Mutagenetix > Incidental Mutation

Incidental Mutation 'R6875:Npnt'

536357

Institutional Source

Beutler Lab

Gene Symbol

Npnt

Ensembl Gene

ENSMUSG00000040998

Gene Name

nephronectin

Synonyms

1110009H02Rik, POEM

MMRRC Submission

044971-MU

Accession Numbers

Essential gene?

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

Stock #

R6875 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

132881745-132950291 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 132909910 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 124 (D124V)

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: D141V

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

SMART Domains

Protein: ENSMUSP00000040071
Gene: ENSMUSG00000040998
AA Change: D141V

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: D124V

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

SMART Domains

Protein: ENSMUSP00000040684
Gene: ENSMUSG00000040998
AA Change: D124V

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: D172V

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

SMART Domains

Protein: ENSMUSP00000091505
Gene: ENSMUSG00000040998
AA Change: D172V

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: D155V

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

SMART Domains

Protein: ENSMUSP00000113419
Gene: ENSMUSG00000040998
AA Change: D155V

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: D20V

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

SMART Domains

Protein: ENSMUSP00000112816
Gene: ENSMUSG00000040998
AA Change: D20V

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: D124V

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

SMART Domains

Protein: ENSMUSP00000113752
Gene: ENSMUSG00000040998
AA Change: D124V

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: 99.5%
20x: 98.2%

Validation Efficiency

98% (58/59)

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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6030458C11Rik	T	C	15: 12,812,068	H270R	probably damaging	Het
Abcb1a	T	C	5: 8,701,628	I336T	probably benign	Het
Adam19	T	A	11: 46,112,875	F177I	probably benign	Het
Ankrd53	T	C	6: 83,768,173	V455A	probably damaging	Het
Arrdc1	A	G	2: 24,925,665	S415P	probably benign	Het
Atp10a	T	C	7: 58,797,352	L614P	probably benign	Het
C130060K24Rik	A	T	6: 65,456,336	N380I	probably benign	Het
Catsper1	G	T	19: 5,343,963	V668F	probably damaging	Het
Cluh	T	A	11: 74,661,918	D596E	probably damaging	Het
Cnot10	A	G	9: 114,615,107	S407P	probably benign	Het
Commd6	T	C	14: 101,634,350	T86A	probably damaging	Het
D5Ertd579e	A	T	5: 36,604,657		probably null	Het
Eif3l	A	G	15: 79,085,560	D252G	probably damaging	Het
Epha2	A	T	4: 141,328,468	S962C	probably damaging	Het
Fcho1	C	A	8: 71,714,425		probably null	Het
Fgf23	G	T	6: 127,073,216	G63C	probably damaging	Het
Flnc	A	T	6: 29,445,749	Y834F	probably damaging	Het
Gcn1l1	T	C	5: 115,588,110	L608P	probably damaging	Het
Hdac5	T	A	11: 102,202,276	E545V	probably damaging	Het
Hecw2	A	T	1: 53,937,132	M166K	probably benign	Het
Ikbkb	T	C	8: 22,665,893	D586G	probably damaging	Het
Il1f9	G	C	2: 24,188,621		probably null	Het
Ipo13	A	T	4: 117,904,911	I422N	possibly damaging	Het
Iqgap3	GGAGAG	GGAG	3: 88,112,771		probably null	Het
Kat6a	G	A	8: 22,932,361	A896T	probably benign	Het
Kif28	A	G	1: 179,735,994	I139T	probably damaging	Het
Klhl25	A	G	7: 75,866,342	E332G	probably damaging	Het
Krt8	C	T	15: 101,997,908	A389T	probably benign	Het
Msrb3	T	C	10: 120,784,106	S175G	probably benign	Het
Muc5ac	C	T	7: 141,809,744		probably benign	Het
Myo10	T	C	15: 25,805,659	Y1709H	probably benign	Het
Nckap5	A	G	1: 126,023,194	S1519P	probably benign	Het
Nr1d1	A	T	11: 98,770,836		probably null	Het
Ogdh	A	G	11: 6,340,477	Y365C	probably benign	Het
Olfr1305	A	T	2: 111,872,961	I298N	possibly damaging	Het
Phf21b	A	T	15: 84,787,446	C416S	probably damaging	Het
Prpsap1	A	G	11: 116,471,438	S373P	probably damaging	Het
Rab28	T	C	5: 41,703,534	T26A	probably damaging	Het
Rbbp8nl	A	G	2: 180,279,226	I455T	probably benign	Het
Rnft2	G	A	5: 118,228,818	A285V	possibly damaging	Het
Rrp36	G	T	17: 46,672,371	Q106K	probably benign	Het
Rsf1	CG	CGACGGCGGAG	7: 97,579,908		probably benign	Het
Runx2	G	A	17: 44,814,192	P80L	probably damaging	Het
Scn5a	A	G	9: 119,486,644	L1666P	probably damaging	Het
Siglecf	A	C	7: 43,355,200	T318P	probably benign	Het
Slc22a1	C	T	17: 12,667,305	W147*	probably null	Het
Smchd1	T	C	17: 71,353,506	I1868V	probably damaging	Het
Snx21	A	G	2: 164,791,902	S203G	probably damaging	Het
Srl	T	C	16: 4,482,831	K792R	probably benign	Het
Srrt	A	G	5: 137,298,673	F100S	probably benign	Het
Stard9	G	T	2: 120,697,436	M1391I	probably benign	Het
Syne2	A	G	12: 76,035,630	E119G	probably damaging	Het
Syt11	G	T	3: 88,762,155	S143R	possibly damaging	Het
Tiparp	T	A	3: 65,531,642	H126Q	probably benign	Het
Tulp2	C	A	7: 45,518,614	T150K	probably benign	Het
Ugt2b37	T	A	5: 87,242,429	Y386F	probably benign	Het
Usp31	C	T	7: 121,649,640	W860*	probably null	Het
Zfp317	A	G	9: 19,643,665	R30G	probably damaging	Het
Zfp709	C	A	8: 71,889,007	N93K	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
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'- CCCATTTAATGTTGGCCTGC -3'
(R):5'- GTTTTGAACGTTTCCCAGCAC -3'

Sequencing Primer
(F):5'- CATGTATATAAATGTGCGCCTCTGG -3'
(R):5'- CTGCCAAGGCTGTGATGTCTC -3'

Posted On

2018-10-18