Mutagenetix > Incidental Mutation

Incidental Mutation 'R0485:Nphs1'

42207

Institutional Source

Beutler Lab

Gene Symbol

Nphs1

Ensembl Gene

ENSMUSG00000006649

Gene Name

nephrosis 1, nephrin

Synonyms

nephrin

MMRRC Submission

038684-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0485 (G1)

Quality Score

213

Status

Validated

Chromosome

Chromosomal Location

30157740-30186648 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 30166940 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 716 (F716L)

Ref Sequence

ENSEMBL: ENSMUSP00000116500 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006825] [ENSMUST00000126297]

AlphaFold

Q9QZS7

Predicted Effect

probably benign
Transcript: ENSMUST00000006825
AA Change: F730L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: F730L

Domain	Start	End	E-Value	Type
signal peptide	1	36	N/A	INTRINSIC
IG	52	146	1.38e-6	SMART
Pfam:C2-set_2	152	242	4.1e-20	PFAM
IG	264	351	9.86e-3	SMART
IG_like	360	452	2.73e1	SMART
IG	464	556	2.99e-2	SMART
IG_like	572	644	8.9e-1	SMART
IG	667	751	1.32e-3	SMART
IG	760	849	7.3e-6	SMART
IGc2	868	941	5.4e-9	SMART
FN3	955	1036	1.01e-11	SMART
transmembrane domain	1078	1100	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000126297
AA Change: F716L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: F716L

Domain	Start	End	E-Value	Type
IG	38	132	1.38e-6	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152625

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.3%
20x: 92.4%

Validation Efficiency

100% (95/95)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the immunoglobulin family of cell adhesion molecules that functions in the glomerular filtration barrier in the kidney. The gene is primarily expressed in renal tissues, and the protein is a type-1 transmembrane protein found at the slit diaphragm of glomerular podocytes. The slit diaphragm is thought to function as an ultrafilter to exclude albumin and other plasma macromolecules in the formation of urine. Mutations in this gene result in Finnish-type congenital nephrosis 1, characterized by severe proteinuria and loss of the slit diaphragm and foot processes.[provided by RefSeq, Oct 2009]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit severe proteinuria associated with kidney defects and die soon after birth. Heterozygotes exhibit fusion of one-third of glomerular foot processes. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700037C18Rik	A	G	16: 3,725,511 (GRCm39)	V5A	probably damaging	Het
Abi3bp	A	G	16: 56,424,375 (GRCm39)		probably null	Het
Acot11	G	A	4: 106,619,224 (GRCm39)	R184C	probably damaging	Het
Adgre5	A	T	8: 84,458,627 (GRCm39)	I133N	probably damaging	Het
Afap1	A	T	5: 36,108,347 (GRCm39)	Q231L	probably damaging	Het
Alg12	T	C	15: 88,695,630 (GRCm39)	T289A	probably benign	Het
Ank3	T	A	10: 69,718,374 (GRCm39)	S542T	possibly damaging	Het
Ankmy2	G	A	12: 36,232,389 (GRCm39)	R138Q	possibly damaging	Het
Ascc2	C	T	11: 4,622,302 (GRCm39)	A456V	probably benign	Het
Atg4c	G	A	4: 99,112,719 (GRCm39)	V289I	probably benign	Het
Bbs7	A	T	3: 36,657,022 (GRCm39)	Y269N	probably damaging	Het
Bcas3	T	A	11: 85,386,676 (GRCm39)	D370E	probably damaging	Het
Bicc1	T	G	10: 70,761,145 (GRCm39)	E955A	probably damaging	Het
Bok	T	C	1: 93,616,999 (GRCm39)	F115S	probably damaging	Het
Caap1	A	T	4: 94,438,758 (GRCm39)		probably null	Het
Cacna2d3	T	A	14: 29,256,476 (GRCm39)	M95L	possibly damaging	Het
Calcrl	T	A	2: 84,200,435 (GRCm39)	D115V	probably benign	Het
Car7	A	T	8: 105,270,170 (GRCm39)	M57L	probably benign	Het
Casq1	G	T	1: 172,037,957 (GRCm39)		probably benign	Het
Cep290	A	T	10: 100,385,206 (GRCm39)	D1894V	possibly damaging	Het
Clec4a2	T	A	6: 123,100,588 (GRCm39)	N14K	probably damaging	Het
Col16a1	G	T	4: 129,984,290 (GRCm39)		probably benign	Het
Col5a1	T	C	2: 27,880,109 (GRCm39)		probably benign	Het
Col5a2	A	T	1: 45,417,642 (GRCm39)	I1311N	probably damaging	Het
Col5a3	T	C	9: 20,694,004 (GRCm39)	T1050A	probably damaging	Het
Colgalt2	A	T	1: 152,360,622 (GRCm39)	I220F	probably damaging	Het
Cpb1	A	T	3: 20,329,792 (GRCm39)	V8E	unknown	Het
Dchs1	C	T	7: 105,421,934 (GRCm39)	R162H	probably benign	Het
Dhx37	A	G	5: 125,499,295 (GRCm39)	Y638H	probably benign	Het
Dhx40	T	G	11: 86,662,088 (GRCm39)		probably benign	Het
Ehd2	T	A	7: 15,686,001 (GRCm39)	Q357L	probably benign	Het
Ewsr1	T	C	11: 5,020,737 (GRCm39)		probably benign	Het
Fcho1	C	T	8: 72,165,204 (GRCm39)	A418T	probably benign	Het
Gid8	T	A	2: 180,355,004 (GRCm39)	Y3*	probably null	Het
Gm10212	A	C	19: 11,548,174 (GRCm39)		noncoding transcript	Het
Grin3b	T	A	10: 79,809,890 (GRCm39)	N465K	possibly damaging	Het
H1f3	A	T	13: 23,739,924 (GRCm39)	K221*	probably null	Het
Htr4	A	T	18: 62,561,225 (GRCm39)	N162I	probably damaging	Het
Irag2	T	C	6: 145,110,938 (GRCm39)	C248R	probably damaging	Het
Itga3	T	C	11: 94,952,796 (GRCm39)	D325G	probably benign	Het
Itpr3	T	G	17: 27,330,903 (GRCm39)	V1737G	probably damaging	Het
Kcnab2	C	T	4: 152,479,439 (GRCm39)	V251I	probably benign	Het
Kcnn2	A	T	18: 45,693,215 (GRCm39)	I264L	probably benign	Het
Klhl41	T	C	2: 69,501,600 (GRCm39)	Y354H	probably damaging	Het
Klra6	T	C	6: 130,000,601 (GRCm39)	I68V	probably benign	Het
Letm2	G	T	8: 26,082,574 (GRCm39)	P178Q	probably damaging	Het
Lypd11	C	A	7: 24,422,170 (GRCm39)	C193F	possibly damaging	Het
Mbtps1	A	T	8: 120,249,340 (GRCm39)		probably benign	Het
Mecom	C	T	3: 30,035,121 (GRCm39)		probably benign	Het
Mrps5	T	A	2: 127,433,745 (GRCm39)	S45T	possibly damaging	Het
Msra	T	A	14: 64,678,210 (GRCm39)	I29F	possibly damaging	Het
Mup5	T	C	4: 61,751,229 (GRCm39)		probably null	Het
Myo1a	T	C	10: 127,555,111 (GRCm39)		probably benign	Het
Myrip	C	A	9: 120,270,443 (GRCm39)	N564K	probably benign	Het
Naa20	T	A	2: 145,757,592 (GRCm39)	D148E	probably damaging	Het
Naga	T	G	15: 82,220,956 (GRCm39)		probably benign	Het
Npc1	A	G	18: 12,346,503 (GRCm39)	V231A	probably benign	Het
Or8s5	T	C	15: 98,238,810 (GRCm39)	H20R	probably benign	Het
Parn	G	C	16: 13,472,299 (GRCm39)		probably benign	Het
Polk	A	T	13: 96,620,272 (GRCm39)	C664S	probably benign	Het
Prkar2b	A	G	12: 32,026,034 (GRCm39)		probably benign	Het
Prkdc	A	G	16: 15,651,604 (GRCm39)	E3747G	probably damaging	Het
Prmt5	A	T	14: 54,748,712 (GRCm39)	M362K	probably damaging	Het
Prob1	T	C	18: 35,786,878 (GRCm39)	T459A	possibly damaging	Het
Rttn	C	T	18: 89,108,543 (GRCm39)		probably benign	Het
Scn1a	T	C	2: 66,104,269 (GRCm39)	M1664V	probably damaging	Het
Sez6	T	A	11: 77,844,639 (GRCm39)	L154H	probably damaging	Het
Sh3tc1	A	G	5: 35,859,356 (GRCm39)		probably benign	Het
Shkbp1	C	T	7: 27,048,006 (GRCm39)	G334D	probably damaging	Het
Slc8a1	A	T	17: 81,955,422 (GRCm39)	F539I	probably damaging	Het
Spata31e5	G	T	1: 28,817,223 (GRCm39)	Q270K	probably damaging	Het
Sptan1	T	C	2: 29,903,860 (GRCm39)		probably benign	Het
Ssc5d	C	T	7: 4,940,470 (GRCm39)	T861M	probably damaging	Het
Tbx5	A	T	5: 120,021,523 (GRCm39)	M510L	probably benign	Het
Tdp1	A	G	12: 99,876,101 (GRCm39)	T351A	probably benign	Het
Tmc8	T	A	11: 117,682,904 (GRCm39)		probably benign	Het
Tmco5	T	A	2: 116,720,588 (GRCm39)	D205E	probably benign	Het
Tmprss2	T	C	16: 97,373,194 (GRCm39)		probably benign	Het
Top6bl	A	T	19: 4,708,442 (GRCm39)	I350N	probably damaging	Het
Tph1	T	A	7: 46,299,448 (GRCm39)	K364N	probably benign	Het
Trim24	T	C	6: 37,934,001 (GRCm39)	L648P	probably damaging	Het
Trmt6	C	A	2: 132,650,950 (GRCm39)		probably benign	Het
Ube2i	A	T	17: 25,488,259 (GRCm39)		probably benign	Het
Vcan	A	C	13: 89,852,779 (GRCm39)	L727R	possibly damaging	Het
Vmn2r28	T	C	7: 5,491,689 (GRCm39)	Y186C	probably damaging	Het
Wars1	C	A	12: 108,841,083 (GRCm39)	D232Y	probably damaging	Het
Xrcc5	T	C	1: 72,378,104 (GRCm39)		probably benign	Het
Zbtb24	T	A	10: 41,340,532 (GRCm39)	S543T	probably damaging	Het
Zfp91	A	G	19: 12,753,353 (GRCm39)		probably benign	Het

Other mutations in Nphs1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00160:Nphs1	APN	7	30,181,976 (GRCm39)	missense	possibly damaging	0.77
IGL00927:Nphs1	APN	7	30,160,164 (GRCm39)	unclassified	probably benign
IGL00976:Nphs1	APN	7	30,160,110 (GRCm39)	missense	possibly damaging	0.78
IGL01397:Nphs1	APN	7	30,186,089 (GRCm39)	missense	probably benign	0.01
IGL01465:Nphs1	APN	7	30,186,139 (GRCm39)	makesense	probably null
IGL01889:Nphs1	APN	7	30,159,936 (GRCm39)	missense	probably damaging	1.00
IGL02383:Nphs1	APN	7	30,181,060 (GRCm39)	splice site	probably benign
R0020:Nphs1	UTSW	7	30,162,633 (GRCm39)	missense	probably benign	0.01
R1024:Nphs1	UTSW	7	30,173,702 (GRCm39)	missense	probably damaging	1.00
R1115:Nphs1	UTSW	7	30,180,803 (GRCm39)	splice site	probably benign
R1144:Nphs1	UTSW	7	30,181,103 (GRCm39)	splice site	probably benign
R1289:Nphs1	UTSW	7	30,170,603 (GRCm39)	missense	probably damaging	1.00
R1317:Nphs1	UTSW	7	30,181,256 (GRCm39)	splice site	probably benign
R1617:Nphs1	UTSW	7	30,181,956 (GRCm39)	missense	probably benign
R1756:Nphs1	UTSW	7	30,160,959 (GRCm39)	missense	probably benign	0.00
R1937:Nphs1	UTSW	7	30,173,798 (GRCm39)	missense	probably damaging	1.00
R2144:Nphs1	UTSW	7	30,160,395 (GRCm39)	missense	probably benign	0.13
R2256:Nphs1	UTSW	7	30,167,417 (GRCm39)	missense	possibly damaging	0.94
R2257:Nphs1	UTSW	7	30,167,417 (GRCm39)	missense	possibly damaging	0.94
R2277:Nphs1	UTSW	7	30,166,989 (GRCm39)	nonsense	probably null
R3104:Nphs1	UTSW	7	30,166,965 (GRCm39)	nonsense	probably null
R3106:Nphs1	UTSW	7	30,166,965 (GRCm39)	nonsense	probably null
R3151:Nphs1	UTSW	7	30,159,665 (GRCm39)	missense	probably benign
R3765:Nphs1	UTSW	7	30,170,635 (GRCm39)	missense	probably damaging	0.98
R4078:Nphs1	UTSW	7	30,166,945 (GRCm39)	nonsense	probably null
R4397:Nphs1	UTSW	7	30,181,390 (GRCm39)	splice site	probably null
R4635:Nphs1	UTSW	7	30,167,432 (GRCm39)	missense	probably benign	0.39
R4650:Nphs1	UTSW	7	30,181,895 (GRCm39)	missense	probably benign	0.21
R4811:Nphs1	UTSW	7	30,159,854 (GRCm39)	missense	probably damaging	1.00
R4850:Nphs1	UTSW	7	30,162,657 (GRCm39)	missense	possibly damaging	0.78
R5272:Nphs1	UTSW	7	30,181,067 (GRCm39)	missense	possibly damaging	0.86
R5327:Nphs1	UTSW	7	30,163,250 (GRCm39)	missense	probably benign	0.00
R5681:Nphs1	UTSW	7	30,186,050 (GRCm39)	missense	probably benign	0.00
R5865:Nphs1	UTSW	7	30,173,810 (GRCm39)	missense	probably damaging	1.00
R5975:Nphs1	UTSW	7	30,165,540 (GRCm39)	missense	possibly damaging	0.82
R6186:Nphs1	UTSW	7	30,165,059 (GRCm39)	missense	probably damaging	0.98
R6198:Nphs1	UTSW	7	30,167,340 (GRCm39)	missense	probably damaging	0.97
R6353:Nphs1	UTSW	7	30,173,969 (GRCm39)	missense	probably damaging	0.99
R7405:Nphs1	UTSW	7	30,162,253 (GRCm39)	missense	possibly damaging	0.46
R7647:Nphs1	UTSW	7	30,181,390 (GRCm39)	splice site	probably null
R7767:Nphs1	UTSW	7	30,162,733 (GRCm39)	missense	probably damaging	1.00
R8132:Nphs1	UTSW	7	30,181,478 (GRCm39)	missense	probably benign	0.02
R8485:Nphs1	UTSW	7	30,165,598 (GRCm39)	missense	probably damaging	0.98
R8678:Nphs1	UTSW	7	30,163,284 (GRCm39)	missense	probably damaging	1.00
R8890:Nphs1	UTSW	7	30,162,080 (GRCm39)	missense	probably damaging	1.00
R8946:Nphs1	UTSW	7	30,162,625 (GRCm39)	missense	probably damaging	1.00
R9133:Nphs1	UTSW	7	30,160,092 (GRCm39)	nonsense	probably null
R9159:Nphs1	UTSW	7	30,165,026 (GRCm39)	missense	possibly damaging	0.93
R9347:Nphs1	UTSW	7	30,170,594 (GRCm39)	missense	probably damaging	1.00
R9547:Nphs1	UTSW	7	30,180,875 (GRCm39)	missense	probably benign	0.00
R9548:Nphs1	UTSW	7	30,180,875 (GRCm39)	missense	probably benign	0.00
R9607:Nphs1	UTSW	7	30,163,012 (GRCm39)	missense	probably damaging	1.00
R9626:Nphs1	UTSW	7	30,166,991 (GRCm39)	missense	probably benign	0.16
R9720:Nphs1	UTSW	7	30,165,499 (GRCm39)	missense	possibly damaging	0.83
R9733:Nphs1	UTSW	7	30,166,955 (GRCm39)	missense	probably damaging	1.00
X0028:Nphs1	UTSW	7	30,166,929 (GRCm39)	missense	probably null	0.01
Z1177:Nphs1	UTSW	7	30,170,328 (GRCm39)	missense	probably damaging	1.00
Z1186:Nphs1	UTSW	7	30,159,775 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTCAACTGGACCTTCCGAGGCTAC -3'
(R):5'- CGACGGTGCAGACTATATCCACAG -3'

Sequencing Primer
(F):5'- CGAGGCTACCGCCTCAG -3'
(R):5'- ACAGCTTGCCCTTTATGGAAGAG -3'

Posted On

2013-05-23