Mutagenetix > Incidental Mutation

Incidental Mutation 'R7347:Nrp2'

570244

Institutional Source

Beutler Lab

Gene Symbol

Nrp2

Ensembl Gene

ENSMUSG00000025969

Gene Name

neuropilin 2

Synonyms

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

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.948) question?

Stock #

R7347 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

62703285-62818695 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 62745504 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 271 (P271S)

Ref Sequence

ENSEMBL: ENSMUSP00000109794 (fasta)

Gene Model

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

AlphaFold

O35375

Predicted Effect

probably benign
Transcript: ENSMUST00000027112
AA Change: P271S

PolyPhen 2 Score 0.053 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000027112
Gene: ENSMUSG00000025969
AA Change: P271S

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 benign
Transcript: ENSMUST00000063594
AA Change: P271S

PolyPhen 2 Score 0.108 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000069379
Gene: ENSMUSG00000025969
AA Change: P271S

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 benign
Transcript: ENSMUST00000075144
AA Change: P271S

PolyPhen 2 Score 0.065 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000074642
Gene: ENSMUSG00000025969
AA Change: P271S

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 benign
Transcript: ENSMUST00000102822
AA Change: P271S

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000099886
Gene: ENSMUSG00000025969
AA Change: P271S

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 benign
Transcript: ENSMUST00000114155
AA Change: P271S

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000109792
Gene: ENSMUSG00000025969
AA Change: P271S

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 benign
Transcript: ENSMUST00000114157
AA Change: P271S

PolyPhen 2 Score 0.038 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000109794
Gene: ENSMUSG00000025969
AA Change: P271S

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

0.1088

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (80/80)

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1300017J02Rik	T	A	9: 103,282,646	E22V	possibly damaging	Het
4930564D02Rik	G	T	3: 105,078,412	R47S	unknown	Het
4931408C20Rik	A	T	1: 26,684,467	L544Q	probably benign	Het
Abtb2	T	G	2: 103,567,412	I229S	probably damaging	Het
Adgre1	T	C	17: 57,420,441	L457P	probably damaging	Het
Amer3	C	A	1: 34,587,902	D407E	probably damaging	Het
Arhgap20	T	C	9: 51,849,035	S729P	probably benign	Het
Asap2	T	G	12: 21,229,457	I418S	probably benign	Het
Atp5j2	T	C	5: 145,188,485		probably null	Het
Brinp3	T	A	1: 146,902,086	V757E	probably benign	Het
Brip1	C	T	11: 86,139,103	G572R	probably benign	Het
C3	C	A	17: 57,223,215	R462L	probably benign	Het
Cat	T	A	2: 103,463,298	H395L	probably benign	Het
Cela3a	T	C	4: 137,402,606	N235D	possibly damaging	Het
Cep89	G	A	7: 35,429,928	R630H	probably damaging	Het
Cntnap1	G	T	11: 101,185,268	G993W	probably damaging	Het
Col9a1	A	G	1: 24,179,403		probably null	Het
Coro2b	G	T	9: 62,489,372	H29N	probably benign	Het
Dll3	C	T	7: 28,299,111	R143H	probably damaging	Het
Dsel	C	T	1: 111,861,573	G411S	probably damaging	Het
Dync1i1	T	A	6: 5,784,530	*114R	probably null	Het
Ecm2	T	C	13: 49,515,078	S86P	probably damaging	Het
Eif5	T	C	12: 111,540,290		probably benign	Het
Ets1	T	A	9: 32,733,032		probably null	Het
Exph5	A	G	9: 53,375,896	N1426D	possibly damaging	Het
Eya2	T	C	2: 165,687,666	F110L	probably benign	Het
Flt1	T	A	5: 147,580,381	E1032V	probably damaging	Het
Galnt5	A	T	2: 58,017,193	H556L	probably benign	Het
Glb1l3	A	T	9: 26,829,003	Y344N	probably benign	Het
Glrx3	C	A	7: 137,459,286	D216E	possibly damaging	Het
Gm45871	T	A	18: 90,591,375	C246S	probably damaging	Het
Gm8251	G	T	1: 44,059,496	P814Q	probably damaging	Het
Gm906	T	C	13: 50,245,744	I849V	probably benign	Het
Gstm4	A	G	3: 108,042,373	L137P	probably benign	Het
Hsd17b13	T	C	5: 103,968,750	T169A	probably damaging	Het
Hydin	A	C	8: 110,600,362	T4778P	probably benign	Het
Ifna15	A	G	4: 88,557,983	L88P	probably damaging	Het
Kcnab1	G	A	3: 65,376,531	R390H	probably benign	Het
Kng1	C	A	16: 23,067,787	H161N	possibly damaging	Het
Lamp5	T	C	2: 136,060,958	V199A	probably benign	Het
Lrig3	G	A	10: 126,009,966	V755M	probably damaging	Het
Mad1l1	C	T	5: 140,144,044	R412H	probably damaging	Het
March6	C	A	15: 31,486,359	C350F	probably benign	Het
Mastl	A	G	2: 23,133,389	S441P	probably damaging	Het
Mfsd13b	A	T	7: 120,991,728	M231L	probably benign	Het
Micalcl	T	C	7: 112,382,151	V444A	probably benign	Het
Ms4a6d	G	A	19: 11,590,073	Q155*	probably null	Het
Myo15	A	G	11: 60,477,961	M516V	probably benign	Het
Myo1b	A	T	1: 51,751,254	F1110L	probably damaging	Het
Nbr1	T	A	11: 101,569,321	L381*	probably null	Het
Nln	T	C	13: 104,050,847	K325E	probably damaging	Het
Nr4a3	T	G	4: 48,051,290	S15A	possibly damaging	Het
Obox6	A	C	7: 15,834,646	L102V	possibly damaging	Het
Olfr1008	T	C	2: 85,689,837	M136T	probably damaging	Het
Olfr1208	T	C	2: 88,897,271	I109V	possibly damaging	Het
Olfr1241	T	C	2: 89,482,455	S227G	probably benign	Het
Olfr853	A	G	9: 19,537,099	M277T	probably damaging	Het
Pde10a	A	G	17: 8,967,462	H567R	probably damaging	Het
Pdgfra	C	T	5: 75,183,098	S760L	possibly damaging	Het
Pid1	T	A	1: 84,159,129	I94L	unknown	Het
Plekhn1	T	C	4: 156,222,671	H474R	probably benign	Het
Prcc	A	T	3: 87,869,681	S329T	possibly damaging	Het
Pros1	G	T	16: 62,919,523	R445L	probably damaging	Het
Pxdn	C	A	12: 30,012,261	H1370Q	probably benign	Het
Sgce	T	A	6: 4,694,106	R283S	probably damaging	Het
Slc25a20	T	G	9: 108,682,458		probably null	Het
Slc6a1	T	C	6: 114,311,818	V446A	probably damaging	Het
Slc6a4	C	G	11: 77,017,085	Y358*	probably null	Het
Sned1	A	C	1: 93,281,736	E857A	probably damaging	Het
Spdye4b	C	T	5: 143,202,390	R213C	possibly damaging	Het
Spry2	T	G	14: 105,893,512	E80A	probably damaging	Het
Stard9	G	A	2: 120,666,534	C142Y	probably benign	Het
Sync	A	T	4: 129,294,306	Q377L	probably benign	Het
Tdrd12	A	G	7: 35,485,692	C718R		Het
Tgoln1	G	C	6: 72,616,278	T73R	probably benign	Het
Tmbim1	T	C	1: 74,291,279	E185G	probably benign	Het
Tyk2	T	C	9: 21,108,034	M1031V	probably damaging	Het
Vmn1r71	C	T	7: 10,748,501	V87I	not run	Het
Vmn2r49	A	G	7: 9,986,814	V250A	probably benign	Het
Yipf3	A	C	17: 46,250,827	T187P	probably damaging	Het
Zfp148	G	T	16: 33,434,790	R50L	possibly damaging	Het
Zfp628	G	A	7: 4,921,818	G1013E	probably damaging	Het

Other mutations in Nrp2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00765:Nrp2	APN	1	62704251	nonsense	probably null
IGL01912:Nrp2	APN	1	62771737	missense	probably damaging	1.00
IGL01996:Nrp2	APN	1	62749260	missense	probably damaging	1.00
IGL02184:Nrp2	APN	1	62718940	nonsense	probably null
IGL02682:Nrp2	APN	1	62771837	missense	probably benign	0.03
IGL02928:Nrp2	APN	1	62815446	missense	probably damaging	1.00
IGL03024:Nrp2	APN	1	62771734	missense	probably damaging	1.00
Euphorbia	UTSW	1	62762813	missense	probably benign	0.02
Sabra	UTSW	1	62783521	missense	probably damaging	1.00
R0068:Nrp2	UTSW	1	62745377	missense	possibly damaging	0.95
R0068:Nrp2	UTSW	1	62745377	missense	possibly damaging	0.95
R0683:Nrp2	UTSW	1	62744318	missense	probably benign	0.41
R0789:Nrp2	UTSW	1	62745450	missense	probably benign	0.44
R1418:Nrp2	UTSW	1	62783332	nonsense	probably null
R1468:Nrp2	UTSW	1	62738299	missense	probably damaging	1.00
R1468:Nrp2	UTSW	1	62738299	missense	probably damaging	1.00
R1544:Nrp2	UTSW	1	62762904	missense	probably damaging	1.00
R1645:Nrp2	UTSW	1	62785124	missense	probably damaging	0.97
R1677:Nrp2	UTSW	1	62783320	missense	probably benign	0.18
R1752:Nrp2	UTSW	1	62738441	missense	probably damaging	1.00
R1840:Nrp2	UTSW	1	62738339	missense	probably damaging	1.00
R1916:Nrp2	UTSW	1	62762747	missense	probably damaging	1.00
R1962:Nrp2	UTSW	1	62718931	missense	probably benign	0.03
R2108:Nrp2	UTSW	1	62744277	missense	probably damaging	1.00
R2164:Nrp2	UTSW	1	62744355	missense	probably damaging	1.00
R2216:Nrp2	UTSW	1	62762918	nonsense	probably null
R2679:Nrp2	UTSW	1	62785078	missense	probably benign	0.00
R4349:Nrp2	UTSW	1	62738417	missense	probably damaging	1.00
R4351:Nrp2	UTSW	1	62738417	missense	probably damaging	1.00
R4352:Nrp2	UTSW	1	62738417	missense	probably damaging	1.00
R4353:Nrp2	UTSW	1	62738417	missense	probably damaging	1.00
R4811:Nrp2	UTSW	1	62719081	missense	probably damaging	1.00
R5362:Nrp2	UTSW	1	62769062	missense	probably benign	0.01
R5387:Nrp2	UTSW	1	62762813	missense	probably benign	0.02
R5461:Nrp2	UTSW	1	62747211	nonsense	probably null
R5704:Nrp2	UTSW	1	62785108	missense	probably benign	0.00
R6143:Nrp2	UTSW	1	62760815	missense	probably damaging	1.00
R6303:Nrp2	UTSW	1	62745406	missense	probably damaging	1.00
R6304:Nrp2	UTSW	1	62745406	missense	probably damaging	1.00
R6376:Nrp2	UTSW	1	62719017	missense	possibly damaging	0.65
R6945:Nrp2	UTSW	1	62760788	missense	probably damaging	1.00
R7393:Nrp2	UTSW	1	62745424	missense	probably damaging	0.98
R7593:Nrp2	UTSW	1	62719044	missense	probably damaging	0.96
R7881:Nrp2	UTSW	1	62771831	missense	probably benign	0.42
R7882:Nrp2	UTSW	1	62783521	missense	probably damaging	1.00
R7948:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R7958:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R7959:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R7960:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R7961:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R8009:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R8012:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R8014:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R8015:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R8068:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R8069:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R8070:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R8071:Nrp2	UTSW	1	62745408	missense	probably damaging	1.00
R8206:Nrp2	UTSW	1	62747215	missense	probably damaging	1.00
R8791:Nrp2	UTSW	1	62749197	missense	probably damaging	1.00
R9090:Nrp2	UTSW	1	62745511	missense	probably benign	0.21
R9271:Nrp2	UTSW	1	62745511	missense	probably benign	0.21
R9287:Nrp2	UTSW	1	62795855	missense	probably damaging	1.00
R9469:Nrp2	UTSW	1	62764871	missense	probably damaging	1.00
R9646:Nrp2	UTSW	1	62738407	missense	probably damaging	1.00
R9752:Nrp2	UTSW	1	62812567	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- TCAAGGCATTGGCAGTGAG -3'
(R):5'- CTTTGCTGGGAAGGAAAACATG -3'

Sequencing Primer
(F):5'- AGCCAGTTTGAGATTTCTCTGAC -3'
(R):5'- GACTTTCCTTGAACTCAGATAGCAC -3'

Posted On

2019-09-13