Mutagenetix > Incidental Mutation

Incidental Mutation 'R4721:Nptn'

354470

Institutional Source

Beutler Lab

Gene Symbol

Nptn

Ensembl Gene

ENSMUSG00000032336

Gene Name

neuroplastin

Synonyms

Sdfr1

MMRRC Submission

041986-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4721 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

58489504-58560162 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 58548059 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 155 (R155C)

Ref Sequence

ENSEMBL: ENSMUSP00000135541 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000085651] [ENSMUST00000114121] [ENSMUST00000175945] [ENSMUST00000176250] [ENSMUST00000176557] [ENSMUST00000176916] [ENSMUST00000177064] [ENSMUST00000177292] [ENSMUST00000177380]

AlphaFold

P97300

Predicted Effect

probably damaging
Transcript: ENSMUST00000085651
AA Change: R155C

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

SMART Domains

Protein: ENSMUSP00000082793
Gene: ENSMUSG00000032336
AA Change: R155C

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
IG	38	118	1.1e-3	SMART
IGc2	133	206	9.3e-7	SMART
transmembrane domain	221	243	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000114121
AA Change: R155C

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000109756
Gene: ENSMUSG00000032336
AA Change: R155C

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
IG	38	118	2.56e-1	SMART
IGc2	133	206	2.34e-4	SMART
transmembrane domain	221	243	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000175945

SMART Domains

Protein: ENSMUSP00000135576
Gene: ENSMUSG00000032336

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176126

Predicted Effect

possibly damaging
Transcript: ENSMUST00000176250
AA Change: R45C

PolyPhen 2 Score 0.906 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000135250
Gene: ENSMUSG00000032336
AA Change: R45C

Domain	Start	End	E-Value	Type
IGc2	23	96	2.34e-4	SMART
transmembrane domain	111	133	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000176557
AA Change: R155C

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000135541
Gene: ENSMUSG00000032336
AA Change: R155C

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
IG	38	118	2.56e-1	SMART
IGc2	133	206	2.34e-4	SMART
transmembrane domain	221	243	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000176896
AA Change: R153C

SMART Domains

Protein: ENSMUSP00000134761
Gene: ENSMUSG00000032336
AA Change: R153C

Domain	Start	End	E-Value	Type
signal peptide	1	27	N/A	INTRINSIC
IG	37	117	2.56e-1	SMART
IGc2	132	205	2.34e-4	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000176916
AA Change: R45C

PolyPhen 2 Score 0.906 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000134977
Gene: ENSMUSG00000032336
AA Change: R45C

Domain	Start	End	E-Value	Type
IGc2	23	96	2.34e-4	SMART
transmembrane domain	111	133	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000177064
AA Change: R67C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000135316
Gene: ENSMUSG00000032336
AA Change: R67C

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
IGc2	45	118	2.34e-4	SMART
transmembrane domain	133	155	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000177292
AA Change: R271C

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000135199
Gene: ENSMUSG00000032336
AA Change: R271C

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
IGc2	43	123	4.09e-9	SMART
IG	154	234	2.56e-1	SMART
IGc2	249	322	2.34e-4	SMART
transmembrane domain	337	359	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000177380

SMART Domains

Protein: ENSMUSP00000135886
Gene: ENSMUSG00000032336

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
IG	38	118	2.56e-1	SMART

Meta Mutation Damage Score

0.2464

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.2%

Validation Efficiency

98% (90/92)

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele exhibit abnormal dendritic spine morphology, decreased CNS synapse formation, abnormal CNS synaptic transmission and impaired hearing. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3425401B19Rik	T	C	14: 32,385,107 (GRCm39)	D286G	probably benign	Het
Abca15	G	A	7: 119,949,998 (GRCm39)	E491K	probably benign	Het
Acsl5	A	G	19: 55,268,962 (GRCm39)	T208A	probably benign	Het
Adamts10	T	A	17: 33,764,511 (GRCm39)		probably null	Het
Ahcyl1	T	C	3: 107,577,233 (GRCm39)	Q313R	possibly damaging	Het
Ccdc71	C	T	9: 108,340,622 (GRCm39)	S145L	possibly damaging	Het
Cep250	A	G	2: 155,812,119 (GRCm39)	T472A	probably damaging	Het
Copa	T	C	1: 171,931,841 (GRCm39)		probably benign	Het
Crybg1	C	A	10: 43,873,883 (GRCm39)	R1075L	probably damaging	Het
Ddr2	T	A	1: 169,832,809 (GRCm39)	K84*	probably null	Het
Ddx59	C	T	1: 136,344,844 (GRCm39)	P172S	probably benign	Het
Dhx34	T	A	7: 15,931,307 (GRCm39)	Q1118L	possibly damaging	Het
Dkkl1	T	A	7: 44,857,232 (GRCm39)	I112F	probably damaging	Het
Dnah8	T	A	17: 30,944,140 (GRCm39)	C1786S	probably damaging	Het
Eml6	T	A	11: 29,788,525 (GRCm39)	D520V	possibly damaging	Het
Ergic1	T	A	17: 26,857,750 (GRCm39)	V192E	probably damaging	Het
Fat3	T	C	9: 15,941,262 (GRCm39)	E1343G	probably damaging	Het
Fxr1	T	C	3: 34,118,381 (GRCm39)	S535P	possibly damaging	Het
Gkn3	C	T	6: 87,360,507 (GRCm39)	A163T	probably damaging	Het
Gm15446	C	T	5: 110,090,866 (GRCm39)	H373Y	probably damaging	Het
Gpr157	A	T	4: 150,183,420 (GRCm39)	N197Y	probably benign	Het
Grid2	G	A	6: 64,643,185 (GRCm39)	M982I	probably benign	Het
Hey2	G	T	10: 30,710,304 (GRCm39)	R150S	possibly damaging	Het
Hmcn1	T	C	1: 150,648,322 (GRCm39)		probably null	Het
Ighv3-3	G	A	12: 114,160,156 (GRCm39)	R85*	probably null	Het
Ighv5-4	A	T	12: 113,561,060 (GRCm39)		probably benign	Het
Igsf21	A	G	4: 139,834,621 (GRCm39)	S84P	probably benign	Het
Kif20b	A	G	19: 34,915,773 (GRCm39)	T517A	probably benign	Het
Krt87	T	C	15: 101,385,863 (GRCm39)	E244G	probably damaging	Het
Lrp1	T	C	10: 127,390,928 (GRCm39)	T2990A	possibly damaging	Het
Lrp1b	T	A	2: 40,605,381 (GRCm39)		probably null	Het
Lrrc42	A	T	4: 107,091,050 (GRCm39)	S382T	probably benign	Het
Magi2	C	T	5: 20,739,467 (GRCm39)	R737W	probably damaging	Het
Mcc	A	G	18: 44,652,623 (GRCm39)	L267P	probably damaging	Het
Mzf1	T	A	7: 12,777,223 (GRCm39)	Q727L	possibly damaging	Het
Mzf1	C	T	7: 12,777,448 (GRCm39)	R652Q	possibly damaging	Het
Nkain3	C	T	4: 20,485,015 (GRCm39)	A21T	probably damaging	Het
Nlrp4e	T	A	7: 23,020,521 (GRCm39)	V336E	possibly damaging	Het
Nr2c2	T	C	6: 92,116,828 (GRCm39)	I10T	possibly damaging	Het
Or12e13	T	A	2: 87,663,515 (GRCm39)	I44N	probably damaging	Het
Or1e26	C	T	11: 73,480,273 (GRCm39)	C97Y	probably damaging	Het
Or1j13	T	C	2: 36,369,836 (GRCm39)	Y102C	probably benign	Het
Pdzk1	G	T	3: 96,776,518 (GRCm39)	E493*	probably null	Het
Plekhh1	GTCAAA	G	12: 79,122,194 (GRCm39)		probably null	Het
Polr3b	T	C	10: 84,491,867 (GRCm39)	V342A	possibly damaging	Het
Prg3	T	C	2: 84,821,750 (GRCm39)	V125A	possibly damaging	Het
Raph1	G	A	1: 60,542,160 (GRCm39)		probably benign	Het
Rassf2	A	G	2: 131,846,358 (GRCm39)	V133A	probably benign	Het
Rbm22	G	A	18: 60,697,463 (GRCm39)	R56H	probably damaging	Het
Rbpjl	A	C	2: 164,246,447 (GRCm39)	S31R	probably benign	Het
Reln	A	G	5: 22,124,220 (GRCm39)	V2762A	probably damaging	Het
Rxrg	T	A	1: 167,452,621 (GRCm39)	I141N	probably damaging	Het
Scn7a	C	A	2: 66,514,529 (GRCm39)	G1082C	probably damaging	Het
Selenon	C	A	4: 134,270,387 (GRCm39)	E322*	probably null	Het
Sipa1	C	T	19: 5,710,413 (GRCm39)	R199Q	probably damaging	Het
Slc26a7	A	T	4: 14,510,261 (GRCm39)		probably null	Het
Slc37a4	T	C	9: 44,312,787 (GRCm39)	S314P	possibly damaging	Het
Smarce1	T	C	11: 99,111,543 (GRCm39)	I59V	probably benign	Het
Stk19	T	C	17: 35,042,120 (GRCm39)		probably null	Het
Susd2	C	T	10: 75,473,964 (GRCm39)	D544N	probably benign	Het
Tcf7l2	G	T	19: 55,919,886 (GRCm39)	R465L	possibly damaging	Het
Tfap2d	T	A	1: 19,174,984 (GRCm39)	S146T	possibly damaging	Het
Tmem156	A	G	5: 65,248,870 (GRCm39)	F10S	probably benign	Het
Tmem63c	G	T	12: 87,103,954 (GRCm39)	A68S	possibly damaging	Het
Tnfrsf21	T	C	17: 43,396,395 (GRCm39)	C560R	probably damaging	Het
Trav10n	C	T	14: 53,359,590 (GRCm39)	T7I	probably benign	Het
Ttc38	C	T	15: 85,722,947 (GRCm39)	R132W	probably benign	Het
Tvp23a	T	C	16: 10,245,275 (GRCm39)	K108R	probably benign	Het
Vmn1r233	T	C	17: 21,214,879 (GRCm39)	M24V	probably benign	Het
Vmn1r88	T	A	7: 12,912,451 (GRCm39)	L269*	probably null	Het
Vmn2r101	T	A	17: 19,832,287 (GRCm39)	M761K	probably damaging	Het
Vps13b	C	T	15: 35,910,864 (GRCm39)	Q3543*	probably null	Het
Wdr37	T	C	13: 8,904,065 (GRCm39)	E101G	possibly damaging	Het
Zc3hc1	A	G	6: 30,374,899 (GRCm39)	V214A	probably benign	Het
Zcchc9	A	T	13: 91,948,728 (GRCm39)		probably null	Het
Zdbf2	A	T	1: 63,347,951 (GRCm39)	Q2110L	possibly damaging	Het
Zfp516	T	G	18: 82,975,236 (GRCm39)	L478R	possibly damaging	Het

Other mutations in Nptn

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00493:Nptn	APN	9	58,550,922 (GRCm39)	missense	probably damaging	1.00
IGL02043:Nptn	APN	9	58,548,012 (GRCm39)	missense	possibly damaging	0.56
kinda_slow	UTSW	9	58,531,035 (GRCm39)	missense	probably damaging	1.00
R0212:Nptn	UTSW	9	58,535,164 (GRCm39)	missense	probably benign	0.03
R1585:Nptn	UTSW	9	58,548,073 (GRCm39)	missense	probably benign	0.17
R1673:Nptn	UTSW	9	58,531,015 (GRCm39)	missense	probably benign	0.12
R2484:Nptn	UTSW	9	58,550,956 (GRCm39)	missense	possibly damaging	0.85
R4151:Nptn	UTSW	9	58,550,825 (GRCm39)	missense	probably benign	0.14
R4389:Nptn	UTSW	9	58,551,055 (GRCm39)	missense	probably damaging	1.00
R5166:Nptn	UTSW	9	58,526,263 (GRCm39)	nonsense	probably null
R5346:Nptn	UTSW	9	58,531,070 (GRCm39)	nonsense	probably null
R6494:Nptn	UTSW	9	58,531,035 (GRCm39)	missense	probably damaging	1.00
R6520:Nptn	UTSW	9	58,551,017 (GRCm39)	missense	probably damaging	1.00
R7506:Nptn	UTSW	9	58,526,156 (GRCm39)	missense	probably damaging	1.00
R8762:Nptn	UTSW	9	58,525,905 (GRCm39)	intron	probably benign
R8867:Nptn	UTSW	9	58,526,264 (GRCm39)	missense	probably damaging	1.00
R9124:Nptn	UTSW	9	58,558,498 (GRCm39)	unclassified	probably benign

Predicted Primers

PCR Primer
(F):5'- GACTCTGAGCCAGTAGGTAAGAC -3'
(R):5'- CAGCAAAAGCTGTGTACAAATCTTG -3'

Sequencing Primer
(F):5'- AAGACCTTTGGTATCTTAGGTGG -3'
(R):5'- CTTGTACACAGTCAATGCTGG -3'

Posted On

2015-10-21