Mutagenetix > Incidental Mutation

Incidental Mutation 'R5538:Npnt'

434908

Institutional Source

Beutler Lab

Gene Symbol

Npnt

Ensembl Gene

ENSMUSG00000040998

Gene Name

nephronectin

Synonyms

POEM, 1110009H02Rik

MMRRC Submission

043096-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.132) question?

Stock #

R5538 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

132587506-132656052 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 132610724 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 285 (N285S)

Ref Sequence

ENSEMBL: ENSMUSP00000113752 (fasta)

Gene Model

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

AlphaFold

Q91V88

Predicted Effect

probably damaging
Transcript: ENSMUST00000042729
AA Change: N302S

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

SMART Domains

Protein: ENSMUSP00000040071
Gene: ENSMUSG00000040998
AA Change: N302S

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 benign
Transcript: ENSMUST00000042744
AA Change: N285S

PolyPhen 2 Score 0.358 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000040684
Gene: ENSMUSG00000040998
AA Change: N285S

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: N333S

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

SMART Domains

Protein: ENSMUSP00000091505
Gene: ENSMUSG00000040998
AA Change: N333S

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: N316S

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

SMART Domains

Protein: ENSMUSP00000113419
Gene: ENSMUSG00000040998
AA Change: N316S

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: N181S

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000112816
Gene: ENSMUSG00000040998
AA Change: N181S

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: N285S

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

SMART Domains

Protein: ENSMUSP00000113752
Gene: ENSMUSG00000040998
AA Change: N285S

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132732

Meta Mutation Damage Score

0.2095

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.3%
20x: 95.1%

Validation Efficiency

94% (73/78)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrv1	C	A	13: 81,581,808 (GRCm39)	R4745S	probably benign	Het
Ank3	A	G	10: 69,823,257 (GRCm39)	E642G	probably damaging	Het
Arhgap11a	G	T	2: 113,667,875 (GRCm39)	D375E	probably benign	Het
Arl8b	C	A	6: 108,760,297 (GRCm39)	L28M	probably damaging	Het
Bbs2	G	A	8: 94,816,391 (GRCm39)	T157M	probably damaging	Het
C2cd3	T	A	7: 100,104,700 (GRCm39)		probably null	Het
C6	T	A	15: 4,844,311 (GRCm39)	I911N	possibly damaging	Het
Cc2d2a	T	C	5: 43,852,518 (GRCm39)	I365T	possibly damaging	Het
Cd46	T	G	1: 194,750,478 (GRCm39)		probably null	Het
Ceacam3	A	T	7: 16,892,346 (GRCm39)	D363V	probably damaging	Het
Cep63	A	T	9: 102,465,992 (GRCm39)	L678*	probably null	Het
Clasrp	A	C	7: 19,318,707 (GRCm39)		probably benign	Het
Clk2	T	A	3: 89,082,962 (GRCm39)	Y412N	probably damaging	Het
Col24a1	C	T	3: 144,998,882 (GRCm39)	A5V	probably damaging	Het
Cox16	T	C	12: 81,531,703 (GRCm39)	N13D	possibly damaging	Het
Cybb	C	G	X: 9,316,989 (GRCm39)	D246H	probably benign	Het
Dhx32	A	T	7: 133,324,946 (GRCm39)	M437K	probably benign	Het
Dnm2	T	C	9: 21,416,923 (GRCm39)	F819L	probably benign	Het
Dpysl4	A	G	7: 138,671,906 (GRCm39)	T85A	probably benign	Het
Dspp	A	T	5: 104,323,096 (GRCm39)	K80*	probably null	Het
Dync2h1	T	C	9: 7,168,630 (GRCm39)		probably benign	Het
Ern1	A	G	11: 106,312,727 (GRCm39)	V218A	possibly damaging	Het
Fbn2	G	A	18: 58,204,973 (GRCm39)	R1157C	probably benign	Het
Fez1	T	A	9: 36,780,172 (GRCm39)	I323N	probably damaging	Het
Fmo9	T	A	1: 166,501,198 (GRCm39)	T199S	probably benign	Het
Fry	T	A	5: 150,419,313 (GRCm39)	L915Q	probably damaging	Het
Gatd1	A	G	7: 140,986,758 (GRCm39)		probably benign	Het
Gm10719	T	C	9: 3,018,962 (GRCm39)	L69S	probably benign	Het
Gnpda2	A	T	5: 69,735,394 (GRCm39)	H230Q	probably damaging	Het
Gramd1c	T	A	16: 43,802,455 (GRCm39)	N652I	probably damaging	Het
H2-T13	T	A	17: 36,392,178 (GRCm39)	H178L	probably benign	Het
Hells	T	A	19: 38,942,096 (GRCm39)	F462Y	probably benign	Het
Htr7	A	G	19: 35,947,235 (GRCm39)	F260L	probably benign	Het
Itsn1	C	A	16: 91,580,990 (GRCm39)	A23D	probably damaging	Het
Jak3	A	G	8: 72,131,417 (GRCm39)	D94G	probably benign	Het
Kctd16	T	A	18: 40,390,319 (GRCm39)	Y97*	probably null	Het
Kif20b	A	T	19: 34,930,364 (GRCm39)	K25*	probably null	Het
Klf2	T	C	8: 73,073,316 (GRCm39)	L40P	probably damaging	Het
Kmt2a	A	G	9: 44,731,639 (GRCm39)		probably benign	Het
Kmt2d	G	A	15: 98,749,990 (GRCm39)		probably benign	Het
Lonrf1	T	A	8: 36,690,178 (GRCm39)		probably null	Het
Lrp1b	A	T	2: 40,587,486 (GRCm39)	I154K	unknown	Het
Mybpc1	T	A	10: 88,381,891 (GRCm39)	I600L	possibly damaging	Het
Or4c12b	T	A	2: 89,646,964 (GRCm39)	F92Y	probably damaging	Het
Or51h5	A	G	7: 102,577,728 (GRCm39)	T298A	probably damaging	Het
Or6c69	T	A	10: 129,747,871 (GRCm39)	Y92F	probably benign	Het
Or6n1	T	C	1: 173,917,544 (GRCm39)	*313R	probably null	Het
Pcnx1	T	C	12: 81,907,183 (GRCm39)	V13A	probably damaging	Het
Phkb	G	A	8: 86,648,756 (GRCm39)	V191I	possibly damaging	Het
Pnpla6	A	G	8: 3,581,508 (GRCm39)	M594V	probably benign	Het
Potefam3e	A	C	8: 19,799,430 (GRCm39)		probably null	Het
Prkdc	A	G	16: 15,469,333 (GRCm39)	E146G	probably damaging	Het
Ror1	T	C	4: 100,298,208 (GRCm39)	M527T	probably benign	Het
Scnm1	A	G	3: 95,037,066 (GRCm39)		probably benign	Het
Skint11	A	T	4: 114,088,959 (GRCm39)	N251I	probably damaging	Het
Slc19a3	T	A	1: 83,000,282 (GRCm39)	N245I	possibly damaging	Het
Slc1a3	A	T	15: 8,675,188 (GRCm39)	D272E	probably damaging	Het
Smok2b	T	A	17: 13,454,440 (GRCm39)	V200D	possibly damaging	Het
Sspo	T	C	6: 48,429,112 (GRCm39)	Y417H	probably damaging	Het
Stk11ip	C	A	1: 75,504,979 (GRCm39)	S388R	probably damaging	Het
Svep1	T	C	4: 58,049,282 (GRCm39)		probably null	Het
Sytl2	A	G	7: 90,038,114 (GRCm39)	I525V	probably benign	Het
Tie1	T	C	4: 118,343,390 (GRCm39)	N158D	probably benign	Het
Tle2	T	C	10: 81,416,418 (GRCm39)	L180P	probably damaging	Het
Txlnb	T	C	10: 17,714,657 (GRCm39)	L363P	probably damaging	Het
Upk3b	C	G	5: 136,072,890 (GRCm39)	A258G	probably benign	Het
Usp32	A	T	11: 84,908,612 (GRCm39)	D1031E	possibly damaging	Het
Vmn2r116	C	T	17: 23,620,041 (GRCm39)	L592F	probably benign	Het
Zfp607b	A	G	7: 27,402,294 (GRCm39)	H250R	probably damaging	Het

Other mutations in Npnt

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00731:Npnt	APN	3	132,610,418 (GRCm39)	critical splice donor site	probably null
IGL01457:Npnt	APN	3	132,591,743 (GRCm39)	missense	probably damaging	1.00
IGL01954:Npnt	APN	3	132,615,724 (GRCm39)	missense	probably damaging	1.00
IGL01999:Npnt	APN	3	132,614,160 (GRCm39)	missense	probably damaging	1.00
IGL02012:Npnt	APN	3	132,614,158 (GRCm39)	missense	probably damaging	1.00
IGL02025:Npnt	APN	3	132,596,523 (GRCm39)	critical splice donor site	probably null
IGL02637:Npnt	APN	3	132,590,271 (GRCm39)	missense	possibly damaging	0.90
R0234:Npnt	UTSW	3	132,620,175 (GRCm39)	missense	possibly damaging	0.82
R0234:Npnt	UTSW	3	132,620,175 (GRCm39)	missense	possibly damaging	0.82
R1680:Npnt	UTSW	3	132,612,563 (GRCm39)	missense	probably benign	0.00
R1729:Npnt	UTSW	3	132,620,158 (GRCm39)	nonsense	probably null
R1773:Npnt	UTSW	3	132,610,454 (GRCm39)	missense	possibly damaging	0.62
R1980:Npnt	UTSW	3	132,653,893 (GRCm39)	missense	probably benign	0.04
R1982:Npnt	UTSW	3	132,653,893 (GRCm39)	missense	probably benign	0.04
R2338:Npnt	UTSW	3	132,597,170 (GRCm39)	missense	probably damaging	1.00
R3800:Npnt	UTSW	3	132,612,524 (GRCm39)	missense	probably damaging	1.00
R4739:Npnt	UTSW	3	132,610,452 (GRCm39)	missense	possibly damaging	0.93
R4790:Npnt	UTSW	3	132,596,523 (GRCm39)	critical splice donor site	probably benign
R5008:Npnt	UTSW	3	132,612,218 (GRCm39)	missense	probably damaging	1.00
R5446:Npnt	UTSW	3	132,614,130 (GRCm39)	missense	probably damaging	1.00
R5471:Npnt	UTSW	3	132,620,148 (GRCm39)	missense	probably benign	0.05
R5673:Npnt	UTSW	3	132,623,258 (GRCm39)	missense	probably damaging	0.97
R5683:Npnt	UTSW	3	132,612,601 (GRCm39)	splice site	probably null
R5827:Npnt	UTSW	3	132,612,536 (GRCm39)	missense	possibly damaging	0.89
R5857:Npnt	UTSW	3	132,614,110 (GRCm39)	missense	probably damaging	1.00
R5910:Npnt	UTSW	3	132,612,179 (GRCm39)	missense	probably damaging	1.00
R6208:Npnt	UTSW	3	132,655,774 (GRCm39)	unclassified	probably benign
R6358:Npnt	UTSW	3	132,610,479 (GRCm39)	missense	probably benign	0.18
R6875:Npnt	UTSW	3	132,615,671 (GRCm39)	missense	probably damaging	1.00
R7025:Npnt	UTSW	3	132,614,157 (GRCm39)	missense	probably damaging	1.00
R7145:Npnt	UTSW	3	132,615,692 (GRCm39)	missense	probably benign	0.01
R7166:Npnt	UTSW	3	132,653,889 (GRCm39)	missense	probably damaging	1.00
R7287:Npnt	UTSW	3	132,612,563 (GRCm39)	missense	probably benign	0.00
R7344:Npnt	UTSW	3	132,614,100 (GRCm39)	splice site	probably null
R8344:Npnt	UTSW	3	132,614,217 (GRCm39)	missense	probably damaging	1.00
R8717:Npnt	UTSW	3	132,614,136 (GRCm39)	missense	probably damaging	1.00
R8873:Npnt	UTSW	3	132,655,816 (GRCm39)	start gained	probably benign
R8903:Npnt	UTSW	3	132,591,764 (GRCm39)	missense	probably damaging	1.00
R9414:Npnt	UTSW	3	132,612,116 (GRCm39)	missense	probably benign	0.00
R9420:Npnt	UTSW	3	132,653,866 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- GTCTGTATCCTGTTGTCAACCG -3'
(R):5'- CAATTGCCATGAGGTGTTTCTG -3'

Sequencing Primer
(F):5'- CAACCGTAATTACTCGTGTAGTGG -3'
(R):5'- CCATGAGGTGTTTCTGTGTATG -3'

Posted On

2016-10-24