Mutagenetix > Incidental Mutation

Incidental Mutation 'R1937:Nphs1'

213544

Institutional Source

Beutler Lab

Gene Symbol

Nphs1

Ensembl Gene

ENSMUSG00000006649

Gene Name

nephrosis 1, nephrin

Synonyms

nephrin

MMRRC Submission

039955-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R1937 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

30458315-30487223 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 30474373 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Leucine at position 985 (Q985L)

Ref Sequence

ENSEMBL: ENSMUSP00000006825 (fasta)

Gene Model

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

AlphaFold

Q9QZS7

Predicted Effect

probably damaging
Transcript: ENSMUST00000006825
AA Change: Q985L

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: Q985L

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

noncoding transcript
Transcript: ENSMUST00000123880

Predicted Effect

probably damaging
Transcript: ENSMUST00000126297
AA Change: Q971L

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: Q971L

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

Predicted Effect

probably benign
Transcript: ENSMUST00000149086

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.7%
20x: 93.5%

Validation Efficiency

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: 106 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006E09Rik	A	T	11: 101,987,163	H17L	probably damaging	Het
5730480H06Rik	C	A	5: 48,374,435	T35K	probably benign	Het
Abhd14a	A	G	9: 106,440,247		probably benign	Het
Abhd8	A	G	8: 71,461,862	F41L	possibly damaging	Het
Ace2	A	T	X: 164,156,528	M123L	possibly damaging	Het
Actr5	T	C	2: 158,636,029	Y440H	possibly damaging	Het
Akr1c6	T	A	13: 4,446,384	N81K	probably benign	Het
Aqp11	T	A	7: 97,737,518	N157I	possibly damaging	Het
Arhgap10	T	C	8: 77,344,653	E568G	probably damaging	Het
Asb7	T	A	7: 66,679,253	Q13L	probably benign	Het
Atf7ip	C	A	6: 136,560,780	A345E	probably benign	Het
Atp8a2	T	C	14: 59,860,270	K770E	probably benign	Het
Bpifb4	A	T	2: 153,944,076	I259F	probably damaging	Het
Cand1	A	T	10: 119,203,020	D1218E	probably damaging	Het
Capg	A	G	6: 72,558,253		probably null	Het
Cep290	C	T	10: 100,497,953	T289M	possibly damaging	Het
Cfap69	T	C	5: 5,593,818	Y548C	probably damaging	Het
Clock	A	G	5: 76,229,493	L652P	probably damaging	Het
Col3a1	C	T	1: 45,334,293		probably benign	Het
Coro7	T	C	16: 4,628,732	E843G	probably benign	Het
Crebrf	T	C	17: 26,742,468	S188P	probably damaging	Het
Cul1	T	C	6: 47,508,355	F307L	probably benign	Het
Cyb561d2	G	A	9: 107,540,316	R79W	probably damaging	Het
Cyp3a59	T	C	5: 146,094,377	S117P	possibly damaging	Het
Ddias	A	G	7: 92,858,622	I695T	probably benign	Het
Dhx29	G	A	13: 112,965,330	G1311D	probably benign	Het
Diexf	A	T	1: 193,122,093	D200E	probably damaging	Het
Dync2h1	A	G	9: 7,139,159		probably null	Het
Ece2	T	A	16: 20,617,866	V146E	probably damaging	Het
Eml2	A	G	7: 19,203,964	K586E	possibly damaging	Het
Eps8l3	A	G	3: 107,884,392	E316G	probably benign	Het
Fam135b	A	T	15: 71,622,014	L22H	probably damaging	Het
Fam166b	T	A	4: 43,427,586	K220N	probably damaging	Het
Focad	T	A	4: 88,401,081	M1K	probably null	Het
Fryl	A	G	5: 73,133,367	S65P	probably damaging	Het
Gm14190	C	T	11: 99,690,730	C4Y	unknown	Het
Gm8909	T	A	17: 36,168,007	T117S	probably damaging	Het
Ift74	T	A	4: 94,662,646	M345K	probably benign	Het
Ispd	G	A	12: 36,390,368	V92I	probably benign	Het
Jag1	C	G	2: 137,083,473	V1070L	possibly damaging	Het
Kcng1	T	C	2: 168,263,021	T302A	probably benign	Het
Kif20b	T	C	19: 34,952,878	V1221A	possibly damaging	Het
Kif23	A	T	9: 61,946,610		probably null	Het
Lpxn	T	G	19: 12,824,910	S200A	probably benign	Het
Meiob	A	G	17: 24,818,331	H61R	probably benign	Het
Mfhas1	C	T	8: 35,589,645	L425F	probably damaging	Het
Myo3a	A	T	2: 22,396,315	S632C	probably damaging	Het
Naip2	T	C	13: 100,161,854	E558G	probably benign	Het
Naip2	C	T	13: 100,161,860	G556D	probably benign	Het
Nbeal1	T	A	1: 60,267,941	Y374*	probably null	Het
Notch3	T	C	17: 32,153,852	S582G	probably benign	Het
Oas1c	T	A	5: 120,802,984	H248L	probably benign	Het
Olfr154	T	C	2: 85,663,997	I146V	probably benign	Het
Olfr193	A	T	16: 59,109,794	M272K	probably benign	Het
Olfr368	A	T	2: 37,331,884	N46Y	probably damaging	Het
Olfr955	A	G	9: 39,470,037	S230P	possibly damaging	Het
Pamr1	A	T	2: 102,642,272	I639F	possibly damaging	Het
Panx1	G	T	9: 15,007,684	T293K	possibly damaging	Het
Papss1	G	T	3: 131,599,871	V226F	probably benign	Het
Pax1	G	T	2: 147,367,889	G301V	possibly damaging	Het
Pdlim5	C	A	3: 142,244,981	R557L	possibly damaging	Het
Pdyn	C	A	2: 129,689,809	M20I	probably benign	Het
Pelp1	G	A	11: 70,393,715		probably null	Het
Pkd2	T	C	5: 104,478,924	V324A	probably damaging	Het
Pkdrej	A	G	15: 85,819,167	I856T	probably benign	Het
Polr1a	T	C	6: 71,936,552		probably null	Het
Pot1a	A	T	6: 25,753,324	D404E	probably benign	Het
Ppp2r2a	A	T	14: 67,016,429	I430N	possibly damaging	Het
Prob1	C	T	18: 35,654,226	R325Q	possibly damaging	Het
Prrc2a	T	C	17: 35,157,908	D742G	probably damaging	Het
Psmc1	C	T	12: 100,114,843	P54S	probably benign	Het
Rab22a	A	G	2: 173,688,211	T61A	probably damaging	Het
Rims1	T	A	1: 22,288,530	K184N	probably damaging	Het
Rnf213	G	A	11: 119,431,685	R1376H	probably damaging	Het
Ryr2	T	C	13: 11,668,962	E3072G	probably damaging	Het
Serpina1b	T	C	12: 103,732,161	K143R	probably benign	Het
Slc22a15	T	G	3: 101,880,189		probably null	Het
Slc25a14	G	A	X: 48,651,963	V210I	probably benign	Het
Slc25a48	A	C	13: 56,448,998	T31P	probably damaging	Het
Slc9a3	C	T	13: 74,166,056		probably null	Het
Slx4	T	C	16: 3,987,166	*105W	probably null	Het
Smc6	A	G	12: 11,299,398	N794S	probably benign	Het
Spata18	G	A	5: 73,676,964	R387Q	probably damaging	Het
Sphkap	C	A	1: 83,267,441	E1486*	probably null	Het
Srsf6	C	T	2: 162,934,483		probably benign	Het
St8sia1	C	T	6: 142,963,672	A33T	probably damaging	Het
Tet2	T	C	3: 133,488,638	T12A	possibly damaging	Het
Tmem144	G	T	3: 79,825,304	S222R	probably damaging	Het
Tnrc6c	A	G	11: 117,756,023	D1450G	possibly damaging	Het
Top1	A	T	2: 160,670,122	K27N	unknown	Het
Tox2	A	G	2: 163,225,556	H30R	probably benign	Het
Tra2b	T	C	16: 22,247,243		probably benign	Het
Trio	A	T	15: 27,833,056	V1165E	probably damaging	Het
Troap	T	A	15: 99,077,388	S145R	probably damaging	Het
Ttc34	G	A	4: 154,865,682	A1031T	possibly damaging	Het
Ttc6	C	T	12: 57,616,323	P302S	probably benign	Het
Ubiad1	A	G	4: 148,444,011	L147P	probably damaging	Het
Ugt2b35	G	T	5: 87,001,282	V131F	probably damaging	Het
Vmn1r167	G	A	7: 23,505,027	T188I	probably benign	Het
Vmn1r46	G	T	6: 89,976,734	M188I	probably benign	Het
Vmn2r115	T	A	17: 23,359,414	N620K	probably damaging	Het
Vmn2r66	A	G	7: 84,995,136	S689P	probably damaging	Het
Wipf2	C	T	11: 98,892,410	R221*	probably null	Het
Zbtb16	T	C	9: 48,659,778	S563G	probably benign	Het
Zfp319	T	C	8: 95,328,571	T335A	probably damaging	Het
Zfp418	A	G	7: 7,182,402	R455G	possibly damaging	Het

Other mutations in Nphs1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00160:Nphs1	APN	7	30482551	missense	possibly damaging	0.77
IGL00927:Nphs1	APN	7	30460739	unclassified	probably benign
IGL00976:Nphs1	APN	7	30460685	missense	possibly damaging	0.78
IGL01397:Nphs1	APN	7	30486664	missense	probably benign	0.01
IGL01465:Nphs1	APN	7	30486714	makesense	probably null
IGL01889:Nphs1	APN	7	30460511	missense	probably damaging	1.00
IGL02383:Nphs1	APN	7	30481635	splice site	probably benign
R0020:Nphs1	UTSW	7	30463208	missense	probably benign	0.01
R0485:Nphs1	UTSW	7	30467515	missense	probably benign
R1024:Nphs1	UTSW	7	30474277	missense	probably damaging	1.00
R1115:Nphs1	UTSW	7	30481378	splice site	probably benign
R1144:Nphs1	UTSW	7	30481678	splice site	probably benign
R1289:Nphs1	UTSW	7	30471178	missense	probably damaging	1.00
R1317:Nphs1	UTSW	7	30481831	splice site	probably benign
R1617:Nphs1	UTSW	7	30482531	missense	probably benign
R1756:Nphs1	UTSW	7	30461534	missense	probably benign	0.00
R2144:Nphs1	UTSW	7	30460970	missense	probably benign	0.13
R2256:Nphs1	UTSW	7	30467992	missense	possibly damaging	0.94
R2257:Nphs1	UTSW	7	30467992	missense	possibly damaging	0.94
R2277:Nphs1	UTSW	7	30467564	nonsense	probably null
R3104:Nphs1	UTSW	7	30467540	nonsense	probably null
R3106:Nphs1	UTSW	7	30467540	nonsense	probably null
R3151:Nphs1	UTSW	7	30460240	missense	probably benign
R3765:Nphs1	UTSW	7	30471210	missense	probably damaging	0.98
R4078:Nphs1	UTSW	7	30467520	nonsense	probably null
R4397:Nphs1	UTSW	7	30481965	splice site	probably null
R4635:Nphs1	UTSW	7	30468007	missense	probably benign	0.39
R4650:Nphs1	UTSW	7	30482470	missense	probably benign	0.21
R4811:Nphs1	UTSW	7	30460429	missense	probably damaging	1.00
R4850:Nphs1	UTSW	7	30463232	missense	possibly damaging	0.78
R5272:Nphs1	UTSW	7	30481642	missense	possibly damaging	0.86
R5327:Nphs1	UTSW	7	30463825	missense	probably benign	0.00
R5681:Nphs1	UTSW	7	30486625	missense	probably benign	0.00
R5865:Nphs1	UTSW	7	30474385	missense	probably damaging	1.00
R5975:Nphs1	UTSW	7	30466115	missense	possibly damaging	0.82
R6186:Nphs1	UTSW	7	30465634	missense	probably damaging	0.98
R6198:Nphs1	UTSW	7	30467915	missense	probably damaging	0.97
R6353:Nphs1	UTSW	7	30474544	missense	probably damaging	0.99
R7405:Nphs1	UTSW	7	30462828	missense	possibly damaging	0.46
R7647:Nphs1	UTSW	7	30481965	splice site	probably null
R7767:Nphs1	UTSW	7	30463308	missense	probably damaging	1.00
R8132:Nphs1	UTSW	7	30482053	missense	probably benign	0.02
R8485:Nphs1	UTSW	7	30466173	missense	probably damaging	0.98
R8678:Nphs1	UTSW	7	30463859	missense	probably damaging	1.00
R8890:Nphs1	UTSW	7	30462655	missense	probably damaging	1.00
R8946:Nphs1	UTSW	7	30463200	missense	probably damaging	1.00
R9133:Nphs1	UTSW	7	30460667	nonsense	probably null
R9159:Nphs1	UTSW	7	30465601	missense	possibly damaging	0.93
R9347:Nphs1	UTSW	7	30471169	missense	probably damaging	1.00
R9547:Nphs1	UTSW	7	30481450	missense	probably benign	0.00
R9548:Nphs1	UTSW	7	30481450	missense	probably benign	0.00
X0028:Nphs1	UTSW	7	30467504	missense	probably null	0.01
Z1177:Nphs1	UTSW	7	30470903	missense	probably damaging	1.00
Z1186:Nphs1	UTSW	7	30460350	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGAACTCATTGAGCACAGCC -3'
(R):5'- CTTCAGCCCAGTCAGTGTGAAG -3'

Sequencing Primer
(F):5'- GAGAACCAACCACTGTTCTCAGGAG -3'
(R):5'- CCAGTCAGTGTGAAGGTGGTG -3'

Posted On

2014-07-14