Mutagenetix > Incidental Mutation

Incidental Mutation 'R1544:Nrp2'

171970

Institutional Source

Beutler Lab

Gene Symbol

Nrp2

Ensembl Gene

ENSMUSG00000025969

Gene Name

neuropilin 2

Synonyms

1110048P06Rik, NP-2, Npn-2, NP2, Npn2

MMRRC Submission

039583-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.951) question?

Stock #

R1544 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

62742476-62857851 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 62802063 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 502 (I502N)

Ref Sequence

ENSEMBL: ENSMUSP00000109794 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027112] [ENSMUST00000063594] [ENSMUST00000075144] [ENSMUST00000102822] [ENSMUST00000114155] [ENSMUST00000114157]

AlphaFold

O35375

Predicted Effect

probably damaging
Transcript: ENSMUST00000027112
AA Change: I502N

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

SMART Domains

Protein: ENSMUSP00000027112
Gene: ENSMUSG00000025969
AA Change: I502N

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
CUB	28	142	3.4e-45	SMART
CUB	149	267	1.04e-40	SMART
FA58C	276	427	1.63e-45	SMART
FA58C	433	592	9.33e-14	SMART
MAM	641	802	2.31e-60	SMART
Pfam:DUF3481	822	906	1.4e-35	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000063594
AA Change: I502N

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

SMART Domains

Protein: ENSMUSP00000069379
Gene: ENSMUSG00000025969
AA Change: I502N

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
CUB	28	142	3.4e-45	SMART
CUB	149	267	1.04e-40	SMART
FA58C	276	427	1.63e-45	SMART
FA58C	433	592	9.33e-14	SMART
MAM	641	802	2.31e-60	SMART
low complexity region	816	831	N/A	INTRINSIC
Pfam:DUF3481	839	923	1.6e-25	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000075144
AA Change: I502N

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

SMART Domains

Protein: ENSMUSP00000074642
Gene: ENSMUSG00000025969
AA Change: I502N

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
CUB	28	142	3.4e-45	SMART
CUB	149	267	1.04e-40	SMART
FA58C	276	427	1.63e-45	SMART
FA58C	433	592	9.33e-14	SMART
MAM	641	802	2.31e-60	SMART
Pfam:DUF3481	827	911	2.3e-25	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000102822
AA Change: I502N

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

SMART Domains

Protein: ENSMUSP00000099886
Gene: ENSMUSG00000025969
AA Change: I502N

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
CUB	28	142	3.4e-45	SMART
CUB	149	267	1.04e-40	SMART
FA58C	276	427	1.63e-45	SMART
FA58C	433	592	9.33e-14	SMART
MAM	641	802	2.31e-60	SMART
Pfam:DUF3481	822	906	2.3e-25	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000114155
AA Change: I502N

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

SMART Domains

Protein: ENSMUSP00000109792
Gene: ENSMUSG00000025969
AA Change: I502N

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
CUB	28	142	3.4e-45	SMART
CUB	149	267	1.04e-40	SMART
FA58C	276	427	1.63e-45	SMART
FA58C	433	592	9.33e-14	SMART
MAM	641	802	2.31e-60	SMART
Pfam:DUF3481	817	901	9.4e-36	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000114157
AA Change: I502N

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

SMART Domains

Protein: ENSMUSP00000109794
Gene: ENSMUSG00000025969
AA Change: I502N

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
CUB	28	142	3.4e-45	SMART
CUB	149	267	1.04e-40	SMART
FA58C	276	427	1.63e-45	SMART
FA58C	433	592	9.33e-14	SMART
MAM	641	802	2.31e-60	SMART
low complexity region	821	836	N/A	INTRINSIC
Pfam:DUF3481	844	928	2.4e-25	PFAM

Meta Mutation Damage Score

0.9642

Coding Region Coverage

1x: 98.9%
3x: 97.9%
10x: 94.7%
20x: 86.9%

Validation Efficiency

99% (114/115)

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 neuropilin family of receptor proteins. The encoded transmembrane protein binds to SEMA3C protein {sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C} and SEMA3F protein {sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F}, and interacts with vascular endothelial growth factor (VEGF). This protein may play a role in cardiovascular development, axon guidance, and tumorigenesis. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Nullizygous mice may exhibit pre- or postnatal lethality, reduced fertility, hydrocephalus, aberrant sensory innervation, reduced interneuron count, seizure susceptibility and abnormal lymphangiogenesis. Homozygotes for a gene trap allele show abnormal neuronal development and axonal trajectories. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 111 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931406B18Rik	A	G	7: 43,147,543 (GRCm39)	I182T	possibly damaging	Het
4933406P04Rik	A	G	10: 20,187,105 (GRCm39)		probably benign	Het
A730018C14Rik	A	G	12: 112,381,924 (GRCm39)		noncoding transcript	Het
Aacs	A	T	5: 125,593,394 (GRCm39)	I666F	possibly damaging	Het
Abcb9	C	T	5: 124,221,694 (GRCm39)	V227I	probably benign	Het
Abcd3	T	C	3: 121,578,122 (GRCm39)	Q168R	probably benign	Het
Adamts4	A	G	1: 171,080,311 (GRCm39)	Q288R	probably benign	Het
Atad2	G	A	15: 57,966,760 (GRCm39)	A611V	probably damaging	Het
Aup1	T	C	6: 83,032,187 (GRCm39)	V118A	possibly damaging	Het
Bend7	T	A	2: 4,768,122 (GRCm39)		probably benign	Het
Brd4	A	G	17: 32,417,646 (GRCm39)		probably benign	Het
C4b	C	A	17: 34,957,941 (GRCm39)	R580L	probably benign	Het
Cct8	G	T	16: 87,288,342 (GRCm39)		probably benign	Het
Cfhr4	A	T	1: 139,664,608 (GRCm39)	C484S	probably damaging	Het
Cilp	T	C	9: 65,183,127 (GRCm39)	Y344H	probably benign	Het
Clic6	A	T	16: 92,288,961 (GRCm39)		probably benign	Het
Colgalt2	T	C	1: 152,360,703 (GRCm39)	S247P	probably damaging	Het
Csf2rb	G	T	15: 78,224,955 (GRCm39)	A212S	probably benign	Het
Csmd3	A	C	15: 47,475,294 (GRCm39)		probably null	Het
Cyp26c1	A	G	19: 37,679,393 (GRCm39)	D366G	probably benign	Het
Dhx33	A	G	11: 70,890,354 (GRCm39)	S222P	probably damaging	Het
Dhx40	T	A	11: 86,697,379 (GRCm39)	I63F	possibly damaging	Het
Dipk2b	A	C	X: 18,286,701 (GRCm39)	L285V	possibly damaging	Het
Dlgap2	T	A	8: 14,879,861 (GRCm39)		probably null	Het
Dnah7b	T	A	1: 46,105,957 (GRCm39)	D20E	unknown	Het
Dnase2b	C	A	3: 146,290,312 (GRCm39)	A220S	probably benign	Het
Dock10	T	C	1: 80,570,352 (GRCm39)	E362G	probably benign	Het
Ect2l	C	T	10: 18,044,182 (GRCm39)	V226I	probably benign	Het
Epha10	C	A	4: 124,779,389 (GRCm39)	N78K	probably damaging	Het
Epha3	A	G	16: 63,593,416 (GRCm39)	V224A	probably damaging	Het
Fcgr4	C	A	1: 170,847,523 (GRCm39)	D40E	probably damaging	Het
Fer1l4	T	C	2: 155,887,553 (GRCm39)	M548V	probably benign	Het
Flii	C	T	11: 60,610,518 (GRCm39)		probably null	Het
Flnc	A	T	6: 29,444,079 (GRCm39)	Y631F	probably benign	Het
Gm6871	A	C	7: 41,195,514 (GRCm39)		probably null	Het
Gtf2ird1	A	T	5: 134,387,772 (GRCm39)	S1028T	possibly damaging	Het
Hycc1	A	T	5: 24,170,139 (GRCm39)	D403E	probably benign	Het
Hydin	A	G	8: 111,301,486 (GRCm39)	H3739R	probably benign	Het
Iqcg	A	T	16: 32,865,895 (GRCm39)	N149K	probably benign	Het
Iqgap3	A	G	3: 88,006,200 (GRCm39)	D537G	probably benign	Het
Itih2	T	G	2: 10,110,025 (GRCm39)	D576A	probably benign	Het
Kcmf1	T	C	6: 72,825,212 (GRCm39)	T243A	probably benign	Het
Kif1a	A	G	1: 93,002,670 (GRCm39)		probably benign	Het
Klf10	C	T	15: 38,297,030 (GRCm39)	G337S	probably damaging	Het
Krt31	T	C	11: 99,938,699 (GRCm39)	N298S	possibly damaging	Het
Lmnb1	A	G	18: 56,882,823 (GRCm39)	E556G	probably benign	Het
Mael	A	T	1: 166,029,859 (GRCm39)	S354T	probably benign	Het
Mast3	T	C	8: 71,238,816 (GRCm39)	D496G	probably damaging	Het
Med12l	A	G	3: 59,172,661 (GRCm39)	T1806A	possibly damaging	Het
Mms19	A	G	19: 41,944,260 (GRCm39)		probably null	Het
Moap1	A	T	12: 102,709,504 (GRCm39)	M15K	possibly damaging	Het
Mpv17l	G	T	16: 13,764,683 (GRCm39)	W70L	probably damaging	Het
Muc4	G	C	16: 32,753,919 (GRCm38)	R1265P	probably benign	Het
Myo7b	T	C	18: 32,127,962 (GRCm39)	I577V	probably benign	Het
Myo9b	T	A	8: 71,743,620 (GRCm39)	L227Q	probably damaging	Het
Myom2	T	C	8: 15,154,059 (GRCm39)		probably benign	Het
Naip6	C	A	13: 100,452,983 (GRCm39)	R26L	probably benign	Het
Nbea	T	C	3: 55,966,248 (GRCm39)	T405A	probably damaging	Het
Nt5el	A	T	13: 105,246,129 (GRCm39)	H230L	probably benign	Het
Nufip2	G	A	11: 77,582,733 (GRCm39)	E216K	possibly damaging	Het
Oaf	A	G	9: 43,133,930 (GRCm39)	Y264H	probably damaging	Het
Or51a42	A	G	7: 103,708,431 (GRCm39)	V126A	probably damaging	Het
Or5m10	T	C	2: 85,717,615 (GRCm39)	L157P	probably damaging	Het
Or6c217	A	T	10: 129,738,293 (GRCm39)	C95*	probably null	Het
Pax1	T	C	2: 147,210,321 (GRCm39)	V352A	probably damaging	Het
Pkd1l2	TGGG	TGG	8: 117,764,974 (GRCm39)		probably null	Het
Plxna3	G	A	X: 73,383,772 (GRCm39)		probably null	Het
Pnpla3	T	C	15: 84,065,247 (GRCm39)	V347A	probably benign	Het
Ppl	T	A	16: 4,920,461 (GRCm39)	K350*	probably null	Het
Pramel28	T	C	4: 143,692,632 (GRCm39)	D123G	probably benign	Het
Prb1a	T	A	6: 132,186,424 (GRCm39)		probably null	Het
Prb1a	C	A	6: 132,186,423 (GRCm39)		probably null	Het
Ptpn11	G	A	5: 121,275,574 (GRCm39)	H540Y	probably benign	Het
Ptprz1	C	A	6: 23,000,747 (GRCm39)	H946N	possibly damaging	Het
Pwwp4a	G	T	X: 72,171,261 (GRCm39)	G218C	probably damaging	Het
Rad51b	A	G	12: 79,349,317 (GRCm39)	E51G	possibly damaging	Het
Rin2	T	C	2: 145,700,366 (GRCm39)	V181A	probably damaging	Het
Rnf157	T	A	11: 116,245,188 (GRCm39)		probably null	Het
Rnf207	A	G	4: 152,398,328 (GRCm39)		probably benign	Het
Ror1	A	T	4: 100,299,183 (GRCm39)	K852M	probably damaging	Het
Sbp	T	A	17: 24,164,043 (GRCm39)	I102K	probably benign	Het
Scaf8	T	C	17: 3,195,429 (GRCm39)	I33T	probably damaging	Het
Scn5a	C	T	9: 119,315,699 (GRCm39)	V1670I	probably damaging	Het
Serhl	C	T	15: 82,989,877 (GRCm39)	T42M	probably damaging	Het
Sin3a	A	G	9: 57,011,281 (GRCm39)		probably benign	Het
Slc12a2	A	G	18: 58,012,374 (GRCm39)	S166G	probably benign	Het
Slc15a4	G	A	5: 127,680,832 (GRCm39)	H396Y	probably benign	Het
Slc2a7	A	T	4: 150,239,143 (GRCm39)	N123Y	probably damaging	Het
Smpd3	G	A	8: 106,992,199 (GRCm39)	T118M	possibly damaging	Het
Spns2	A	T	11: 72,347,193 (GRCm39)	I427N	probably benign	Het
Ssmem1	T	A	6: 30,519,650 (GRCm39)	S112T	probably damaging	Het
Stard10	A	T	7: 100,993,233 (GRCm39)	D190V	probably damaging	Het
Stil	A	T	4: 114,881,049 (GRCm39)	K531M	probably damaging	Het
Strc	T	C	2: 121,203,219 (GRCm39)		probably null	Het
Svil	T	A	18: 5,046,817 (GRCm39)	I21N	possibly damaging	Het
Syt11	T	C	3: 88,656,110 (GRCm39)	M14V	probably benign	Het
Tasor2	A	T	13: 3,640,413 (GRCm39)	H241Q	possibly damaging	Het
Tg	A	T	15: 66,577,081 (GRCm39)	Q1468L	probably benign	Het
Tjp1	A	G	7: 64,952,669 (GRCm39)	V1555A	probably benign	Het
Tmprss11d	A	C	5: 86,486,658 (GRCm39)	S77R	probably damaging	Het
Tsnaxip1	A	G	8: 106,554,383 (GRCm39)		probably benign	Het
Tyr	C	A	7: 87,141,914 (GRCm39)	L138F	probably damaging	Het
Ubash3b	A	G	9: 40,927,901 (GRCm39)	V469A	probably damaging	Het
Ugt8a	T	C	3: 125,709,098 (GRCm39)	Y4C	probably benign	Het
Vmn1r201	A	T	13: 22,658,968 (GRCm39)	T61S	probably benign	Het
Vmn1r204	A	G	13: 22,740,465 (GRCm39)	H32R	probably benign	Het
Vmn1r228	T	A	17: 20,997,285 (GRCm39)	I78L	probably benign	Het
Wdr90	T	C	17: 26,068,284 (GRCm39)	D1348G	possibly damaging	Het
Zfp563	T	A	17: 33,324,187 (GRCm39)	C261S	probably benign	Het
Zfp809	T	A	9: 22,146,395 (GRCm39)	L28Q	probably damaging	Het
Znrf3	T	A	11: 5,239,066 (GRCm39)	Q99L	probably damaging	Het

Other mutations in Nrp2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00765:Nrp2	APN	1	62,743,410 (GRCm39)	nonsense	probably null
IGL01912:Nrp2	APN	1	62,810,896 (GRCm39)	missense	probably damaging	1.00
IGL01996:Nrp2	APN	1	62,788,419 (GRCm39)	missense	probably damaging	1.00
IGL02184:Nrp2	APN	1	62,758,099 (GRCm39)	nonsense	probably null
IGL02682:Nrp2	APN	1	62,810,996 (GRCm39)	missense	probably benign	0.03
IGL02928:Nrp2	APN	1	62,854,605 (GRCm39)	missense	probably damaging	1.00
IGL03024:Nrp2	APN	1	62,810,893 (GRCm39)	missense	probably damaging	1.00
Euphorbia	UTSW	1	62,801,972 (GRCm39)	missense	probably benign	0.02
Sabra	UTSW	1	62,822,680 (GRCm39)	missense	probably damaging	1.00
R0068:Nrp2	UTSW	1	62,784,536 (GRCm39)	missense	possibly damaging	0.95
R0068:Nrp2	UTSW	1	62,784,536 (GRCm39)	missense	possibly damaging	0.95
R0683:Nrp2	UTSW	1	62,783,477 (GRCm39)	missense	probably benign	0.41
R0789:Nrp2	UTSW	1	62,784,609 (GRCm39)	missense	probably benign	0.44
R1418:Nrp2	UTSW	1	62,822,491 (GRCm39)	nonsense	probably null
R1468:Nrp2	UTSW	1	62,777,458 (GRCm39)	missense	probably damaging	1.00
R1468:Nrp2	UTSW	1	62,777,458 (GRCm39)	missense	probably damaging	1.00
R1645:Nrp2	UTSW	1	62,824,283 (GRCm39)	missense	probably damaging	0.97
R1677:Nrp2	UTSW	1	62,822,479 (GRCm39)	missense	probably benign	0.18
R1752:Nrp2	UTSW	1	62,777,600 (GRCm39)	missense	probably damaging	1.00
R1840:Nrp2	UTSW	1	62,777,498 (GRCm39)	missense	probably damaging	1.00
R1916:Nrp2	UTSW	1	62,801,906 (GRCm39)	missense	probably damaging	1.00
R1962:Nrp2	UTSW	1	62,758,090 (GRCm39)	missense	probably benign	0.03
R2108:Nrp2	UTSW	1	62,783,436 (GRCm39)	missense	probably damaging	1.00
R2164:Nrp2	UTSW	1	62,783,514 (GRCm39)	missense	probably damaging	1.00
R2216:Nrp2	UTSW	1	62,802,077 (GRCm39)	nonsense	probably null
R2679:Nrp2	UTSW	1	62,824,237 (GRCm39)	missense	probably benign	0.00
R4349:Nrp2	UTSW	1	62,777,576 (GRCm39)	missense	probably damaging	1.00
R4351:Nrp2	UTSW	1	62,777,576 (GRCm39)	missense	probably damaging	1.00
R4352:Nrp2	UTSW	1	62,777,576 (GRCm39)	missense	probably damaging	1.00
R4353:Nrp2	UTSW	1	62,777,576 (GRCm39)	missense	probably damaging	1.00
R4811:Nrp2	UTSW	1	62,758,240 (GRCm39)	missense	probably damaging	1.00
R5362:Nrp2	UTSW	1	62,808,221 (GRCm39)	missense	probably benign	0.01
R5387:Nrp2	UTSW	1	62,801,972 (GRCm39)	missense	probably benign	0.02
R5461:Nrp2	UTSW	1	62,786,370 (GRCm39)	nonsense	probably null
R5704:Nrp2	UTSW	1	62,824,267 (GRCm39)	missense	probably benign	0.00
R6143:Nrp2	UTSW	1	62,799,974 (GRCm39)	missense	probably damaging	1.00
R6303:Nrp2	UTSW	1	62,784,565 (GRCm39)	missense	probably damaging	1.00
R6304:Nrp2	UTSW	1	62,784,565 (GRCm39)	missense	probably damaging	1.00
R6376:Nrp2	UTSW	1	62,758,176 (GRCm39)	missense	possibly damaging	0.65
R6945:Nrp2	UTSW	1	62,799,947 (GRCm39)	missense	probably damaging	1.00
R7347:Nrp2	UTSW	1	62,784,663 (GRCm39)	missense	probably benign	0.04
R7393:Nrp2	UTSW	1	62,784,583 (GRCm39)	missense	probably damaging	0.98
R7593:Nrp2	UTSW	1	62,758,203 (GRCm39)	missense	probably damaging	0.96
R7881:Nrp2	UTSW	1	62,810,990 (GRCm39)	missense	probably benign	0.42
R7882:Nrp2	UTSW	1	62,822,680 (GRCm39)	missense	probably damaging	1.00
R7948:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R7958:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R7959:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R7960:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R7961:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R8009:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R8012:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R8014:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R8015:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R8068:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R8069:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R8070:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R8071:Nrp2	UTSW	1	62,784,567 (GRCm39)	missense	probably damaging	1.00
R8206:Nrp2	UTSW	1	62,786,374 (GRCm39)	missense	probably damaging	1.00
R8791:Nrp2	UTSW	1	62,788,356 (GRCm39)	missense	probably damaging	1.00
R9090:Nrp2	UTSW	1	62,784,670 (GRCm39)	missense	probably benign	0.21
R9271:Nrp2	UTSW	1	62,784,670 (GRCm39)	missense	probably benign	0.21
R9287:Nrp2	UTSW	1	62,835,014 (GRCm39)	missense	probably damaging	1.00
R9469:Nrp2	UTSW	1	62,804,030 (GRCm39)	missense	probably damaging	1.00
R9646:Nrp2	UTSW	1	62,777,566 (GRCm39)	missense	probably damaging	1.00
R9752:Nrp2	UTSW	1	62,851,726 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CATTGCTGATACCCAGATCTCTGCC -3'
(R):5'- GCGCAACATTGCCTCTTGGATG -3'

Sequencing Primer
(F):5'- CTCCTCCACCCGAGAGTACC -3'
(R):5'- AACATTGCCTCTTGGATGATACC -3'

Posted On

2014-04-13