Mutagenetix > Incidental Mutation

Incidental Mutation 'R7287:Npnt'

566071

Institutional Source

Beutler Lab

Gene Symbol

Npnt

Ensembl Gene

ENSMUSG00000040998

Gene Name

nephronectin

Synonyms

1110009H02Rik, POEM

MMRRC Submission

045321-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.146) question?

Stock #

R7287 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

132881745-132950291 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 132906802 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 74 (V74A)

Ref Sequence

ENSEMBL: ENSMUSP00000112816 (fasta)

Gene Model

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

AlphaFold

Q91V88

Predicted Effect

probably benign
Transcript: ENSMUST00000042729
AA Change: V195A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000040071
Gene: ENSMUSG00000040998
AA Change: V195A

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: V178A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000040684
Gene: ENSMUSG00000040998
AA Change: V178A

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 benign
Transcript: ENSMUST00000093971
AA Change: V226A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000091505
Gene: ENSMUSG00000040998
AA Change: V226A

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 benign
Transcript: ENSMUST00000117164
AA Change: V209A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000113419
Gene: ENSMUSG00000040998
AA Change: V209A

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 benign
Transcript: ENSMUST00000117456
AA Change: V74A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000112816
Gene: ENSMUSG00000040998
AA Change: V74A

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 benign
Transcript: ENSMUST00000117811
AA Change: V178A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000113752
Gene: ENSMUSG00000040998
AA Change: V178A

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

100% (71/71)

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
2610507B11Rik	G	A	11: 78,272,883	R1059H	possibly damaging	Het
Abca3	A	G	17: 24,385,887	D656G	possibly damaging	Het
Abcc3	C	T	11: 94,357,047	A1207T	probably benign	Het
Abcc8	T	C	7: 46,113,110	H1209R	probably damaging	Het
Adam26a	T	C	8: 43,570,343	T37A	possibly damaging	Het
Adamts9	C	T	6: 92,890,003	R685Q	possibly damaging	Het
Anapc7	T	A	5: 122,433,436	N191K	probably benign	Het
Ankrd26	C	T	6: 118,549,637		probably null	Het
Ap5z1	T	C	5: 142,474,047	L484P	probably damaging	Het
Arhgap32	A	G	9: 32,152,697	D77G		Het
Atp10a	T	A	7: 58,827,269	D1213E	probably damaging	Het
B3gnt8	T	C	7: 25,628,970	L275P	probably damaging	Het
Cab39	A	G	1: 85,818,461	E21G	probably benign	Het
Capn15	G	T	17: 25,960,455	S948R	probably damaging	Het
Cbarp	T	C	10: 80,137,320	T15A	unknown	Het
Ccdc81	C	T	7: 89,893,123	A182T	probably damaging	Het
Ccpg1	A	G	9: 73,015,406	H766R	probably benign	Het
Cfl1	T	C	19: 5,492,534	V14A	probably benign	Het
Chd6	A	G	2: 161,008,392	I875T	probably benign	Het
Cidec	T	A	6: 113,428,398	E121D	probably benign	Het
Clpx	C	A	9: 65,300,013	Y64*	probably null	Het
Cntn1	T	A	15: 92,245,952		probably null	Het
Cyp24a1	A	G	2: 170,485,906	L472P	probably damaging	Het
Dcdc2c	G	T	12: 28,516,686	D159E	probably benign	Het
Emp1	T	C	6: 135,380,169	F82L	probably benign	Het
Fem1b	T	C	9: 62,796,122	T619A	probably benign	Het
Fgf15	A	T	7: 144,896,794	D39V	probably benign	Het
Galnt12	T	G	4: 47,108,525	F221V	probably damaging	Het
Herc6	A	G	6: 57,651,980		probably null	Het
Hspg2	G	A	4: 137,529,556	V1537I	probably benign	Het
Ido2	T	C	8: 24,535,138		probably null	Het
Insr	G	A	8: 3,169,717	T935I	probably benign	Het
Itgax	G	A	7: 128,148,505	C1031Y	probably damaging	Het
Kif13a	C	T	13: 46,752,455	V671M	possibly damaging	Het
Kmt5b	T	C	19: 3,804,501	Y255H	possibly damaging	Het
Lrriq1	A	T	10: 103,216,016	Y292N	probably benign	Het
Mrpl37	A	G	4: 107,060,520	F318S	probably damaging	Het
Nav2	A	G	7: 49,420,328	N311D	probably benign	Het
Nbeal1	G	C	1: 60,237,151	V684L	probably benign	Het
Nlrp9b	T	C	7: 20,028,456	C673R	probably damaging	Het
Olfr1335	T	A	4: 118,809,742	T41S	probably benign	Het
Olfr378	T	A	11: 73,425,843	I47F	probably benign	Het
Plce1	A	T	19: 38,701,903	Q677L	probably benign	Het
Pmel	C	T	10: 128,715,226	Q113*	probably null	Het
Pom121l2	T	A	13: 21,984,332	F924L	probably benign	Het
Poteg	G	A	8: 27,453,344	R214K	probably null	Het
Pprc1	G	T	19: 46,071,354	S1480I	unknown	Het
Secisbp2l	A	G	2: 125,740,369	S1056P	probably benign	Het
Selenoo	T	C	15: 89,098,700	F477L	probably benign	Het
Senp2	A	G	16: 22,018,364	D121G	probably damaging	Het
Slc25a11	T	C	11: 70,645,355	D211G	probably benign	Het
Slc44a2	A	G	9: 21,342,456	D131G	probably benign	Het
Tcf25	G	A	8: 123,373,972	A34T	possibly damaging	Het
Tm9sf3	A	G	19: 41,217,379	Y530H	probably damaging	Het
Tmco3	G	A	8: 13,319,605		probably null	Het
Tmem132d	G	T	5: 127,984,351	Q396K	probably damaging	Het
Tmem154	A	G	3: 84,690,563	T136A	possibly damaging	Het
Tnrc6b	A	G	15: 80,879,541	T415A	possibly damaging	Het
Tonsl	T	C	15: 76,633,725		probably null	Het
Ttyh1	T	C	7: 4,125,658	Y185H	probably benign	Het
Ufl1	T	A	4: 25,254,852	T535S	probably benign	Het
Vmn1r15	T	C	6: 57,258,216	L23P	possibly damaging	Het
Vmn2r25	T	A	6: 123,852,081	H78L	possibly damaging	Het
Vmn2r68	T	C	7: 85,222,252	T608A	probably benign	Het
Vwf	A	G	6: 125,637,467	I1104V		Het
Zbtb2	C	T	10: 4,368,986	D347N	possibly damaging	Het
Zfyve9	A	T	4: 108,718,256	S543T	probably benign	Het
Zhx1	T	C	15: 58,053,296	N518S	probably damaging	Het
Zmym6	T	C	4: 127,122,982	V852A	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
R7025:Npnt	UTSW	3	132908396	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
R7344:Npnt	UTSW	3	132908339	splice site	probably null
R8344:Npnt	UTSW	3	132908456	missense	probably damaging	1.00
R8717:Npnt	UTSW	3	132908375	missense	probably damaging	1.00
R8873:Npnt	UTSW	3	132950055	start gained	probably benign
R8903:Npnt	UTSW	3	132886003	missense	probably damaging	1.00
R9414:Npnt	UTSW	3	132906355	missense	probably benign	0.00
R9420:Npnt	UTSW	3	132948105	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- AGCTGGAGACTTCTCAACGC -3'
(R):5'- AAGTAGATGGTGTCGTATCTACTGC -3'

Sequencing Primer
(F):5'- TGGAGACTTCTCAACGCTACAGG -3'
(R):5'- TGGTTGTGAGCGCAGAAGAATTC -3'

Posted On

2019-06-26