Mutagenetix > Incidental Mutation

Incidental Mutation 'R0396:Npas3'

32073

Institutional Source

Beutler Lab

Gene Symbol

Npas3

Ensembl Gene

ENSMUSG00000021010

Gene Name

neuronal PAS domain protein 3

Synonyms

bHLHe12, 4930423H22Rik

MMRRC Submission

038602-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.927) question?

Stock #

R0396 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

53294940-54118958 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 53878528 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 150 (Y150C)

Ref Sequence

ENSEMBL: ENSMUSP00000152411 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000101432] [ENSMUST00000223057] [ENSMUST00000223358]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000101432
AA Change: Y178C

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000098975
Gene: ENSMUSG00000021010
AA Change: Y178C

Domain	Start	End	E-Value	Type
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 damaging
Transcript: ENSMUST00000223057
AA Change: Y160C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Predicted Effect

probably damaging
Transcript: ENSMUST00000223358
AA Change: Y150C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Meta Mutation Damage Score

0.8652

Coding Region Coverage

1x: 99.0%
3x: 98.0%
10x: 95.5%
20x: 89.8%

Validation Efficiency

92% (96/104)

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: 101 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933405L10Rik	G	A	8: 106,436,412 (GRCm39)	V194I	probably benign	Het
Acsm1	A	T	7: 119,235,678 (GRCm39)	I133F	probably damaging	Het
Adamts9	T	A	6: 92,774,986 (GRCm39)	T1676S	probably benign	Het
Adcy4	T	C	14: 56,009,745 (GRCm39)	D769G	probably benign	Het
Aif1	T	C	17: 35,390,085 (GRCm39)	*148W	probably null	Het
Akna	C	T	4: 63,310,363 (GRCm39)		probably benign	Het
Arhgap32	G	A	9: 32,156,551 (GRCm39)		probably null	Het
Atpaf1	G	A	4: 115,642,449 (GRCm39)	E92K	possibly damaging	Het
Bltp2	T	C	11: 78,159,203 (GRCm39)	V467A	possibly damaging	Het
C1s1	T	C	6: 124,510,313 (GRCm39)	E378G	probably benign	Het
Caprin1	T	A	2: 103,599,914 (GRCm39)	Q108L	probably damaging	Het
Car13	A	T	3: 14,721,299 (GRCm39)	H154L	probably benign	Het
Cdon	C	A	9: 35,381,426 (GRCm39)	N605K	probably damaging	Het
Ceacam10	G	A	7: 24,480,439 (GRCm39)	G70E	probably damaging	Het
Cfap221	G	A	1: 119,881,930 (GRCm39)	T286M	probably benign	Het
Cfap61	T	C	2: 145,791,864 (GRCm39)	F107S	possibly damaging	Het
Coil	C	A	11: 88,872,449 (GRCm39)	T270N	probably benign	Het
Crocc2	T	G	1: 93,151,936 (GRCm39)		probably benign	Het
Crot	T	C	5: 9,019,959 (GRCm39)	E461G	probably damaging	Het
D130052B06Rik	G	T	11: 33,573,391 (GRCm39)	R41L	unknown	Het
D630045J12Rik	T	C	6: 38,173,671 (GRCm39)	S166G	possibly damaging	Het
Dennd4a	T	G	9: 64,769,673 (GRCm39)	V460G	probably damaging	Het
Depdc7	A	T	2: 104,557,668 (GRCm39)		probably benign	Het
Dgkb	G	A	12: 38,240,134 (GRCm39)		probably null	Het
Dhx57	T	G	17: 80,582,226 (GRCm39)	S407R	probably benign	Het
Dnase2a	G	T	8: 85,636,392 (GRCm39)		probably benign	Het
Dqx1	T	G	6: 83,035,986 (GRCm39)	M106R	probably benign	Het
Eno1b	T	C	18: 48,180,806 (GRCm39)	I328T	probably benign	Het
Ephx2	T	G	14: 66,345,512 (GRCm39)	I151L	probably benign	Het
Gdf3	C	T	6: 122,584,094 (GRCm39)	G91D	probably damaging	Het
Gpc5	T	A	14: 115,665,620 (GRCm39)	N481K	possibly damaging	Het
Gsdme	T	A	6: 50,198,087 (GRCm39)	H291L	probably benign	Het
H2-T13	A	G	17: 36,394,614 (GRCm39)	I103T	possibly damaging	Het
Hif3a	G	A	7: 16,785,946 (GRCm39)		probably benign	Het
Hmox2	A	T	16: 4,583,627 (GRCm39)	I232L	probably benign	Het
Itgb2	A	G	10: 77,397,023 (GRCm39)	Y686C	probably damaging	Het
Jmjd1c	A	G	10: 67,055,302 (GRCm39)	T528A	possibly damaging	Het
Kdr	T	C	5: 76,121,388 (GRCm39)	I541V	possibly damaging	Het
Khdrbs2	C	A	1: 32,559,054 (GRCm39)	V343L	probably damaging	Het
Kif16b	C	T	2: 142,695,579 (GRCm39)	R175H	probably damaging	Het
Klri2	T	G	6: 129,717,251 (GRCm39)	E44A	possibly damaging	Het
Kmt2b	G	T	7: 30,276,180 (GRCm39)	T1773K	probably damaging	Het
Lair1	A	G	7: 4,013,785 (GRCm39)	L154P	probably damaging	Het
Larp1b	G	A	3: 40,924,996 (GRCm39)	V158M	probably damaging	Het
Lgi3	T	A	14: 70,772,280 (GRCm39)	I275N	probably damaging	Het
Lrba	A	G	3: 86,202,486 (GRCm39)	N246D	probably damaging	Het
Lrrc45	T	A	11: 120,605,733 (GRCm39)		probably benign	Het
Mdh2	G	T	5: 135,818,533 (GRCm39)	V263L	probably benign	Het
Myom1	T	A	17: 71,341,688 (GRCm39)	V149E	probably damaging	Het
Nanos1	A	T	19: 60,745,479 (GRCm39)	D259V	probably damaging	Het
Nedd4l	T	A	18: 65,294,725 (GRCm39)		probably benign	Het
Or10ab4	A	T	7: 107,655,170 (GRCm39)	H327L	probably benign	Het
Or10ag59	T	A	2: 87,405,911 (GRCm39)	V161D	possibly damaging	Het
Or2h1b	C	T	17: 37,462,446 (GRCm39)	C139Y	probably damaging	Het
Or2y1f	A	T	11: 49,184,165 (GRCm39)	I6F	probably benign	Het
Or52e15	G	A	7: 104,645,913 (GRCm39)	A66V	probably damaging	Het
Or8k28	T	C	2: 86,286,363 (GRCm39)	N84S	possibly damaging	Het
Pde4c	A	G	8: 71,202,725 (GRCm39)	N637S	probably benign	Het
Pds5b	T	A	5: 150,702,740 (GRCm39)	V824D	possibly damaging	Het
Pole2	A	T	12: 69,269,160 (GRCm39)		probably benign	Het
Ppig	C	T	2: 69,566,320 (GRCm39)		probably benign	Het
Prep	A	G	10: 44,968,772 (GRCm39)	Y90C	probably damaging	Het
Proca1	A	T	11: 78,085,731 (GRCm39)	R11S	probably damaging	Het
Prph	T	A	15: 98,954,872 (GRCm39)	W313R	probably benign	Het
Prune2	C	T	19: 17,100,444 (GRCm39)	P1983S	probably benign	Het
Ptbp2	G	A	3: 119,517,847 (GRCm39)		probably benign	Het
Rsph6a	C	T	7: 18,808,031 (GRCm39)	P398L	probably damaging	Het
Sdk2	T	C	11: 113,720,793 (GRCm39)	I1379V	probably benign	Het
Sf3b1	C	T	1: 55,058,430 (GRCm39)	G53E	probably damaging	Het
Slc9a3	T	C	13: 74,305,903 (GRCm39)		probably null	Het
Smarcal1	A	T	1: 72,665,632 (GRCm39)	H710L	probably benign	Het
Soat2	GAGAAG	GAG	15: 102,059,142 (GRCm39)		probably benign	Het
Sptan1	T	C	2: 29,881,045 (GRCm39)	V438A	probably damaging	Het
Sstr4	T	A	2: 148,238,181 (GRCm39)	V264D	probably damaging	Het
Susd2	A	G	10: 75,475,745 (GRCm39)	L418P	probably damaging	Het
Synj1	A	G	16: 90,735,528 (GRCm39)	V1475A	probably benign	Het
Szt2	G	A	4: 118,233,544 (GRCm39)		probably benign	Het
Tbc1d4	T	C	14: 101,695,499 (GRCm39)		probably null	Het
Tesk1	A	G	4: 43,446,000 (GRCm39)	E311G	probably damaging	Het
Tmed5	A	T	5: 108,273,882 (GRCm39)	V119E	probably damaging	Het
Tmem260	T	C	14: 48,724,324 (GRCm39)	S201P	possibly damaging	Het
Tnxb	A	G	17: 34,890,707 (GRCm39)	Y350C	probably damaging	Het
Tpte	T	C	8: 22,825,624 (GRCm39)		probably benign	Het
Trim37	A	T	11: 87,037,794 (GRCm39)	D161V	probably damaging	Het
Trrap	C	A	5: 144,751,366 (GRCm39)	Q1640K	probably damaging	Het
Tspoap1	T	C	11: 87,667,172 (GRCm39)		probably benign	Het
Ttk	T	A	9: 83,729,313 (GRCm39)		probably benign	Het
Vmn1r172	A	G	7: 23,359,957 (GRCm39)	S281G	probably benign	Het
Vmn1r177	A	G	7: 23,565,022 (GRCm39)	S285P	probably damaging	Het
Vmn1r231	C	T	17: 21,110,661 (GRCm39)	V85I	probably damaging	Het
Vmn2r100	C	A	17: 19,742,382 (GRCm39)	P252Q	possibly damaging	Het
Vmn2r118	T	C	17: 55,915,643 (GRCm39)	I436V	probably benign	Het
Vmn2r12	T	C	5: 109,240,765 (GRCm39)	K116R	probably benign	Het
Vmn2r28	T	A	7: 5,491,513 (GRCm39)	I245L	probably benign	Het
Wdr26	A	T	1: 181,008,216 (GRCm39)		probably benign	Het
Xrcc3	A	T	12: 111,776,391 (GRCm39)	H67Q	probably benign	Het
Zbbx	A	T	3: 74,985,802 (GRCm39)	S417T	possibly damaging	Het
Zc3h13	A	G	14: 75,560,922 (GRCm39)	D504G	unknown	Het
Zfp1005	G	A	2: 150,109,973 (GRCm39)	G221D	probably damaging	Het
Zfp217	C	T	2: 169,957,382 (GRCm39)	A539T	probably benign	Het
Zyg11b	A	T	4: 108,112,505 (GRCm39)	F388I	probably damaging	Het

Other mutations in Npas3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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'- AGCCTACTGGTTTGATGGCAGTTAC -3'
(R):5'- GAGCGCAAGTTTATTCTGAAAGCCC -3'

Sequencing Primer
(F):5'- GATGGCAGTTACTACTGAATCCC -3'
(R):5'- ACAGGCTCCTCTGACTTGG -3'

Posted On

2013-04-24