Mutagenetix > Incidental Mutation

Incidental Mutation 'R0507:Negr1'

47652

Institutional Source

Beutler Lab

Gene Symbol

Negr1

Ensembl Gene

ENSMUSG00000040037

Gene Name

neuronal growth regulator 1

Synonyms

neurotractin, Ntra, 5330422G01Rik

MMRRC Submission

038702-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0507 (G1)

Quality Score

162

Status

Validated

Chromosome

Chromosomal Location

156267431-157022082 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 156267862 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 11 (S11T)

Ref Sequence

ENSEMBL: ENSMUSP00000101680 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000041425] [ENSMUST00000074015] [ENSMUST00000106065] [ENSMUST00000175773]

AlphaFold

Q80Z24

Predicted Effect

possibly damaging
Transcript: ENSMUST00000041425
AA Change: S11T

PolyPhen 2 Score 0.697 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000041132
Gene: ENSMUSG00000040037
AA Change: S11T

Domain	Start	End	E-Value	Type
signal peptide	1	31	N/A	INTRINSIC
IG	39	130	2.52e-9	SMART
IGc2	145	204	3.22e-16	SMART
IGc2	230	298	3.82e-9	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000074015
AA Change: S11T

PolyPhen 2 Score 0.697 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000073664
Gene: ENSMUSG00000040037
AA Change: S11T

Domain	Start	End	E-Value	Type
signal peptide	1	31	N/A	INTRINSIC
IG	39	130	2.52e-9	SMART
IGc2	145	204	3.22e-16	SMART
IGc2	230	298	3.82e-9	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000106065
AA Change: S11T

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000101680
Gene: ENSMUSG00000040037
AA Change: S11T

Domain	Start	End	E-Value	Type
signal peptide	1	31	N/A	INTRINSIC
IG	39	130	2.52e-9	SMART
IGc2	145	204	3.22e-16	SMART
IGc2	230	298	3.82e-9	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139363

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140941

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148224

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149387

Predicted Effect

possibly damaging
Transcript: ENSMUST00000175773
AA Change: S11T

PolyPhen 2 Score 0.823 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000135531
Gene: ENSMUSG00000040037
AA Change: S11T

Domain	Start	End	E-Value	Type
low complexity region	15	26	N/A	INTRINSIC
IG	39	101	6.97e-3	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000197246

Meta Mutation Damage Score

0.4811

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.1%
20x: 95.0%

Validation Efficiency

100% (72/72)

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out or ENU-induced allele exhibit reduced body weight. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca7	T	A	10: 79,838,655 (GRCm39)		probably benign	Het
Adamts16	T	C	13: 70,916,766 (GRCm39)	D742G	probably benign	Het
Akap9	G	A	5: 4,119,043 (GRCm39)	E3517K	probably benign	Het
Arfgef3	T	C	10: 18,467,369 (GRCm39)	T1944A	probably damaging	Het
Bsx	A	G	9: 40,787,796 (GRCm39)		probably benign	Het
Cct2	A	T	10: 116,891,151 (GRCm39)		probably null	Het
Cdkl4	T	C	17: 80,851,237 (GRCm39)	D155G	probably benign	Het
Cep250	C	T	2: 155,834,452 (GRCm39)	R2126C	possibly damaging	Het
Cep97	A	T	16: 55,726,245 (GRCm39)		probably benign	Het
Cpne3	C	T	4: 19,532,544 (GRCm39)		probably benign	Het
Csmd1	T	C	8: 16,235,358 (GRCm39)		probably benign	Het
Cx3cr1	C	A	9: 119,881,022 (GRCm39)	D127Y	probably damaging	Het
Dcdc2a	A	G	13: 25,286,572 (GRCm39)	Q165R	probably damaging	Het
Ddx17	A	G	15: 79,421,758 (GRCm39)		probably benign	Het
Dicer1	A	G	12: 104,657,917 (GRCm39)	S1886P	probably damaging	Het
Egf	T	C	3: 129,474,828 (GRCm39)	D571G	possibly damaging	Het
Fyb1	A	G	15: 6,664,297 (GRCm39)	D460G	probably benign	Het
Gbp2	G	T	3: 142,335,794 (GRCm39)	D165Y	probably damaging	Het
Gm14412	A	T	2: 177,006,325 (GRCm39)	N523K	possibly damaging	Het
Gsap	C	T	5: 21,474,961 (GRCm39)	T540I	possibly damaging	Het
Gucy2d	C	A	7: 98,108,209 (GRCm39)		probably null	Het
Icam4	C	A	9: 20,940,799 (GRCm39)	P17Q	possibly damaging	Het
Lyz1	A	T	10: 117,125,022 (GRCm39)		probably null	Het
Matcap1	T	C	8: 106,011,351 (GRCm39)	N261S	probably damaging	Het
Mbd6	A	G	10: 127,119,389 (GRCm39)		probably benign	Het
Mroh3	A	T	1: 136,118,718 (GRCm39)	I533N	probably damaging	Het
Muc4	A	T	16: 32,569,887 (GRCm39)	M316L	probably benign	Het
Myof	A	G	19: 37,889,725 (GRCm39)	I1282T	possibly damaging	Het
Ncald	T	G	15: 37,397,528 (GRCm39)	I51L	probably benign	Het
Obscn	T	C	11: 58,920,167 (GRCm39)	N6735D	probably damaging	Het
Or52n4b	T	C	7: 108,144,292 (GRCm39)	S185P	probably damaging	Het
Or5b105	G	A	19: 13,080,642 (GRCm39)	R3C	possibly damaging	Het
Or6c1b	A	T	10: 129,273,157 (GRCm39)	M159L	probably benign	Het
Or9q1	T	A	19: 13,805,140 (GRCm39)	I207F	possibly damaging	Het
Otogl	A	G	10: 107,702,601 (GRCm39)	V684A	possibly damaging	Het
Palm3	A	G	8: 84,754,958 (GRCm39)	T157A	probably benign	Het
Pard3	T	A	8: 128,097,967 (GRCm39)		probably benign	Het
Pcdh15	A	G	10: 74,457,129 (GRCm39)	D1302G	probably damaging	Het
Pi16	G	A	17: 29,546,826 (GRCm39)	E467K	possibly damaging	Het
Plec	A	T	15: 76,056,983 (GRCm39)	I4183N	probably damaging	Het
Ppp1r13l	T	C	7: 19,109,739 (GRCm39)	L720P	possibly damaging	Het
Prag1	A	G	8: 36,571,277 (GRCm39)	E620G	probably damaging	Het
Ralbp1	G	A	17: 66,156,955 (GRCm39)	T646M	probably benign	Het
Rnf182	T	G	13: 43,821,823 (GRCm39)	S125A	probably benign	Het
Rpe	C	T	1: 66,754,300 (GRCm39)	T124I	probably benign	Het
Rufy4	T	C	1: 74,185,875 (GRCm39)	I514T	probably benign	Het
Sec13	A	T	6: 113,712,080 (GRCm39)	I85N	probably damaging	Het
Siglec1	C	T	2: 130,916,445 (GRCm39)		probably benign	Het
Skint5	T	C	4: 113,425,127 (GRCm39)		probably null	Het
Slc4a3	T	A	1: 75,532,725 (GRCm39)	I995K	probably damaging	Het
Smyd4	T	A	11: 75,290,534 (GRCm39)	S545T	possibly damaging	Het
Steap3	C	T	1: 120,169,313 (GRCm39)	R328H	possibly damaging	Het
Tgm6	G	A	2: 129,980,751 (GRCm39)	E183K	possibly damaging	Het
Themis	T	A	10: 28,657,828 (GRCm39)	V132E	possibly damaging	Het
Thsd1	T	A	8: 22,748,695 (GRCm39)	I461N	probably damaging	Het
Ttk	T	G	9: 83,750,120 (GRCm39)	S692A	probably damaging	Het
Twf1	A	G	15: 94,483,411 (GRCm39)	M99T	probably damaging	Het
Uchl3	T	A	14: 101,904,443 (GRCm39)	L89*	probably null	Het
Uhmk1	A	G	1: 170,034,760 (GRCm39)	V316A	probably damaging	Het
Unc80	A	G	1: 66,567,052 (GRCm39)	N886S	possibly damaging	Het
Vash2	G	T	1: 190,699,115 (GRCm39)		probably benign	Het
Vmn1r200	G	A	13: 22,579,718 (GRCm39)	E174K	probably benign	Het
Vps16	T	C	2: 130,279,632 (GRCm39)		probably null	Het
Wdr73	T	C	7: 80,541,594 (GRCm39)	E316G	possibly damaging	Het
Xpo1	T	C	11: 23,244,682 (GRCm39)	V1020A	possibly damaging	Het
Ylpm1	T	A	12: 85,075,886 (GRCm39)	N870K	probably benign	Het
Zfhx4	C	T	3: 5,466,048 (GRCm39)	Q2069*	probably null	Het
Zfp1005	T	A	2: 150,110,044 (GRCm39)	C245S	possibly damaging	Het
Zfp512b	C	A	2: 181,226,757 (GRCm39)		probably benign	Het

Other mutations in Negr1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01284:Negr1	APN	3	156,851,854 (GRCm39)	missense	probably damaging	1.00
IGL01635:Negr1	APN	3	156,267,929 (GRCm39)	missense	probably benign	0.00
IGL02006:Negr1	APN	3	156,721,810 (GRCm39)	splice site	probably benign
IGL02427:Negr1	APN	3	156,267,827 (GRCm39)	start gained	probably benign
IGL02542:Negr1	APN	3	156,267,862 (GRCm39)	missense	probably damaging	1.00
PIT4466001:Negr1	UTSW	3	156,565,235 (GRCm39)	missense	probably benign	0.44
R0241:Negr1	UTSW	3	156,914,036 (GRCm39)	intron	probably benign
R0496:Negr1	UTSW	3	156,721,904 (GRCm39)	missense	probably damaging	1.00
R0506:Negr1	UTSW	3	156,866,385 (GRCm39)	splice site	probably benign
R0634:Negr1	UTSW	3	156,721,903 (GRCm39)	missense	possibly damaging	0.51
R1324:Negr1	UTSW	3	156,774,860 (GRCm39)	missense	probably damaging	1.00
R1923:Negr1	UTSW	3	156,267,836 (GRCm39)	missense	probably benign	0.06
R4569:Negr1	UTSW	3	156,914,013 (GRCm39)	intron	probably benign
R4592:Negr1	UTSW	3	156,914,023 (GRCm39)	intron	probably benign
R4874:Negr1	UTSW	3	156,565,082 (GRCm39)	missense	probably damaging	0.98
R5137:Negr1	UTSW	3	156,721,833 (GRCm39)	missense	probably damaging	0.99
R5330:Negr1	UTSW	3	156,774,913 (GRCm39)	nonsense	probably null
R5331:Negr1	UTSW	3	156,774,913 (GRCm39)	nonsense	probably null
R5974:Negr1	UTSW	3	156,774,923 (GRCm39)	missense	probably damaging	1.00
R6560:Negr1	UTSW	3	157,018,494 (GRCm39)	missense	probably benign
R7506:Negr1	UTSW	3	156,774,870 (GRCm39)	nonsense	probably null
R7677:Negr1	UTSW	3	156,774,823 (GRCm39)	nonsense	probably null
R8080:Negr1	UTSW	3	156,866,357 (GRCm39)	missense	probably damaging	1.00
R8523:Negr1	UTSW	3	156,866,297 (GRCm39)	missense	probably damaging	1.00
R8950:Negr1	UTSW	3	156,721,906 (GRCm39)	missense	probably damaging	1.00
R8997:Negr1	UTSW	3	156,721,918 (GRCm39)	missense	probably damaging	1.00
R9082:Negr1	UTSW	3	156,774,876 (GRCm39)	nonsense	probably null
R9317:Negr1	UTSW	3	156,904,081 (GRCm39)	missense	probably benign	0.00
R9691:Negr1	UTSW	3	156,267,898 (GRCm39)	missense	probably damaging	0.98
R9715:Negr1	UTSW	3	156,774,936 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- ACTACGCCCGACAACTAGGGAG -3'
(R):5'- TCGCTTACGGAGTGAAGCAGAAAC -3'

Sequencing Primer
(F):5'- ACAACTAGGGAGGGGGC -3'
(R):5'- TTCACTCTGGGTGTAAAGCAAG -3'

Posted On

2013-06-12