Mutagenetix > Incidental Mutations

Incidental Mutation 'R7025:Npnt'

545896

Institutional Source

Beutler Lab

Gene Symbol

Npnt

Ensembl Gene

ENSMUSG00000040998

Gene Name

nephronectin

Synonyms

1110009H02Rik, POEM

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.130) question?

Stock #

R7025 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

132881745-132950291 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 132908396 bp

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Tyrosine at position 47 (C47Y)

Ref Sequence

ENSEMBL: ENSMUSP00000112816 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000042729] [ENSMUST00000042744] [ENSMUST00000093971] [ENSMUST00000117164] [ENSMUST00000117456] [ENSMUST00000117811]

Predicted Effect

probably damaging
Transcript: ENSMUST00000042729
AA Change: C168Y

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

SMART Domains

Protein: ENSMUSP00000040071
Gene: ENSMUSG00000040998
AA Change: C168Y

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
EGF	76	104	1.53e-1	SMART
EGF_CA	106	145	1.85e-9	SMART
EGF	149	185	1.73e1	SMART
EGF	189	230	7.53e-1	SMART
EGF_CA	231	271	5.31e-10	SMART
low complexity region	324	383	N/A	INTRINSIC
Pfam:MAM	439	578	8.2e-28	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000042744
AA Change: C151Y

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

SMART Domains

Protein: ENSMUSP00000040684
Gene: ENSMUSG00000040998
AA Change: C151Y

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
EGF	59	87	7.6e-4	SMART
EGF_CA	89	128	9e-12	SMART
EGF	132	168	8.5e-2	SMART
EGF	172	213	3.5e-3	SMART
EGF_CA	214	254	2.6e-12	SMART
low complexity region	307	366	N/A	INTRINSIC
MAM	417	560	1.4e-11	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000093971
AA Change: C199Y

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

SMART Domains

Protein: ENSMUSP00000091505
Gene: ENSMUSG00000040998
AA Change: C199Y

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
EGF	76	104	1.53e-1	SMART
EGF_CA	137	176	1.85e-9	SMART
EGF	180	216	1.73e1	SMART
EGF	220	261	7.53e-1	SMART
EGF_CA	262	302	5.31e-10	SMART
low complexity region	355	414	N/A	INTRINSIC
Pfam:MAM	470	609	1.9e-23	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000117164
AA Change: C182Y

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

SMART Domains

Protein: ENSMUSP00000113419
Gene: ENSMUSG00000040998
AA Change: C182Y

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
EGF	59	87	1.53e-1	SMART
EGF_CA	120	159	1.85e-9	SMART
EGF	163	199	1.73e1	SMART
EGF	203	244	7.53e-1	SMART
EGF_CA	245	285	5.31e-10	SMART
low complexity region	338	397	N/A	INTRINSIC
Pfam:MAM	453	592	8.6e-28	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000117456
AA Change: C47Y

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

SMART Domains

Protein: ENSMUSP00000112816
Gene: ENSMUSG00000040998
AA Change: C47Y

Domain	Start	End	E-Value	Type
EGF	28	64	1.73e1	SMART
EGF	68	109	7.53e-1	SMART
EGF_CA	110	150	5.31e-10	SMART
low complexity region	203	262	N/A	INTRINSIC
Pfam:MAM	318	457	5.3e-28	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000117811
AA Change: C151Y

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

SMART Domains

Protein: ENSMUSP00000113752
Gene: ENSMUSG00000040998
AA Change: C151Y

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
EGF	59	87	1.53e-1	SMART
EGF_CA	89	128	1.85e-9	SMART
EGF	132	168	1.73e1	SMART
EGF	172	213	7.53e-1	SMART
EGF_CA	214	254	5.31e-10	SMART
low complexity region	307	366	N/A	INTRINSIC
Pfam:MAM	393	532	3.3e-28	PFAM

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.6%
20x: 98.8%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Mice homozygous for a null allele frequently exhibit kidney agenesis or hypoplasia attributed to a delay in the invasion of the metanephric mesenchyme by the ureteric bud at an early stage of kidney development. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acbd4	T	A	11: 103,104,538	L90M	probably damaging	Het
Acot7	T	C	4: 152,178,189	S7P	unknown	Het
Ahcyl2	T	C	6: 29,908,421	Y388H	probably damaging	Het
Atp1a2	T	A	1: 172,284,550	R593*	probably null	Het
Bicral	T	C	17: 46,801,668	T869A	probably benign	Het
Brca2	C	T	5: 150,540,478	P1236S	probably benign	Het
Cacna2d1	C	T	5: 16,352,668	Q699*	probably null	Het
Ccser2	T	C	14: 36,940,007	N407D	probably damaging	Het
Cd300lg	A	G	11: 102,043,074	Y49C	probably damaging	Het
Cdh12	C	A	15: 21,358,814	T108K	probably damaging	Het
Ctnnd1	A	T	2: 84,610,606	I715K	possibly damaging	Het
Cyp17a1	T	A	19: 46,670,980	D137V	probably damaging	Het
Dbr1	A	G	9: 99,575,983	T19A	probably damaging	Het
Dnah3	C	T	7: 120,030,010	A1441T	possibly damaging	Het
Dpt	G	A	1: 164,796,939	D70N	probably damaging	Het
Elk4	C	A	1: 132,019,369	P366Q	probably damaging	Het
Eml4	A	C	17: 83,425,311	D131A	probably benign	Het
Faap24	A	G	7: 35,392,871	I207T	possibly damaging	Het
Fam198b	T	C	3: 79,886,548	Y108H	probably damaging	Het
Fam219a	T	C	4: 41,521,925	S41G	probably benign	Het
Gm15448	T	A	7: 3,821,262	K629*	probably null	Het
Ifi203	T	C	1: 173,928,385		probably benign	Het
Inpp4a	T	C	1: 37,369,423	V295A	probably benign	Het
Kif2a	A	G	13: 106,982,594	Y267H	probably damaging	Het
Kprp	T	A	3: 92,825,197	Q182L	probably benign	Het
Krt90	T	C	15: 101,557,175	K337R	possibly damaging	Het
Lrp2	T	A	2: 69,483,028	Y2453F	possibly damaging	Het
Magel2	A	C	7: 62,379,787	Y813S	unknown	Het
Myh7	C	A	14: 54,974,644	E1548*	probably null	Het
Myh8	A	G	11: 67,297,539	T1009A	probably benign	Het
Nab2	T	A	10: 127,666,508		probably benign	Het
Neb	T	C	2: 52,296,273	D929G	possibly damaging	Het
Nelfb	A	C	2: 25,210,493	V155G	probably damaging	Het
Nmur1	C	A	1: 86,387,848	M65I	possibly damaging	Het
Nop56	C	T	2: 130,277,881	R81*	probably null	Het
Nrp1	G	T	8: 128,480,954	C610F	probably damaging	Het
Olfr1175-ps	T	C	2: 88,323,262	K148E	probably damaging	Het
Olfr1243	T	A	2: 89,527,604	I269F	probably damaging	Het
Olfr766-ps1	T	A	10: 129,064,675	M1L	probably benign	Het
Pax5	G	A	4: 44,679,501	Q93*	probably null	Het
Pcnt	G	T	10: 76,403,835	Q1273K	probably damaging	Het
Pde4dip	G	A	3: 97,724,183	Q1137*	probably null	Het
Pfas	A	T	11: 68,990,760	D959E	probably benign	Het
Prex1	TCCGACCCC	TCCGACCCCGACCCC	2: 166,613,187		probably benign	Het
Prpf40b	C	T	15: 99,306,400	Q182*	probably null	Het
Ptk2	G	A	15: 73,221,809	P854S	possibly damaging	Het
Rpe65	A	C	3: 159,622,685	E406A	probably damaging	Het
Serpina3k	A	T	12: 104,341,142	Y211F	probably benign	Het
Shkbp1	T	C	7: 27,355,281	I65V	possibly damaging	Het
Slc22a29	G	A	19: 8,160,580	P544S	probably benign	Het
Stab2	T	C	10: 86,850,837	D2281G	probably damaging	Het
Tjp2	A	G	19: 24,132,688	M64T	probably benign	Het
Tnfrsf8	C	T	4: 145,274,403	V378I	possibly damaging	Het
Trpm1	A	T	7: 64,226,714		probably null	Het
Ubqln3	A	G	7: 104,141,275	I536T	probably benign	Het
Vmn1r44	A	G	6: 89,893,754	T161A	possibly damaging	Het
Vmn2r108	T	A	17: 20,471,083	I393F	possibly damaging	Het

Other mutations in Npnt

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00731:Npnt	APN	3	132904657	critical splice donor site	probably null
IGL01457:Npnt	APN	3	132885982	missense	probably damaging	1.00
IGL01954:Npnt	APN	3	132909963	missense	probably damaging	1.00
IGL01999:Npnt	APN	3	132908399	missense	probably damaging	1.00
IGL02012:Npnt	APN	3	132908397	missense	probably damaging	1.00
IGL02025:Npnt	APN	3	132890762	critical splice donor site	probably null
IGL02637:Npnt	APN	3	132884510	missense	possibly damaging	0.90
R0234:Npnt	UTSW	3	132914414	missense	possibly damaging	0.82
R0234:Npnt	UTSW	3	132914414	missense	possibly damaging	0.82
R1680:Npnt	UTSW	3	132906802	missense	probably benign	0.00
R1729:Npnt	UTSW	3	132914397	nonsense	probably null
R1773:Npnt	UTSW	3	132904693	missense	possibly damaging	0.62
R1980:Npnt	UTSW	3	132948132	missense	probably benign	0.04
R1982:Npnt	UTSW	3	132948132	missense	probably benign	0.04
R2338:Npnt	UTSW	3	132891409	missense	probably damaging	1.00
R3800:Npnt	UTSW	3	132906763	missense	probably damaging	1.00
R4739:Npnt	UTSW	3	132904691	missense	possibly damaging	0.93
R4790:Npnt	UTSW	3	132890762	critical splice donor site	probably benign
R5008:Npnt	UTSW	3	132906457	missense	probably damaging	1.00
R5446:Npnt	UTSW	3	132908369	missense	probably damaging	1.00
R5471:Npnt	UTSW	3	132914387	missense	probably benign	0.05
R5538:Npnt	UTSW	3	132904963	missense	probably damaging	1.00
R5673:Npnt	UTSW	3	132917497	missense	probably damaging	0.97
R5683:Npnt	UTSW	3	132906840	splice site	probably null
R5827:Npnt	UTSW	3	132906775	missense	possibly damaging	0.89
R5857:Npnt	UTSW	3	132908349	missense	probably damaging	1.00
R5910:Npnt	UTSW	3	132906418	missense	probably damaging	1.00
R6208:Npnt	UTSW	3	132950013	unclassified	probably benign
R6358:Npnt	UTSW	3	132904718	missense	probably benign	0.18
R6875:Npnt	UTSW	3	132909910	missense	probably damaging	1.00
R7145:Npnt	UTSW	3	132909931	missense	probably benign	0.01
R7166:Npnt	UTSW	3	132948128	missense	probably damaging	1.00
R7287:Npnt	UTSW	3	132906802	missense	probably benign	0.00
R7344:Npnt	UTSW	3	132908339	splice site	probably null
R8344:Npnt	UTSW	3	132908456	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGTTGGTCCATTCACAGGAATCC -3'
(R):5'- GAGGGCTGGTTCATTGACTC -3'

Sequencing Primer
(F):5'- GTCCATTCACAGGAATCCTCGTC -3'
(R):5'- GACTCTCTGTTGTTGAATCGCTGAC -3'

Posted On

2019-05-13