Mutagenetix > Incidental Mutation

Incidental Mutation 'R2256:Nphs1'

243370

Institutional Source

Beutler Lab

Gene Symbol

Nphs1

Ensembl Gene

ENSMUSG00000006649

Gene Name

nephrosis 1, nephrin

Synonyms

nephrin

MMRRC Submission

040256-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2256 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

30458315-30487223 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 30467992 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 782 (I782F)

Ref Sequence

ENSEMBL: ENSMUSP00000006825 (fasta)

Gene Model

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

AlphaFold

Q9QZS7

Predicted Effect

possibly damaging
Transcript: ENSMUST00000006825
AA Change: I782F

PolyPhen 2 Score 0.940 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: I782F

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

possibly damaging
Transcript: ENSMUST00000126297
AA Change: I768F

PolyPhen 2 Score 0.927 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: I768F

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152625

Meta Mutation Damage Score

0.2908

Coding Region Coverage

1x: 99.3%
3x: 98.8%
10x: 97.7%
20x: 96.3%

Validation Efficiency

98% (97/99)

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: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb4	T	C	5: 8,958,431 (GRCm38)	S1200P	probably damaging	Het
Acadsb	A	G	7: 131,443,653 (GRCm38)	Y438C	probably benign	Het
Acp7	A	C	7: 28,614,413 (GRCm38)	W399G	probably damaging	Het
Actr3b	A	G	5: 25,822,405 (GRCm38)	T113A	possibly damaging	Het
Adgrv1	T	C	13: 81,506,140 (GRCm38)	D2204G	probably benign	Het
Ago1	A	G	4: 126,441,911 (GRCm38)	V669A	possibly damaging	Het
Ang5	T	A	14: 43,962,521 (GRCm38)	L14Q	probably null	Het
Aoc1	T	C	6: 48,906,440 (GRCm38)	Y417H	possibly damaging	Het
Arhgap32	T	C	9: 32,247,497 (GRCm38)	I186T	probably damaging	Het
Atf2	A	T	2: 73,845,511 (GRCm38)		probably null	Het
Atg4a	A	G	X: 140,990,235 (GRCm38)	I91V	probably benign	Het
Atp7b	T	G	8: 21,998,266 (GRCm38)	T1102P	probably damaging	Het
Bend5	A	C	4: 111,431,010 (GRCm38)		probably benign	Het
Camkk2	T	C	5: 122,746,335 (GRCm38)	D341G	probably damaging	Het
Cast	T	A	13: 74,739,905 (GRCm38)	I208L	probably damaging	Het
Ccdc141	A	T	2: 77,132,262 (GRCm38)	W113R	probably damaging	Het
Cdk14	T	A	5: 4,888,924 (GRCm38)	M433L	probably benign	Het
Cel	A	G	2: 28,561,192 (GRCm38)	F51S	probably damaging	Het
Cenpc1	A	G	5: 86,016,203 (GRCm38)	L853S	probably damaging	Het
Cep162	C	A	9: 87,206,914 (GRCm38)	D972Y	probably damaging	Het
Cimip3	AC	A	17: 47,433,423 (GRCm38)		probably benign	Het
Clasrp	A	G	7: 19,586,585 (GRCm38)		probably benign	Het
Cntnap5c	T	A	17: 58,330,315 (GRCm38)	N1062K	probably benign	Het
Col3a1	A	G	1: 45,321,632 (GRCm38)	D74G	unknown	Het
Copb1	T	A	7: 114,253,875 (GRCm38)	D29V	possibly damaging	Het
Cox6a1	C	T	5: 115,348,848 (GRCm38)	E35K	possibly damaging	Het
Cyp2b9	G	A	7: 26,173,605 (GRCm38)		probably null	Het
Ddx46	A	G	13: 55,647,708 (GRCm38)	K177E	possibly damaging	Het
Dmbt1	T	C	7: 131,090,494 (GRCm38)	F823L	probably benign	Het
Drc7	A	T	8: 95,075,009 (GRCm38)	H666L	probably benign	Het
Fam228a	T	C	12: 4,737,775 (GRCm38)		probably benign	Het
Fam83e	A	T	7: 45,728,770 (GRCm38)	K406M	possibly damaging	Het
Fam83e	A	T	7: 45,728,769 (GRCm38)	K406*	probably null	Het
Fam90a1a	T	A	8: 21,963,517 (GRCm38)	L296Q	possibly damaging	Het
Fat1	A	G	8: 44,950,371 (GRCm38)	Y53C	probably damaging	Het
Fhdc1	T	C	3: 84,446,046 (GRCm38)	E624G	probably benign	Het
Fryl	T	A	5: 73,072,844 (GRCm38)	N1657Y	possibly damaging	Het
Fsip2	T	A	2: 82,962,751 (GRCm38)	D417E	probably benign	Het
Garin5b	T	A	7: 4,771,021 (GRCm38)	M31L	probably benign	Het
Greb1l	A	G	18: 10,503,307 (GRCm38)	M453V	possibly damaging	Het
Gtf2b	A	G	3: 142,781,424 (GRCm38)	D207G	probably benign	Het
Has3	C	A	8: 106,874,256 (GRCm38)	L117I	probably damaging	Het
Iqca1l	C	T	5: 24,552,040 (GRCm38)		probably benign	Het
Jmjd1c	T	A	10: 67,225,294 (GRCm38)	I1142N	probably damaging	Het
Lipt2	C	T	7: 100,159,394 (GRCm38)	T38I	probably benign	Het
Magea2	A	T	X: 155,027,859 (GRCm38)	L243Q	probably damaging	Het
Mast4	A	T	13: 102,735,751 (GRCm38)	C2178S	possibly damaging	Het
Mctp2	A	G	7: 72,185,820 (GRCm38)	L543P	probably damaging	Het
Mmut	A	T	17: 40,956,319 (GRCm38)	I595F	probably benign	Het
Mphosph9	C	T	5: 124,283,659 (GRCm38)	V740I	probably benign	Het
Mtrex	A	T	13: 112,876,512 (GRCm38)	M890K	probably damaging	Het
Myo1e	G	A	9: 70,378,373 (GRCm38)		probably null	Het
Nlrc4	A	G	17: 74,445,630 (GRCm38)	I586T	probably damaging	Het
Nom1	T	A	5: 29,437,752 (GRCm38)	V417D	probably damaging	Het
Numa1	A	G	7: 102,000,791 (GRCm38)	E1243G	probably damaging	Het
Or4a81	T	C	2: 89,788,470 (GRCm38)	H294R	probably benign	Het
Or4k42	T	C	2: 111,489,978 (GRCm38)	Y60C	probably damaging	Het
Or52e7	A	G	7: 105,035,819 (GRCm38)	Y207C	probably benign	Het
Or5g23	T	A	2: 85,608,463 (GRCm38)	Y149F	possibly damaging	Het
Or5p54	A	T	7: 107,955,037 (GRCm38)	Y132F	probably damaging	Het
Orai2	C	T	5: 136,161,600 (GRCm38)	V52I	probably damaging	Het
Osbpl5	A	G	7: 143,709,094 (GRCm38)	C186R	probably damaging	Het
Osbpl6	A	G	2: 76,584,474 (GRCm38)	E403G	probably damaging	Het
Padi4	G	A	4: 140,759,940 (GRCm38)	T217I	possibly damaging	Het
Parm1	C	T	5: 91,594,121 (GRCm38)	T116I	possibly damaging	Het
Pde4dip	T	A	3: 97,718,184 (GRCm38)	Q1366L	probably damaging	Het
Phgdh	T	C	3: 98,328,291 (GRCm38)	K108E	probably benign	Het
Pold1	T	C	7: 44,533,799 (GRCm38)		probably null	Het
Ppp1r37	G	T	7: 19,562,018 (GRCm38)		probably benign	Het
Sdk2	T	C	11: 113,830,794 (GRCm38)	N1332S	probably benign	Het
Sema6d	A	G	2: 124,664,150 (GRCm38)	D626G	probably damaging	Het
Slc18b1	A	G	10: 23,810,922 (GRCm38)	N212S	probably benign	Het
Slc2a9	T	C	5: 38,453,199 (GRCm38)	T86A	probably damaging	Het
Slco1a6	A	T	6: 142,091,016 (GRCm38)	M555K	probably benign	Het
Sntg2	C	T	12: 30,236,688 (GRCm38)	W302*	probably null	Het
Spata22	T	A	11: 73,340,475 (GRCm38)	M185K	possibly damaging	Het
Stk35	T	A	2: 129,810,507 (GRCm38)	Y309*	probably null	Het
Taar8c	A	G	10: 24,101,071 (GRCm38)	V281A	probably benign	Het
Thoc1	C	A	18: 9,993,466 (GRCm38)	D608E	possibly damaging	Het
Tmem121b	A	T	6: 120,492,069 (GRCm38)	Y562*	probably null	Het
Tmem121b	A	G	6: 120,492,071 (GRCm38)	Y562H	probably damaging	Het
Tmtc4	A	T	14: 122,941,408 (GRCm38)	I449N	probably benign	Het
Tmub1	G	A	5: 24,447,177 (GRCm38)		probably benign	Het
Tmub1	C	A	5: 24,446,924 (GRCm38)	G14V	possibly damaging	Het
Tshz2	A	G	2: 169,886,477 (GRCm38)	T529A	probably damaging	Het
Ugdh	A	T	5: 65,417,115 (GRCm38)		probably benign	Het
Usp25	A	G	16: 77,113,794 (GRCm38)	K913E	probably benign	Het
Vgf	A	G	5: 137,031,547 (GRCm38)		probably benign	Het
Vmn2r19	T	A	6: 123,329,886 (GRCm38)	F451Y	probably benign	Het
Vmn2r59	A	T	7: 42,012,245 (GRCm38)	C715*	probably null	Het
Vps9d1	C	A	8: 123,245,121 (GRCm38)	A582S	probably benign	Het
Xbp1	T	G	11: 5,524,841 (GRCm38)	H247Q	probably damaging	Het
Zfp1008	A	T	13: 62,607,396 (GRCm38)	I36N	probably benign	Het
Zfp319	A	T	8: 95,328,501 (GRCm38)	M358K	possibly damaging	Het
Zfp438	A	T	18: 5,213,508 (GRCm38)	N483K	probably damaging	Het
Zfp518b	T	C	5: 38,671,636 (GRCm38)	N1009D	possibly damaging	Het
Zfp644	A	T	5: 106,635,845 (GRCm38)	H945Q	probably damaging	Het
Zgrf1	T	A	3: 127,561,997 (GRCm38)	S291T	probably benign	Het

Other mutations in Nphs1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00160:Nphs1	APN	7	30,482,551 (GRCm38)	missense	possibly damaging	0.77
IGL00927:Nphs1	APN	7	30,460,739 (GRCm38)	unclassified	probably benign
IGL00976:Nphs1	APN	7	30,460,685 (GRCm38)	missense	possibly damaging	0.78
IGL01397:Nphs1	APN	7	30,486,664 (GRCm38)	missense	probably benign	0.01
IGL01465:Nphs1	APN	7	30,486,714 (GRCm38)	makesense	probably null
IGL01889:Nphs1	APN	7	30,460,511 (GRCm38)	missense	probably damaging	1.00
IGL02383:Nphs1	APN	7	30,481,635 (GRCm38)	splice site	probably benign
R0020:Nphs1	UTSW	7	30,463,208 (GRCm38)	missense	probably benign	0.01
R0485:Nphs1	UTSW	7	30,467,515 (GRCm38)	missense	probably benign
R1024:Nphs1	UTSW	7	30,474,277 (GRCm38)	missense	probably damaging	1.00
R1115:Nphs1	UTSW	7	30,481,378 (GRCm38)	splice site	probably benign
R1144:Nphs1	UTSW	7	30,481,678 (GRCm38)	splice site	probably benign
R1289:Nphs1	UTSW	7	30,471,178 (GRCm38)	missense	probably damaging	1.00
R1317:Nphs1	UTSW	7	30,481,831 (GRCm38)	splice site	probably benign
R1617:Nphs1	UTSW	7	30,482,531 (GRCm38)	missense	probably benign
R1756:Nphs1	UTSW	7	30,461,534 (GRCm38)	missense	probably benign	0.00
R1937:Nphs1	UTSW	7	30,474,373 (GRCm38)	missense	probably damaging	1.00
R2144:Nphs1	UTSW	7	30,460,970 (GRCm38)	missense	probably benign	0.13
R2257:Nphs1	UTSW	7	30,467,992 (GRCm38)	missense	possibly damaging	0.94
R2277:Nphs1	UTSW	7	30,467,564 (GRCm38)	nonsense	probably null
R3104:Nphs1	UTSW	7	30,467,540 (GRCm38)	nonsense	probably null
R3106:Nphs1	UTSW	7	30,467,540 (GRCm38)	nonsense	probably null
R3151:Nphs1	UTSW	7	30,460,240 (GRCm38)	missense	probably benign
R3765:Nphs1	UTSW	7	30,471,210 (GRCm38)	missense	probably damaging	0.98
R4078:Nphs1	UTSW	7	30,467,520 (GRCm38)	nonsense	probably null
R4397:Nphs1	UTSW	7	30,481,965 (GRCm38)	splice site	probably null
R4635:Nphs1	UTSW	7	30,468,007 (GRCm38)	missense	probably benign	0.39
R4650:Nphs1	UTSW	7	30,482,470 (GRCm38)	missense	probably benign	0.21
R4811:Nphs1	UTSW	7	30,460,429 (GRCm38)	missense	probably damaging	1.00
R4850:Nphs1	UTSW	7	30,463,232 (GRCm38)	missense	possibly damaging	0.78
R5272:Nphs1	UTSW	7	30,481,642 (GRCm38)	missense	possibly damaging	0.86
R5327:Nphs1	UTSW	7	30,463,825 (GRCm38)	missense	probably benign	0.00
R5681:Nphs1	UTSW	7	30,486,625 (GRCm38)	missense	probably benign	0.00
R5865:Nphs1	UTSW	7	30,474,385 (GRCm38)	missense	probably damaging	1.00
R5975:Nphs1	UTSW	7	30,466,115 (GRCm38)	missense	possibly damaging	0.82
R6186:Nphs1	UTSW	7	30,465,634 (GRCm38)	missense	probably damaging	0.98
R6198:Nphs1	UTSW	7	30,467,915 (GRCm38)	missense	probably damaging	0.97
R6353:Nphs1	UTSW	7	30,474,544 (GRCm38)	missense	probably damaging	0.99
R7405:Nphs1	UTSW	7	30,462,828 (GRCm38)	missense	possibly damaging	0.46
R7647:Nphs1	UTSW	7	30,481,965 (GRCm38)	splice site	probably null
R7767:Nphs1	UTSW	7	30,463,308 (GRCm38)	missense	probably damaging	1.00
R8132:Nphs1	UTSW	7	30,482,053 (GRCm38)	missense	probably benign	0.02
R8485:Nphs1	UTSW	7	30,466,173 (GRCm38)	missense	probably damaging	0.98
R8678:Nphs1	UTSW	7	30,463,859 (GRCm38)	missense	probably damaging	1.00
R8890:Nphs1	UTSW	7	30,462,655 (GRCm38)	missense	probably damaging	1.00
R8946:Nphs1	UTSW	7	30,463,200 (GRCm38)	missense	probably damaging	1.00
R9133:Nphs1	UTSW	7	30,460,667 (GRCm38)	nonsense	probably null
R9159:Nphs1	UTSW	7	30,465,601 (GRCm38)	missense	possibly damaging	0.93
R9347:Nphs1	UTSW	7	30,471,169 (GRCm38)	missense	probably damaging	1.00
R9547:Nphs1	UTSW	7	30,481,450 (GRCm38)	missense	probably benign	0.00
R9548:Nphs1	UTSW	7	30,481,450 (GRCm38)	missense	probably benign	0.00
R9607:Nphs1	UTSW	7	30,463,587 (GRCm38)	missense	probably damaging	1.00
R9626:Nphs1	UTSW	7	30,467,566 (GRCm38)	missense	probably benign	0.16
R9720:Nphs1	UTSW	7	30,466,074 (GRCm38)	missense	possibly damaging	0.83
R9733:Nphs1	UTSW	7	30,467,530 (GRCm38)	missense	probably damaging	1.00
X0028:Nphs1	UTSW	7	30,467,504 (GRCm38)	missense	probably null	0.01
Z1177:Nphs1	UTSW	7	30,470,903 (GRCm38)	missense	probably damaging	1.00
Z1186:Nphs1	UTSW	7	30,460,350 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATCACAGAGGCACAACGATG -3'
(R):5'- TCAGTTCCCAGAAGATACCCTG -3'

Sequencing Primer
(F):5'- TCTCTTCCATAAAGGGCAAGCTG -3'
(R):5'- TGACCTGTACAGTCACACATGG -3'

Posted On

2014-10-16