Mutagenetix > Incidental Mutation

Incidental Mutation 'R7145:Npnt'

553694

Institutional Source

Beutler Lab

Gene Symbol

Npnt

Ensembl Gene

ENSMUSG00000040998

Gene Name

nephronectin

Synonyms

POEM, 1110009H02Rik

MMRRC Submission

045223-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.162) question?

Stock #

R7145 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

132587506-132656052 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 132615692 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 165 (N165S)

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: N134S

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000040071
Gene: ENSMUSG00000040998
AA Change: N134S

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: N117S

PolyPhen 2 Score 0.069 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000040684
Gene: ENSMUSG00000040998
AA Change: N117S

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: N165S

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000091505
Gene: ENSMUSG00000040998
AA Change: N165S

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: N148S

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000113419
Gene: ENSMUSG00000040998
AA Change: N148S

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: N13S

PolyPhen 2 Score 0.069 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000112816
Gene: ENSMUSG00000040998
AA Change: N13S

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: N117S

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000113752
Gene: ENSMUSG00000040998
AA Change: N117S

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: 99.9%
10x: 99.7%
20x: 99.2%

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	T	C	3: 137,775,820 (GRCm39)	Y1670H	probably damaging	Het
Abca12	T	C	1: 71,346,212 (GRCm39)	K886R	possibly damaging	Het
Adcy3	G	A	12: 4,250,992 (GRCm39)	E584K	probably benign	Het
Ano3	A	T	2: 110,693,205 (GRCm39)	V131D	probably benign	Het
Arhgdig	C	T	17: 26,418,337 (GRCm39)	W215*	probably null	Het
Cad	G	T	5: 31,224,956 (GRCm39)	W953L	possibly damaging	Het
Calhm2	T	C	19: 47,124,080 (GRCm39)	Y88C	probably benign	Het
Cdk5rap2	A	T	4: 70,156,468 (GRCm39)	D1681E	probably benign	Het
Cenpl	T	A	1: 160,910,482 (GRCm39)	L143H	possibly damaging	Het
Cherp	T	C	8: 73,222,230 (GRCm39)	K270E		Het
Cmss1	A	G	16: 57,131,718 (GRCm39)	I136T	probably benign	Het
Col23a1	T	C	11: 51,456,050 (GRCm39)		probably null	Het
Crnn	C	A	3: 93,055,689 (GRCm39)	D158E	probably damaging	Het
Dnmt3a	A	T	12: 3,922,844 (GRCm39)	Q149L	probably benign	Het
Dst	T	A	1: 34,228,963 (GRCm39)	N2185K	probably benign	Het
Eif1ad18	G	T	12: 88,050,597 (GRCm39)	C44F	probably benign	Het
Elp2	T	A	18: 24,737,126 (GRCm39)	N25K	probably benign	Het
Ephb4	A	T	5: 137,370,308 (GRCm39)	D845V	probably damaging	Het
Esyt3	T	C	9: 99,201,627 (GRCm39)	T561A	probably damaging	Het
F3	G	T	3: 121,525,235 (GRCm39)	V159L	probably damaging	Het
Fam81a	A	T	9: 70,017,560 (GRCm39)	D128E	probably damaging	Het
Flot1	T	G	17: 36,135,835 (GRCm39)	H155Q	probably benign	Het
Fut9	T	A	4: 25,620,507 (GRCm39)	K102N	probably damaging	Het
Gm6309	T	C	5: 146,107,100 (GRCm39)	Q82R	possibly damaging	Het
H13	A	G	2: 152,522,992 (GRCm39)	N102D	probably damaging	Het
Lamc2	C	G	1: 153,006,518 (GRCm39)	A878P	possibly damaging	Het
Lepr	C	T	4: 101,609,394 (GRCm39)	T327I	probably benign	Het
Lrp2	A	G	2: 69,285,152 (GRCm39)		probably null	Het
Ly86	A	G	13: 37,560,986 (GRCm39)	K116E	probably damaging	Het
Mapk8ip2	T	A	15: 89,343,201 (GRCm39)	F648I	possibly damaging	Het
Muc16	G	A	9: 18,566,876 (GRCm39)	T1881I	unknown	Het
Myh13	T	G	11: 67,245,566 (GRCm39)	S1069A	probably benign	Het
Myh4	T	A	11: 67,151,054 (GRCm39)	I1903N	possibly damaging	Het
Myo18b	A	T	5: 112,965,545 (GRCm39)	L1341*	probably null	Het
Naa25	G	T	5: 121,555,552 (GRCm39)		probably null	Het
Nbeal1	G	C	1: 60,276,310 (GRCm39)	V684L	probably benign	Het
Ncapg	C	T	5: 45,827,372 (GRCm39)	A3V	possibly damaging	Het
Ncln	T	C	10: 81,324,086 (GRCm39)	H481R	probably benign	Het
Nek4	C	A	14: 30,704,305 (GRCm39)	Q607K	probably damaging	Het
Neo1	T	C	9: 58,796,462 (GRCm39)	Y1182C	probably damaging	Het
Or2l5	C	G	16: 19,333,649 (GRCm39)	V246L	probably damaging	Het
Or4p22	C	T	2: 88,317,721 (GRCm39)	S215L	probably damaging	Het
Or8b8	A	G	9: 37,808,859 (GRCm39)	H53R	probably benign	Het
Or8k30	T	C	2: 86,338,872 (GRCm39)	L23P	probably damaging	Het
Otulin	T	C	15: 27,608,856 (GRCm39)	Y229C	probably damaging	Het
Palld	A	T	8: 61,985,051 (GRCm39)	D1071E	unknown	Het
Pcdhb20	T	C	18: 37,638,142 (GRCm39)	S223P	probably damaging	Het
Pcdhga6	T	A	18: 37,840,781 (GRCm39)	I167N	probably damaging	Het
Pcdhgb4	A	G	18: 37,854,843 (GRCm39)	N413D	probably benign	Het
Pcdhgb8	T	A	18: 37,896,050 (GRCm39)	Y373*	probably null	Het
Plxna2	G	T	1: 194,331,830 (GRCm39)	V419L	probably benign	Het
Rpgrip1l	A	T	8: 91,959,434 (GRCm39)		probably null	Het
Rsrc2	A	G	5: 123,877,630 (GRCm39)		probably benign	Het
Scaper	C	T	9: 55,819,395 (GRCm39)	D107N	unknown	Het
Scgb2b3	T	A	7: 31,059,573 (GRCm39)	Y67F	probably benign	Het
Scn5a	G	A	9: 119,315,437 (GRCm39)	T1757I	probably damaging	Het
Sgo2b	G	A	8: 64,381,218 (GRCm39)	P538L	probably damaging	Het
Slc9a3	A	G	13: 74,298,797 (GRCm39)	K72R	probably damaging	Het
Smchd1	T	A	17: 71,685,202 (GRCm39)	T1409S	probably benign	Het
Stab1	A	T	14: 30,867,030 (GRCm39)		probably null	Het
Sult2b1	T	C	7: 45,383,056 (GRCm39)	E242G	probably damaging	Het
Tcaf1	A	T	6: 42,663,687 (GRCm39)	H64Q	probably damaging	Het
Tle6	T	C	10: 81,435,910 (GRCm39)	T2A	possibly damaging	Het
Tmem115	T	C	9: 107,412,285 (GRCm39)	V203A	probably benign	Het
Tmem45b	G	A	9: 31,340,337 (GRCm39)	T108I	probably damaging	Het
Tmf1	A	T	6: 97,153,079 (GRCm39)	D331E	probably damaging	Het
Txndc9	T	C	1: 38,029,377 (GRCm39)	Y157C	probably damaging	Het
Vmn2r111	T	C	17: 22,778,032 (GRCm39)	N549S	possibly damaging	Het
Vmn2r27	C	A	6: 124,168,711 (GRCm39)	R806S	probably benign	Het
Vmn2r59	G	A	7: 41,695,188 (GRCm39)	A408V	probably damaging	Het
Ythdc1	T	C	5: 86,964,467 (GRCm39)	V92A	probably benign	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
R5538:Npnt	UTSW	3	132,610,724 (GRCm39)	missense	probably damaging	1.00
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
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'- GATCTTTCATTCCTCGGGCG -3'
(R):5'- CGGACTTTTATCTGTCACCGAAG -3'

Sequencing Primer
(F):5'- GGCGCGCACACAAACAC -3'
(R):5'- ACCGAAGTGATGCTTTCGC -3'

Posted On

2019-05-15