Mutagenetix > Incidental Mutation

Incidental Mutation 'R6494:Nptn'

522967

Institutional Source

Beutler Lab

Gene Symbol

Nptn

Ensembl Gene

ENSMUSG00000032336

Gene Name

neuroplastin

Synonyms

Sdfr1

MMRRC Submission

044626-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6494 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

58582240-58657955 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 58623752 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Glycine at position 169 (C169G)

Ref Sequence

ENSEMBL: ENSMUSP00000135199 (fasta)

Gene Model

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

AlphaFold

P97300

Predicted Effect

probably damaging
Transcript: ENSMUST00000085651
AA Change: C53G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000082793
Gene: ENSMUSG00000032336
AA Change: C53G

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: C53G

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

SMART Domains

Protein: ENSMUSP00000109756
Gene: ENSMUSG00000032336
AA Change: C53G

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

probably damaging
Transcript: ENSMUST00000176557
AA Change: C53G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000135541
Gene: ENSMUSG00000032336
AA Change: C53G

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: C51G

SMART Domains

Protein: ENSMUSP00000134761
Gene: ENSMUSG00000032336
AA Change: C51G

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

probably benign
Transcript: ENSMUST00000177064

SMART Domains

Protein: ENSMUSP00000135316
Gene: ENSMUSG00000032336

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: C169G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000135199
Gene: ENSMUSG00000032336
AA Change: C169G

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 damaging
Transcript: ENSMUST00000177380
AA Change: C53G

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

SMART Domains

Protein: ENSMUSP00000135886
Gene: ENSMUSG00000032336
AA Change: C53G

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

Meta Mutation Damage Score

0.9610

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 97.8%
20x: 92.4%

Validation Efficiency

98% (44/45)

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: 45 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700022I11Rik	A	G	4: 42,971,924	N419S	possibly damaging	Het
Akt2	T	C	7: 27,616,349	L52P	possibly damaging	Het
Chd1l	G	A	3: 97,587,167	A399V	probably damaging	Het
Chic2	T	C	5: 75,044,282	E6G	probably benign	Het
Clca4a	T	A	3: 144,957,298	T597S	probably benign	Het
Col5a2	C	A	1: 45,378,327	D1363Y	probably damaging	Het
Csmd1	C	T	8: 16,211,695		probably null	Het
Dnah7b	A	T	1: 46,099,431	Y211F	probably damaging	Het
Efcab3	A	T	11: 105,100,019	Y5460F	possibly damaging	Het
Efcab6	T	A	15: 84,044,322		probably null	Het
Eno4	T	A	19: 58,962,794	Y237N	probably damaging	Het
Fer1l4	T	A	2: 156,045,470	D602V	probably benign	Het
Fgfr2	T	C	7: 130,198,550	N337S	probably damaging	Het
Fras1	C	T	5: 96,759,564	R3203C	possibly damaging	Het
Gbp2	T	A	3: 142,632,008	V295E	probably damaging	Het
Gm10549	C	A	18: 33,464,305		probably benign	Het
Hyal4	A	G	6: 24,765,746	I366M	possibly damaging	Het
Itsn2	C	T	12: 4,634,792	R448*	probably null	Het
Klhl35	G	T	7: 99,472,899	W69L	probably damaging	Het
Kpnb1	T	C	11: 97,181,648	I154V	probably benign	Het
Lax1	T	A	1: 133,680,448	Y185F	probably damaging	Het
Mmp12	C	T	9: 7,353,479	P208L	probably damaging	Het
Ndufb8	C	T	19: 44,555,305	V33M	probably null	Het
Nuggc	A	T	14: 65,648,222	E766V	probably damaging	Het
Olfr1117-ps1	A	T	2: 87,309,176	N149I	possibly damaging	Het
Olfr1150-ps1	A	T	2: 87,357,632	K63*	probably null	Het
Pcdhga6	T	A	18: 37,708,541	I438N	probably damaging	Het
Pkn2	T	C	3: 142,803,668	N721S	possibly damaging	Het
Pole	T	C	5: 110,324,722	W1590R	possibly damaging	Het
Prph2	A	G	17: 46,911,081	T129A	probably benign	Het
Ptpro	A	T	6: 137,382,642	K403N	probably benign	Het
Rbck1	T	C	2: 152,330,966	D54G	possibly damaging	Het
Serpinb7	T	A	1: 107,435,346	L80*	probably null	Het
Setdb2	T	A	14: 59,402,414	Y676F	probably benign	Het
Skint1	G	T	4: 112,010,712	C12F	probably benign	Het
Slc22a26	T	A	19: 7,802,286	D55V	probably damaging	Het
Slc9a8	G	A	2: 167,424,291	V63I	probably damaging	Het
Sox2	T	A	3: 34,651,097	S228T	probably benign	Het
Spg11	A	G	2: 122,113,225	S149P	probably damaging	Het
Tbc1d19	T	A	5: 53,829,383	S45T	probably benign	Het
Tsacc	T	C	3: 88,295,396	E11G	probably benign	Het
Ttc7b	C	T	12: 100,495,407	A104T	possibly damaging	Het
Uox	C	T	3: 146,624,577	R163*	probably null	Het
Zfp108	T	A	7: 24,261,357	F458I	probably damaging	Het
Zfp616	A	T	11: 74,085,192	K762N	probably damaging	Het

Other mutations in Nptn

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00493:Nptn	APN	9	58643639	missense	probably damaging	1.00
IGL02043:Nptn	APN	9	58640729	missense	possibly damaging	0.56
kinda_slow	UTSW	9	58623752	missense	probably damaging	1.00
R0212:Nptn	UTSW	9	58627881	missense	probably benign	0.03
R1585:Nptn	UTSW	9	58640790	missense	probably benign	0.17
R1673:Nptn	UTSW	9	58623732	missense	probably benign	0.12
R2484:Nptn	UTSW	9	58643673	missense	possibly damaging	0.85
R4151:Nptn	UTSW	9	58643542	missense	probably benign	0.14
R4389:Nptn	UTSW	9	58643772	missense	probably damaging	1.00
R4721:Nptn	UTSW	9	58640776	missense	probably damaging	1.00
R5166:Nptn	UTSW	9	58618980	nonsense	probably null
R5346:Nptn	UTSW	9	58623787	nonsense	probably null
R6520:Nptn	UTSW	9	58643734	missense	probably damaging	1.00
R7506:Nptn	UTSW	9	58618873	missense	probably damaging	1.00
R8762:Nptn	UTSW	9	58618622	intron	probably benign
R8867:Nptn	UTSW	9	58618981	missense	probably damaging	1.00
R9124:Nptn	UTSW	9	58651215	unclassified	probably benign

Predicted Primers

PCR Primer
(F):5'- CAGTGTAGTCCTGTCTGCC -3'
(R):5'- TTTAGTATATGCACCACACATGC -3'

Sequencing Primer
(F):5'- GTGTAGTCCTGTCTGCCTTCCC -3'
(R):5'- AAGCACCGTTACCTGCTGAG -3'

Posted On

2018-06-06