Mutagenetix > Incidental Mutation

Incidental Mutation 'R2144:Nphs1'

236624

Institutional Source

Beutler Lab

Gene Symbol

Nphs1

Ensembl Gene

ENSMUSG00000006649

Gene Name

nephrosis 1, nephrin

Synonyms

nephrin

MMRRC Submission

040147-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2144 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

30157740-30186648 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 30160395 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 169 (E169G)

Ref Sequence

ENSEMBL: ENSMUSP00000006825 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006825] [ENSMUST00000045817] [ENSMUST00000126297]

AlphaFold

Q9QZS7

Predicted Effect

probably benign
Transcript: ENSMUST00000006825
AA Change: E169G

PolyPhen 2 Score 0.131 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: E169G

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: ENSMUST00000045817

SMART Domains

Protein: ENSMUSP00000039395
Gene: ENSMUSG00000036915

Domain	Start	End	E-Value	Type
IG	27	117	9.18e-12	SMART
IG	128	219	5.13e-1	SMART
IG_like	230	306	8.06e0	SMART
IGc2	321	379	3.06e-8	SMART
IG_like	401	500	4.65e1	SMART
transmembrane domain	509	531	N/A	INTRINSIC
low complexity region	547	565	N/A	INTRINSIC
low complexity region	607	629	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000117923

Predicted Effect

probably benign
Transcript: ENSMUST00000126297
AA Change: E155G

PolyPhen 2 Score 0.108 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: E155G

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140565

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152625

Predicted Effect

probably benign
Transcript: ENSMUST00000169893

SMART Domains

Protein: ENSMUSP00000131161
Gene: ENSMUSG00000036915

Domain	Start	End	E-Value	Type
IG	27	117	9.18e-12	SMART
IG_like	118	189	5.91e-1	SMART
IG_like	211	287	8.06e0	SMART
IGc2	302	360	3.06e-8	SMART
IG_like	382	481	4.65e1	SMART
transmembrane domain	490	512	N/A	INTRINSIC
low complexity region	528	546	N/A	INTRINSIC
low complexity region	588	610	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.1%

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: 117 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930553M12Rik	T	A	4: 88,786,412 (GRCm39)	T69S	unknown	Het
4930553M12Rik	G	A	4: 88,786,411 (GRCm39)	T69I	unknown	Het
Acsl6	A	T	11: 54,232,604 (GRCm39)	Q485L	probably damaging	Het
Adam5	C	A	8: 25,305,496 (GRCm39)	V81F	probably benign	Het
Aoc1l1	A	G	6: 48,952,225 (GRCm39)	H50R	probably benign	Het
Bag2	A	G	1: 33,785,912 (GRCm39)	S137P	possibly damaging	Het
Birc6	A	T	17: 74,967,408 (GRCm39)	Q4103L	possibly damaging	Het
Camta2	A	G	11: 70,562,401 (GRCm39)	F999L	probably benign	Het
Cap2	A	T	13: 46,713,978 (GRCm39)		probably null	Het
Ccnk	T	A	12: 108,155,349 (GRCm39)	L102Q	probably null	Het
Cd52	T	C	4: 133,821,048 (GRCm39)		probably benign	Het
Cdc123	A	T	2: 5,815,617 (GRCm39)	I160K	probably benign	Het
Cep85l	T	C	10: 53,234,222 (GRCm39)	N52S	probably benign	Het
Cntnap5a	C	T	1: 116,029,440 (GRCm39)	T298I	probably benign	Het
Cpsf4	G	T	5: 145,115,572 (GRCm39)	S192I	probably benign	Het
Cpxm1	A	G	2: 130,239,330 (GRCm39)	S33P	probably benign	Het
Cyp2a12	A	T	7: 26,734,194 (GRCm39)	T376S	possibly damaging	Het
Cyp3a16	A	G	5: 145,392,894 (GRCm39)	F137S	probably damaging	Het
Des	A	G	1: 75,343,448 (GRCm39)	T444A	probably benign	Het
Dgcr8	C	T	16: 18,102,120 (GRCm39)	G54D	probably damaging	Het
Dmac2l	A	G	12: 69,787,828 (GRCm39)	Q88R	probably damaging	Het
Dsc3	A	G	18: 20,113,743 (GRCm39)	F393S	possibly damaging	Het
Dstyk	T	A	1: 132,391,113 (GRCm39)	M838K	probably damaging	Het
Dvl1	G	A	4: 155,932,273 (GRCm39)	V28I	possibly damaging	Het
Eml5	A	C	12: 98,776,864 (GRCm39)	F1417C	probably damaging	Het
Ep400	A	T	5: 110,851,384 (GRCm39)	M1366K	unknown	Het
Epg5	G	T	18: 77,997,412 (GRCm39)	C425F	possibly damaging	Het
Epha3	C	G	16: 63,593,680 (GRCm39)	R136P	possibly damaging	Het
Extl1	C	A	4: 134,098,355 (GRCm39)	E225D	probably benign	Het
Fam186b	A	G	15: 99,178,538 (GRCm39)	Y263H	probably benign	Het
Fbn2	A	G	18: 58,186,065 (GRCm39)	V1761A	possibly damaging	Het
Fer1l6	T	A	15: 58,499,383 (GRCm39)	M1251K	probably benign	Het
Gart	A	T	16: 91,426,969 (GRCm39)	I555N	probably damaging	Het
Gm11596	A	T	11: 99,683,789 (GRCm39)	C110*	probably null	Het
Gnptab	C	T	10: 88,264,368 (GRCm39)	S262L	possibly damaging	Het
Gpr21	T	C	2: 37,408,243 (GRCm39)	V263A	probably benign	Het
Gxylt1	T	C	15: 93,152,361 (GRCm39)	I224V	probably benign	Het
H2-Aa	A	G	17: 34,502,801 (GRCm39)	S122P	probably damaging	Het
Hsph1	A	C	5: 149,553,802 (GRCm39)		probably null	Het
Hunk	G	A	16: 90,229,420 (GRCm39)	D94N	probably damaging	Het
Ikbke	C	A	1: 131,201,211 (GRCm39)	V176L	probably damaging	Het
Inpp5k	A	T	11: 75,538,017 (GRCm39)		probably null	Het
Ints10	A	G	8: 69,249,457 (GRCm39)	T96A	probably damaging	Het
Kansl2	A	T	15: 98,424,512 (GRCm39)	V306E	probably benign	Het
Kif20a	A	G	18: 34,758,657 (GRCm39)	D42G	possibly damaging	Het
Klhl7	A	T	5: 24,305,861 (GRCm39)	M37L	probably benign	Het
Krtap1-5	T	C	11: 99,471,644 (GRCm39)	I50V	probably benign	Het
Ktn1	A	G	14: 47,952,109 (GRCm39)	E983G	probably damaging	Het
Lrrk1	G	A	7: 65,945,911 (GRCm39)	S566L	probably damaging	Het
M6pr	A	G	6: 122,292,326 (GRCm39)	M174V	probably benign	Het
Man2a2	A	G	7: 80,013,264 (GRCm39)	S510P	probably damaging	Het
Mmrn1	G	A	6: 60,922,059 (GRCm39)	S172N	possibly damaging	Het
Mpv17	A	G	5: 31,311,533 (GRCm39)		probably null	Het
Mrgpra9	T	C	7: 46,885,211 (GRCm39)	E152G	probably benign	Het
Mst1r	T	C	9: 107,790,367 (GRCm39)	V660A	probably benign	Het
Myof	A	G	19: 37,969,669 (GRCm39)		probably null	Het
Myrf	G	A	19: 10,206,038 (GRCm39)	P126L	probably benign	Het
Nckap1l	C	T	15: 103,384,103 (GRCm39)	A567V	probably damaging	Het
Npy1r	T	A	8: 67,157,836 (GRCm39)	V382D	probably benign	Het
Nrl	A	T	14: 55,758,307 (GRCm39)	M140K	possibly damaging	Het
Odad2	C	T	18: 7,127,229 (GRCm39)	E995K	probably damaging	Het
Or14c39	T	A	7: 86,344,488 (GRCm39)	F275I	probably damaging	Het
Or2ag1b	A	T	7: 106,288,164 (GRCm39)	M258K	probably damaging	Het
Or4f56	A	G	2: 111,703,768 (GRCm39)	I144T	probably damaging	Het
Or5ac17	C	T	16: 59,036,389 (GRCm39)	V196M	probably benign	Het
Or8d2	C	T	9: 38,759,635 (GRCm39)	T75I	probably damaging	Het
Orc5	T	A	5: 22,752,925 (GRCm39)	L36F	possibly damaging	Het
Osbpl1a	A	T	18: 13,004,230 (GRCm39)	S396T	probably benign	Het
Pappa	T	A	4: 65,099,186 (GRCm39)	Y568*	probably null	Het
Pask	C	T	1: 93,249,019 (GRCm39)	A794T	probably benign	Het
Pclo	C	T	5: 14,908,766 (GRCm39)	L5025F	unknown	Het
Pde3a	T	C	6: 141,435,837 (GRCm39)	V924A	probably benign	Het
Pdpr	A	G	8: 111,844,668 (GRCm39)	N355S	probably damaging	Het
Pepd	A	T	7: 34,620,843 (GRCm39)	K36M	probably benign	Het
Pet100	T	G	8: 3,672,355 (GRCm39)	L14R	probably damaging	Het
Pfkfb2	T	C	1: 130,626,460 (GRCm39)	T438A	probably benign	Het
Pik3r6	T	A	11: 68,434,437 (GRCm39)	L546*	probably null	Het
Pira2	A	T	7: 3,847,344 (GRCm39)	L115Q	probably damaging	Het
Plxdc1	T	C	11: 97,824,838 (GRCm39)	Y339C	probably damaging	Het
Primpol	A	T	8: 47,039,378 (GRCm39)	M414K	probably damaging	Het
Prol1	A	T	5: 88,476,254 (GRCm39)	T215S	unknown	Het
Prss22	A	G	17: 24,213,656 (GRCm39)	Y212H	probably damaging	Het
Ralgapa2	C	A	2: 146,230,524 (GRCm39)	V1014L	probably damaging	Het
Rap1gap2	G	A	11: 74,316,802 (GRCm39)	T245M	probably damaging	Het
Rbm26	T	A	14: 105,352,638 (GRCm39)	R1009*	probably null	Het
Rbm42	A	G	7: 30,340,535 (GRCm39)	*450Q	probably null	Het
Rere	T	C	4: 150,701,388 (GRCm39)	V1256A	probably damaging	Het
Rmi1	G	T	13: 58,555,797 (GRCm39)	L15F	probably damaging	Het
Rnf213	T	C	11: 119,334,516 (GRCm39)	S3242P	probably damaging	Het
Rtel1	T	A	2: 180,965,499 (GRCm39)	V167E	probably damaging	Het
Scgb1b2	G	T	7: 30,991,188 (GRCm39)		probably benign	Het
Sin3b	T	C	8: 73,457,893 (GRCm39)	L203P	probably damaging	Het
Skint6	T	C	4: 113,093,457 (GRCm39)	S229G	possibly damaging	Het
Slco1a4	T	C	6: 141,755,104 (GRCm39)	Y566C	probably damaging	Het
Smgc	T	G	15: 91,728,624 (GRCm39)	D121E	possibly damaging	Het
Sned1	T	A	1: 93,199,406 (GRCm39)	F495L	probably damaging	Het
St7	A	T	6: 17,886,006 (GRCm39)	N52I	possibly damaging	Het
Sycn	C	A	7: 28,240,494 (GRCm39)	Q54K	probably benign	Het
Syngr4	A	G	7: 45,536,464 (GRCm39)	V186A	probably benign	Het
Tars3	G	A	7: 65,305,539 (GRCm39)	M254I	possibly damaging	Het
Tcaf2	A	T	6: 42,619,738 (GRCm39)	H96Q	probably benign	Het
Tcp11l2	T	C	10: 84,449,363 (GRCm39)	Y443H	probably damaging	Het
Tmem200c	A	T	17: 69,149,244 (GRCm39)	Q609L	possibly damaging	Het
Tmx3	G	A	18: 90,535,614 (GRCm39)	G83R	probably damaging	Het
Tpgs2	A	C	18: 25,301,598 (GRCm39)	V23G	possibly damaging	Het
Trhr	T	C	15: 44,060,579 (GRCm39)	V33A	probably benign	Het
Trim66	A	T	7: 109,074,320 (GRCm39)	I647N	probably damaging	Het
Trnt1	A	G	6: 106,755,000 (GRCm39)	K244E	probably damaging	Het
Tsfm	G	A	10: 126,864,314 (GRCm39)	Q134*	probably null	Het
Ttll9	A	G	2: 152,844,927 (GRCm39)	T432A	probably benign	Het
Vmn2r78	C	T	7: 86,603,690 (GRCm39)	L623F	probably damaging	Het
Wdr55	A	G	18: 36,895,419 (GRCm39)	N132S	possibly damaging	Het
Wipf2	A	T	11: 98,787,040 (GRCm39)	R356S	possibly damaging	Het
Wnk1	A	G	6: 119,925,949 (GRCm39)		probably benign	Het
Zfp260	A	G	7: 29,804,765 (GRCm39)	K222E	probably damaging	Het
Zfp300	A	G	X: 20,948,190 (GRCm39)	S525P	possibly damaging	Het
Zfp592	A	G	7: 80,687,950 (GRCm39)	T959A	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
R0485:Nphs1	UTSW	7	30,166,940 (GRCm39)	missense	probably benign
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
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'- CCTTTCAGAACCCACCAAGTTG -3'
(R):5'- ACCTGGGGTGGTAATATCTTCAG -3'

Sequencing Primer
(F):5'- AAGTTGGGCTCCAGCTCTC -3'
(R):5'- CTTCAGGGAAGACATATTTTGGG -3'

Posted On

2014-10-01