Mutagenetix > Incidental Mutation

Incidental Mutation 'R6994:Npas3'

544065

Institutional Source

Beutler Lab

Gene Symbol

Npas3

Ensembl Gene

ENSMUSG00000021010

Gene Name

neuronal PAS domain protein 3

Synonyms

bHLHe12, 4930423H22Rik

MMRRC Submission

045100-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.924) question?

Stock #

R6994 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

53294940-54118958 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 54115576 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Lysine at position 802 (Q802K)

Ref Sequence

ENSEMBL: ENSMUSP00000152411 (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: Q833K

PolyPhen 2 Score 0.767 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000098975
Gene: ENSMUSG00000021010
AA Change: Q833K

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 benign
Transcript: ENSMUST00000223057
AA Change: Q815K

PolyPhen 2 Score 0.347 (Sensitivity: 0.90; Specificity: 0.89)

Predicted Effect

probably damaging
Transcript: ENSMUST00000223358
AA Change: Q802K

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

96% (82/85)

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl4	T	G	4: 144,349,849 (GRCm39)	W369G	probably damaging	Het
Abhd16b	C	T	2: 181,135,461 (GRCm39)	T121M	possibly damaging	Het
Adam5	A	T	8: 25,276,262 (GRCm39)	C468*	probably null	Het
Aim2	C	T	1: 173,283,152 (GRCm39)	A78V	possibly damaging	Het
Alg9	G	A	9: 50,703,422 (GRCm39)	W254*	probably null	Het
Ankrd55	G	C	13: 112,504,834 (GRCm39)	E499Q	probably benign	Het
Atp6v0a2	T	C	5: 124,791,209 (GRCm39)	F546S	probably damaging	Het
Bean1	CT	C	8: 104,908,664 (GRCm39)		probably null	Het
Bpi	A	T	2: 158,100,164 (GRCm39)		probably benign	Het
Bves	A	G	10: 45,215,514 (GRCm39)	H63R	probably benign	Het
Ccdc183	T	C	2: 25,507,057 (GRCm39)	M45V	probably benign	Het
Cfhr4	T	A	1: 139,664,668 (GRCm39)	I464L	possibly damaging	Het
Cmklr1	T	C	5: 113,752,983 (GRCm39)	Y6C	probably damaging	Het
Colgalt1	C	T	8: 72,076,165 (GRCm39)	R539C	probably damaging	Het
Ctsm	T	A	13: 61,687,698 (GRCm39)	E53D	probably damaging	Het
Cyp2a22	A	G	7: 26,638,606 (GRCm39)		probably null	Het
Ddx10	A	G	9: 53,115,411 (GRCm39)	V641A	probably damaging	Het
Ddx6	T	C	9: 44,540,020 (GRCm39)	V316A	probably damaging	Het
Dhx34	T	C	7: 15,937,799 (GRCm39)	D767G	probably benign	Het
Dnaaf6rt	T	C	1: 31,261,990 (GRCm39)		probably benign	Het
Dtnbp1	T	A	13: 45,155,405 (GRCm39)	D15V	probably damaging	Het
Dtx3l	C	T	16: 35,751,742 (GRCm39)		probably null	Het
Entpd8	T	C	2: 24,973,321 (GRCm39)	I162T	probably damaging	Het
Fam186a	G	T	15: 99,840,347 (GRCm39)	Q1966K	probably benign	Het
Fbxo27	A	C	7: 28,392,785 (GRCm39)	D22A	probably damaging	Het
Fermt3	A	T	19: 6,977,095 (GRCm39)	I577N	probably damaging	Het
Frmd8	A	T	19: 5,923,209 (GRCm39)	S81T	probably damaging	Het
Gm5108	T	A	5: 68,102,012 (GRCm39)		probably benign	Het
Gm9195	T	C	14: 72,718,271 (GRCm39)	Y135C	probably damaging	Het
Gpatch2l	G	A	12: 86,290,958 (GRCm39)	R47H	probably damaging	Het
Kcnh8	A	T	17: 53,284,723 (GRCm39)	I898F	probably benign	Het
Kri1	C	T	9: 21,199,083 (GRCm39)		probably benign	Het
Krt32	T	A	11: 99,977,271 (GRCm39)	I210F	probably damaging	Het
Lama1	G	A	17: 68,060,820 (GRCm39)	C716Y		Het
Lamc2	G	A	1: 153,012,508 (GRCm39)	T722M	probably benign	Het
Lpin3	C	T	2: 160,746,803 (GRCm39)	P766L	probably damaging	Het
Macroh2a1	T	C	13: 56,237,643 (GRCm39)	N206D	probably benign	Het
Marf1	T	C	16: 13,946,721 (GRCm39)	T1169A	probably damaging	Het
Morc1	G	A	16: 48,385,984 (GRCm39)	V536M	probably benign	Het
Morc1	A	T	16: 48,438,909 (GRCm39)	H768L	probably benign	Het
Mpped2	T	A	2: 106,529,878 (GRCm39)	H42Q	possibly damaging	Het
Nfatc1	G	T	18: 80,696,779 (GRCm39)		probably null	Het
Nfkbid	G	A	7: 30,125,192 (GRCm39)	S263N	probably benign	Het
Or52s1b	T	C	7: 102,822,119 (GRCm39)	T242A	probably damaging	Het
Or5ac20	T	G	16: 59,104,453 (GRCm39)	M136L	possibly damaging	Het
Or5p67	T	A	7: 107,922,101 (GRCm39)	I261F	possibly damaging	Het
Pabpc4l	C	A	3: 46,401,345 (GRCm39)	V100L	possibly damaging	Het
Pagr1a	A	G	7: 126,615,613 (GRCm39)		probably null	Het
Pcdh1	A	T	18: 38,331,553 (GRCm39)	N483K	probably damaging	Het
Pikfyve	C	A	1: 65,291,689 (GRCm39)	P1303T	probably damaging	Het
Plekhh3	T	A	11: 101,056,519 (GRCm39)		probably null	Het
Pnkd	T	A	1: 74,332,335 (GRCm39)		probably null	Het
Pparg	A	T	6: 115,428,011 (GRCm39)	Q166L	probably benign	Het
Psenen	A	G	7: 30,262,932 (GRCm39)		probably null	Het
Rab4a	T	C	8: 124,557,105 (GRCm39)	S142P	probably damaging	Het
Reg3a	T	C	6: 78,358,132 (GRCm39)	V21A	probably benign	Het
Relt	A	C	7: 100,502,321 (GRCm39)		probably benign	Het
Rftn1	T	A	17: 50,344,019 (GRCm39)	T90S	possibly damaging	Het
Ripor3	T	G	2: 167,839,186 (GRCm39)	D105A	probably damaging	Het
Rnase10	T	A	14: 51,247,138 (GRCm39)	I135N	probably damaging	Het
Rsrc1	C	T	3: 66,901,982 (GRCm39)	P44L	unknown	Het
Rttn	A	G	18: 89,047,023 (GRCm39)	E895G	probably damaging	Het
Serpina3a	G	A	12: 104,079,089 (GRCm39)		probably null	Het
Slco5a1	C	T	1: 12,951,617 (GRCm39)	C562Y	probably damaging	Het
Spen	T	C	4: 141,220,770 (GRCm39)	T396A	unknown	Het
Tgfbr3	A	G	5: 107,280,892 (GRCm39)	S623P	probably damaging	Het
Tmem8b	A	G	4: 43,690,192 (GRCm39)	I876V	probably damaging	Het
Tmod3	T	C	9: 75,416,669 (GRCm39)	K221R	probably damaging	Het
Tomm40	G	T	7: 19,436,831 (GRCm39)	D40E	probably damaging	Het
Trav6d-4	G	T	14: 52,991,048 (GRCm39)	G28V	probably damaging	Het
Trav8d-2	G	T	14: 53,279,933 (GRCm39)	A17S	probably benign	Het
Triml2	T	C	8: 43,643,115 (GRCm39)	C158R	possibly damaging	Het
Trip10	A	G	17: 57,562,331 (GRCm39)	E283G	probably damaging	Het
Tubb2b	T	C	13: 34,311,518 (GRCm39)	Y425C	probably damaging	Het
Ubr1	T	C	2: 120,794,074 (GRCm39)	T37A	probably benign	Het
Unc13b	A	G	4: 43,171,403 (GRCm39)		probably benign	Het
Unc13b	A	G	4: 43,173,203 (GRCm39)		probably benign	Het
Vcan	A	T	13: 89,841,526 (GRCm39)	D379E	possibly damaging	Het
Vmn1r44	T	A	6: 89,871,140 (GRCm39)	H295Q	probably benign	Het
Vmn2r16	A	T	5: 109,487,969 (GRCm39)	S281C	probably damaging	Het
Vmn2r84	C	T	10: 130,226,876 (GRCm39)	A321T	possibly damaging	Het
Vsig10l	A	T	7: 43,114,491 (GRCm39)	H271L	possibly damaging	Het
Vwa8	A	T	14: 79,145,596 (GRCm39)	H91L	possibly damaging	Het
Zfp957	T	A	14: 79,451,130 (GRCm39)	E223V	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
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
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'- AACTCCTTGCTGTACACTGGG -3'
(R):5'- TACCGTTGCTGTAGACTGGG -3'

Sequencing Primer
(F):5'- GGGACCTGGAGGCCCTG -3'
(R):5'- TGGTGAACACGTTGCCAC -3'

Posted On

2019-05-13