IGL01330:Npas3 APN 12 54,095,602 (GRCm39) missense probably damaging 1.00
IGL01376:Npas3 APN 12 54,091,369 (GRCm39) missense probably benign 0.01
IGL01634:Npas3 APN 12 53,993,946 (GRCm39) missense probably damaging 1.00
IGL02456:Npas3 APN 12 54,095,550 (GRCm39) missense probably damaging 0.99
IGL02663:Npas3 APN 12 54,115,691 (GRCm39) missense probably damaging 1.00
IGL02731:Npas3 APN 12 54,114,578 (GRCm39) missense probably benign 0.01
IGL02955:Npas3 APN 12 53,548,048 (GRCm39) missense probably damaging 0.96
IGL03001:Npas3 APN 12 53,547,975 (GRCm39) missense probably damaging 1.00
IGL03047:Npas3 APN 12 53,878,470 (GRCm39) splice site probably benign
IGL02837:Npas3 UTSW 12 53,993,980 (GRCm39) missense possibly damaging 0.79
R0042:Npas3 UTSW 12 54,095,624 (GRCm39) missense probably damaging 1.00
R0042:Npas3 UTSW 12 54,095,624 (GRCm39) missense probably damaging 1.00
R0396:Npas3 UTSW 12 53,878,528 (GRCm39) missense probably damaging 1.00
R1687:Npas3 UTSW 12 54,095,658 (GRCm39) splice site probably null
R1863:Npas3 UTSW 12 54,115,609 (GRCm39) missense probably damaging 1.00
R2004:Npas3 UTSW 12 54,114,680 (GRCm39) missense possibly damaging 0.63
R2047:Npas3 UTSW 12 54,115,612 (GRCm39) missense probably damaging 0.99
R2049:Npas3 UTSW 12 54,108,871 (GRCm39) missense probably damaging 1.00
R2278:Npas3 UTSW 12 53,687,285 (GRCm39) missense possibly damaging 0.92
R2323:Npas3 UTSW 12 54,115,129 (GRCm39) missense probably damaging 1.00
R2871:Npas3 UTSW 12 54,114,796 (GRCm39) nonsense probably null
R2871:Npas3 UTSW 12 54,114,796 (GRCm39) nonsense probably null
R3116:Npas3 UTSW 12 54,114,508 (GRCm39) splice site probably null
R3431:Npas3 UTSW 12 54,115,832 (GRCm39) missense probably damaging 0.99
R3731:Npas3 UTSW 12 53,401,175 (GRCm39) missense probably benign 0.11
R3767:Npas3 UTSW 12 54,115,857 (GRCm39) makesense probably null
R4332:Npas3 UTSW 12 54,108,852 (GRCm39) missense probably damaging 0.99
R4593:Npas3 UTSW 12 54,115,280 (GRCm39) missense probably benign 0.08
R4601:Npas3 UTSW 12 54,091,361 (GRCm39) missense probably damaging 0.99
R4654:Npas3 UTSW 12 54,108,915 (GRCm39) critical splice donor site probably null
R4946:Npas3 UTSW 12 54,112,618 (GRCm39) missense probably damaging 1.00
R5140:Npas3 UTSW 12 53,547,897 (GRCm39) nonsense probably null
R5302:Npas3 UTSW 12 54,115,619 (GRCm39) missense probably damaging 1.00
R5524:Npas3 UTSW 12 54,115,721 (GRCm39) missense possibly damaging 0.64
R5735:Npas3 UTSW 12 54,050,262 (GRCm39) missense probably benign 0.00
R6252:Npas3 UTSW 12 54,115,673 (GRCm39) missense probably damaging 1.00
R6438:Npas3 UTSW 12 54,115,481 (GRCm39) missense probably damaging 0.99
R6987:Npas3 UTSW 12 54,115,036 (GRCm39) missense possibly damaging 0.94
R6994:Npas3 UTSW 12 54,115,576 (GRCm39) missense probably damaging 0.96
R7304:Npas3 UTSW 12 54,115,824 (GRCm39) missense probably damaging 1.00
R7684:Npas3 UTSW 12 54,115,609 (GRCm39) missense probably damaging 1.00
R7724:Npas3 UTSW 12 54,115,124 (GRCm39) missense possibly damaging 0.90
R7739:Npas3 UTSW 12 54,115,501 (GRCm39) missense probably damaging 1.00
R7826:Npas3 UTSW 12 53,878,539 (GRCm39) missense possibly damaging 0.92
R8017:Npas3 UTSW 12 54,091,462 (GRCm39) missense probably damaging 1.00
R8019:Npas3 UTSW 12 54,091,462 (GRCm39) missense probably damaging 1.00
R8034:Npas3 UTSW 12 53,687,312 (GRCm39) missense probably damaging 1.00
R8422:Npas3 UTSW 12 54,115,292 (GRCm39) missense probably benign
R9172:Npas3 UTSW 12 54,112,653 (GRCm39) missense probably benign 0.08
R9207:Npas3 UTSW 12 54,114,818 (GRCm39) missense possibly damaging 0.87
R9774:Npas3 UTSW 12 53,994,108 (GRCm39) missense probably damaging 1.00
X0003:Npas3 UTSW 12 54,091,511 (GRCm39) splice site probably null
X0064:Npas3 UTSW 12 53,401,167 (GRCm39) missense probably damaging 0.96
Z1176:Npas3 UTSW 12 53,547,963 (GRCm39) missense probably damaging 0.99
Z1177:Npas3 UTSW 12 53,993,989 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CGACATGAACTGCAACGACGATGG -3'
(R):5'- GTCTTGATCTTGAGCACAGAGGCG -3'

Sequencing Primer
(F):5'- TGACAGCGACGACAGCTTC -3'
(R):5'- TGTGCGGCGATGACAGCA -3'
Posted On 2015-02-04