Incidental Mutation 'R3731:Npas3'
ID 271002
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 # R3731 (G1)
Quality Score 225
Status Not validated
Chromosome 12
Chromosomal Location 53294940-54118958 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 53401175 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 40 (I40T)
Ref Sequence ENSEMBL: ENSMUSP00000098975 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000101432] [ENSMUST00000220986] [ENSMUST00000223057] [ENSMUST00000223358]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000101432
AA Change: I40T

PolyPhen 2 Score 0.108 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000098975
Gene: ENSMUSG00000021010
AA Change: I40T

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 probably benign
Transcript: ENSMUST00000220986
Predicted Effect probably benign
Transcript: ENSMUST00000223057
Predicted Effect probably benign
Transcript: ENSMUST00000223358
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
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: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A630010A05Rik T A 16: 14,427,485 (GRCm39) probably null Het
Abcc5 A T 16: 20,217,684 (GRCm39) Y5* probably null Het
Acbd6 T A 1: 155,434,471 (GRCm39) S30T probably benign Het
Adar T C 3: 89,653,962 (GRCm39) I325T probably damaging Het
Akap13 T C 7: 75,261,125 (GRCm39) S92P probably benign Het
Atp1a4 A T 1: 172,061,528 (GRCm39) V771E probably damaging Het
Cfh A G 1: 140,047,708 (GRCm39) S492P possibly damaging Het
Crlf1 A G 8: 70,952,092 (GRCm39) T95A probably benign Het
Dennd2d T G 3: 106,407,271 (GRCm39) F441V probably damaging Het
Dhx33 T C 11: 70,879,978 (GRCm39) D344G probably benign Het
Disp3 A G 4: 148,337,284 (GRCm39) S844P probably benign Het
Dock2 T C 11: 34,599,722 (GRCm39) K286E probably damaging Het
Fam228a T C 12: 4,768,671 (GRCm39) E203G probably benign Het
Fbxo38 GTGCTGCTGCTGCTGCTGCTGC GTGCTGCTGCTGCTGCTGC 18: 62,648,399 (GRCm39) probably benign Het
Frmpd4 G A X: 166,269,803 (GRCm39) T493M probably damaging Het
Galnt13 A G 2: 54,823,519 (GRCm39) N365S possibly damaging Het
Hrob A G 11: 102,148,732 (GRCm39) E381G possibly damaging Het
Ighv1-19 C A 12: 114,672,497 (GRCm39) C40F probably damaging Het
Ints4 A G 7: 97,155,308 (GRCm39) Q320R probably benign Het
Kctd5 T C 17: 24,278,212 (GRCm39) D146G probably benign Het
Loxl3 T C 6: 83,027,652 (GRCm39) probably null Het
Lrp2 G A 2: 69,294,923 (GRCm39) P3465L probably damaging Het
Lrp2 A T 2: 69,365,251 (GRCm39) probably null Het
Manba G A 3: 135,260,611 (GRCm39) V599I probably benign Het
Mbd6 A G 10: 127,121,637 (GRCm39) probably benign Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Nepn A T 10: 52,280,110 (GRCm39) N401Y probably damaging Het
Nol10 A T 12: 17,474,674 (GRCm39) K622I probably benign Het
Or1e29 T C 11: 73,667,565 (GRCm39) E196G probably benign Het
Or1j19 A T 2: 36,676,578 (GRCm39) I14F possibly damaging Het
Or2d4 T A 7: 106,543,684 (GRCm39) N175Y probably damaging Het
Or4n4b T A 14: 50,535,962 (GRCm39) D268V probably damaging Het
Or5p73 T C 7: 108,064,633 (GRCm39) I34T possibly damaging Het
Or8g33 T A 9: 39,338,365 (GRCm39) M1L probably benign Het
Phtf1 A G 3: 103,893,095 (GRCm39) M120V probably benign Het
Plxna2 A G 1: 194,471,193 (GRCm39) Y988C probably benign Het
Rgs12 G A 5: 35,189,595 (GRCm39) E658K probably damaging Het
Ripor3 C G 2: 167,834,739 (GRCm39) E251Q probably damaging Het
Sec24b T C 3: 129,827,482 (GRCm39) K203R possibly damaging Het
Serpina1d T A 12: 103,734,164 (GRCm39) N47Y possibly damaging Het
Setx GTGGCT GT 2: 29,044,073 (GRCm39) 1814 probably null Het
Sirpb1c T C 3: 15,887,287 (GRCm39) K184R probably damaging Het
Slc16a10 G C 10: 39,932,620 (GRCm39) H314D possibly damaging Het
Upp2 T C 2: 58,645,379 (GRCm39) S41P probably benign Het
Vmn1r10 A G 6: 57,090,719 (GRCm39) T104A probably damaging Het
Wdhd1 A C 14: 47,485,349 (GRCm39) S838R possibly damaging Het
Zer1 A G 2: 30,000,923 (GRCm39) V166A probably benign Het
Zfp217 T C 2: 169,956,308 (GRCm39) N897D probably benign Het
Zfp960 T A 17: 17,308,633 (GRCm39) L449H probably damaging 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
ANU05:Npas3 UTSW 12 54,114,857 (GRCm39) missense possibly damaging 0.49
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
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'- GCTACAGTGTACACATTACAGTTG -3'
(R):5'- CCCACCCTTGATTTCAGAGG -3'

Sequencing Primer
(F):5'- CACATTACAGTTGTGAGTAGAGCC -3'
(R):5'- GAATAGCTGGCAACCACA -3'
Posted On 2015-03-18