Mutagenetix > Incidental Mutation

Incidental Mutation 'R6358:Npnt'

513325

Institutional Source

Beutler Lab

Gene Symbol

Npnt

Ensembl Gene

ENSMUSG00000040998

Gene Name

nephronectin

Synonyms

1110009H02Rik, POEM

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.113) question?

Stock #

R6358 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

132881745-132950291 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 132904718 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 415 (V415I)

Ref Sequence

ENSEMBL: ENSMUSP00000091505 (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: V384I

PolyPhen 2 Score 0.181 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000040071
Gene: ENSMUSG00000040998
AA Change: V384I

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: V367I

PolyPhen 2 Score 0.114 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000040684
Gene: ENSMUSG00000040998
AA Change: V367I

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: V415I

PolyPhen 2 Score 0.181 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000091505
Gene: ENSMUSG00000040998
AA Change: V415I

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: V398I

PolyPhen 2 Score 0.064 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000113419
Gene: ENSMUSG00000040998
AA Change: V398I

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: V263I

PolyPhen 2 Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000112816
Gene: ENSMUSG00000040998
AA Change: V263I

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: V367I

PolyPhen 2 Score 0.180 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000113752
Gene: ENSMUSG00000040998
AA Change: V367I

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

0.0898

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 94.8%

Validation Efficiency

100% (61/61)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam39	T	C	8: 40,826,681	V703A	probably benign	Het
Adgrv1	T	A	13: 81,414,583	Q5389L	probably damaging	Het
Aldh18a1	A	T	19: 40,577,678	I42N	possibly damaging	Het
Ankrd28	A	C	14: 31,710,864	C575W	probably damaging	Het
Car14	T	A	3: 95,898,175	T329S	possibly damaging	Het
Cdhr2	T	C	13: 54,736,546	F1298S	probably damaging	Het
Crhr2	A	G	6: 55,093,043	I341T	probably benign	Het
D5Ertd579e	T	A	5: 36,616,236		probably null	Het
Emilin1	A	G	5: 30,918,218	E601G	probably damaging	Het
Erbin	T	A	13: 103,845,565	Q456L	probably damaging	Het
Glp1r	T	C	17: 30,932,644	V405A	probably benign	Het
Gm10220	C	G	5: 26,120,305		probably null	Het
Gm2016	A	G	12: 87,877,000	E139G	unknown	Het
Gm527	A	T	12: 64,923,548	H219L	possibly damaging	Het
Gorasp2	T	A	2: 70,672,760	M1K	probably null	Het
H2-DMa	T	A	17: 34,137,984	L152H	probably damaging	Het
Hsd3b7	T	A	7: 127,801,537	H54Q	probably damaging	Het
Hspa12b	T	C	2: 131,137,066		probably benign	Het
Iars	C	A	13: 49,727,143	T1006K	possibly damaging	Het
Jmjd1c	T	C	10: 67,225,939	V1357A	probably benign	Het
Magi3	T	C	3: 104,050,952	M606V	probably damaging	Het
Mia	T	C	7: 27,180,978	D24G	probably benign	Het
Mon2	A	T	10: 123,013,504	L1297Q	probably damaging	Het
Musk	T	A	4: 58,373,171	S691T	possibly damaging	Het
Myo5c	A	T	9: 75,296,012	E1463D	possibly damaging	Het
Ndufs6	C	T	13: 73,320,319	G87D	probably damaging	Het
Ntsr2	A	G	12: 16,656,768	I266V	probably benign	Het
Olfr259	T	C	2: 87,108,434		probably benign	Het
Olfr736	A	T	14: 50,393,388	I211F	possibly damaging	Het
Pkmyt1	T	A	17: 23,733,656		probably null	Het
Polr1e	T	C	4: 45,026,813	L166P	probably damaging	Het
Ppib	T	G	9: 66,061,474	F48C	probably damaging	Het
Ppl	C	A	16: 5,087,929	E1501*	probably null	Het
Prpf8	T	C	11: 75,491,495	V384A	probably benign	Het
Ptch1	T	G	13: 63,513,689	S1212R	probably damaging	Het
Ralb	C	A	1: 119,476,005	D131Y	probably damaging	Het
Rfx4	T	A	10: 84,844,235	M141K	probably damaging	Het
Rgl2	T	A	17: 33,937,131		probably null	Het
Rpl27	A	G	11: 101,443,956		probably benign	Het
Sdc1	A	C	12: 8,791,297	T213P	probably damaging	Het
Setx	T	A	2: 29,171,348	N2256K	possibly damaging	Het
Shank2	A	G	7: 144,031,297	M12V	probably benign	Het
Slc22a28	T	A	19: 8,071,888	K332M	probably damaging	Het
Slf2	A	T	19: 44,935,425	H226L	probably benign	Het
Tbc1d10b	T	C	7: 127,203,412	S362G	probably benign	Het
Tbxas1	G	A	6: 38,952,112		probably benign	Het
Tctn1	A	G	5: 122,261,512	V83A	probably damaging	Het
Tgm4	A	G	9: 123,056,518	E375G	probably damaging	Het
Tmeff2	T	A	1: 51,133,114	Y247*	probably null	Het
Tmem167b	C	T	3: 108,558,895	R79H	possibly damaging	Het
Tmprss7	T	G	16: 45,669,573	M429L	probably benign	Het
Tnfsf18	T	A	1: 161,503,579	D99E	probably benign	Het
Tnrc18	A	T	5: 142,727,981	S2534T	probably damaging	Het
Tnxb	A	G	17: 34,678,994	E872G	probably damaging	Het
Tomm40l	C	T	1: 171,219,637	V237I	possibly damaging	Het
Trbv2	A	G	6: 41,047,902	Q84R	probably benign	Het
Tspan18	T	C	2: 93,209,874	R179G	probably benign	Het
Tspan8	G	T	10: 115,833,227	V56L	probably benign	Het
Zbtb22	T	C	17: 33,918,737	S619P	probably damaging	Het
Zfp2	A	T	11: 50,900,601	I205N	probably damaging	Het
Zfpm1	A	G	8: 122,337,111		probably benign	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
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
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
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'- TGCCTAGAGTTGAACGCCATC -3'
(R):5'- GTCATTACCAACAGGCCTACTTCC -3'

Sequencing Primer
(F):5'- GCAGTCATAGTTCTTGCAACG -3'
(R):5'- CAGGCCTACTTCCAAGCC -3'

Posted On

2018-04-27