Mutagenetix > Incidental Mutation

Incidental Mutation 'R0433:Nphp4'

38914

Institutional Source

Beutler Lab

Gene Symbol

Nphp4

Ensembl Gene

ENSMUSG00000039577

Gene Name

nephronophthisis 4 (juvenile) homolog (human)

Synonyms

nmf192, 4930564O18Rik

MMRRC Submission

038635-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.142) question?

Stock #

R0433 (G1)

Quality Score

222

Status

Validated

Chromosome

Chromosomal Location

152561163-152647640 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 152602629 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 401 (V401A)

Ref Sequence

ENSEMBL: ENSMUSP00000080128 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056567] [ENSMUST00000081393]

AlphaFold

P59240

Predicted Effect

probably benign
Transcript: ENSMUST00000056567
AA Change: V401A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: V401A

Domain	Start	End	E-Value	Type
low complexity region	317	333	N/A	INTRINSIC
low complexity region	367	380	N/A	INTRINSIC
low complexity region	473	484	N/A	INTRINSIC
low complexity region	507	530	N/A	INTRINSIC
low complexity region	896	909	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000081393
AA Change: V401A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: V401A

Domain	Start	End	E-Value	Type
low complexity region	317	333	N/A	INTRINSIC
low complexity region	367	380	N/A	INTRINSIC
low complexity region	473	484	N/A	INTRINSIC
low complexity region	507	530	N/A	INTRINSIC
low complexity region	896	909	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123635

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142027

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 94.3%

Validation Efficiency

99% (108/109)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein involved in renal tubular development and function. This protein interacts with nephrocystin, and belongs to a multifunctional complex that is localized to actin- and microtubule-based structures. Mutations in this gene are associated with nephronophthisis type 4, a renal disease, and with Senior-Loken syndrome type 4, a combination of nephronophthisis and retinitis pigmentosa. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]
PHENOTYPE: Mutant mice have a mottled retina with photoreceptor degeneration and male infertility associated with oligozoospermia and asthenozoospermia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 102 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110032F04Rik	T	C	3: 68,777,636 (GRCm39)	V199A	possibly damaging	Het
Abcb5	T	C	12: 118,841,545 (GRCm39)	M967V	probably benign	Het
Adcy10	T	A	1: 165,379,591 (GRCm39)	L951Q	probably damaging	Het
Amer2	A	T	14: 60,616,032 (GRCm39)	S76C	probably damaging	Het
Atad1	T	C	19: 32,675,877 (GRCm39)	I182M	probably benign	Het
Bpi	A	G	2: 158,100,339 (GRCm39)	D42G	probably damaging	Het
C7	G	T	15: 5,018,398 (GRCm39)	T815K	probably damaging	Het
Cacna1g	T	A	11: 94,350,033 (GRCm39)	D604V	probably benign	Het
Camk1g	A	G	1: 193,036,366 (GRCm39)	F165L	probably damaging	Het
Ccdc69	C	T	11: 54,943,716 (GRCm39)		probably null	Het
Ccser2	A	C	14: 36,640,486 (GRCm39)	F37L	probably damaging	Het
Cfap43	A	G	19: 47,814,210 (GRCm39)	F208S	probably benign	Het
Cfap54	G	A	10: 92,814,942 (GRCm39)		probably benign	Het
Cfap69	A	C	5: 5,699,853 (GRCm39)	D62E	probably damaging	Het
Cnksr2	A	T	X: 156,671,554 (GRCm39)	M483K	probably benign	Het
Cnksr2	C	A	X: 156,671,553 (GRCm39)	M483I	probably benign	Het
Cog8	T	C	8: 107,783,110 (GRCm39)	S60G	possibly damaging	Het
Col4a3	C	T	1: 82,647,940 (GRCm39)	P484S	unknown	Het
Col6a4	C	T	9: 105,945,193 (GRCm39)	G974R	probably damaging	Het
Cplane1	T	C	15: 8,246,046 (GRCm39)	S1473P	probably benign	Het
Dbnl	T	G	11: 5,746,825 (GRCm39)		probably null	Het
Dhcr7	T	C	7: 143,394,200 (GRCm39)	C114R	possibly damaging	Het
Dnah2	C	A	11: 69,350,114 (GRCm39)	D2340Y	probably damaging	Het
Dnai4	T	C	4: 102,960,450 (GRCm39)	N67D	probably benign	Het
Dusp10	T	A	1: 183,801,393 (GRCm39)	Y387N	probably damaging	Het
Eipr1	C	T	12: 28,909,330 (GRCm39)	T199I	possibly damaging	Het
Emc2	T	G	15: 43,360,520 (GRCm39)		probably null	Het
Enpp3	A	G	10: 24,696,495 (GRCm39)	S147P	probably benign	Het
Fam133b	T	A	5: 3,608,560 (GRCm39)		probably benign	Het
Fat1	C	A	8: 45,477,686 (GRCm39)	T2244K	possibly damaging	Het
Fbn1	A	G	2: 125,190,135 (GRCm39)	S1453P	possibly damaging	Het
Fez2	A	T	17: 78,725,476 (GRCm39)	F13I	probably damaging	Het
Ggnbp2	T	C	11: 84,727,246 (GRCm39)	K530R	probably damaging	Het
Gpa33	T	C	1: 165,991,330 (GRCm39)		probably benign	Het
Gpr142	T	C	11: 114,696,823 (GRCm39)	I123T	probably damaging	Het
Il21	T	G	3: 37,286,684 (GRCm39)	I11L	possibly damaging	Het
Klhl7	A	G	5: 24,332,700 (GRCm39)	E86G	probably damaging	Het
Klk10	G	T	7: 43,430,989 (GRCm39)	A11S	possibly damaging	Het
Knl1	A	T	2: 118,934,542 (GRCm39)	D2115V	probably damaging	Het
Lonp2	A	G	8: 87,360,582 (GRCm39)	D185G	probably damaging	Het
Lrrc47	T	C	4: 154,102,822 (GRCm39)		probably benign	Het
Lrrcc1	A	G	3: 14,624,434 (GRCm39)	I698V	probably damaging	Het
Lzts2	T	C	19: 45,010,115 (GRCm39)	V83A	possibly damaging	Het
Melk	C	A	4: 44,340,614 (GRCm39)		probably benign	Het
Mical1	G	A	10: 41,355,486 (GRCm39)	V150I	probably benign	Het
Morn3	C	A	5: 123,177,396 (GRCm39)	M129I	probably benign	Het
Mroh2b	T	A	15: 4,971,116 (GRCm39)	D1040E	probably benign	Het
Mroh5	T	C	15: 73,661,877 (GRCm39)	N438S	probably benign	Het
Mroh5	T	A	15: 73,662,657 (GRCm39)	Q387L	probably damaging	Het
Myh15	A	G	16: 48,965,599 (GRCm39)	D1168G	probably damaging	Het
Nek10	A	G	14: 14,860,927 (GRCm38)	E493G	probably benign	Het
Nipsnap3a	A	G	4: 53,000,316 (GRCm39)	Y227C	probably damaging	Het
Nlrp9c	T	A	7: 26,085,244 (GRCm39)	T112S	probably benign	Het
Nr1h2	A	G	7: 44,199,411 (GRCm39)	*365Q	probably null	Het
Or13p5	T	C	4: 118,592,287 (GRCm39)	V187A	probably benign	Het
Or5p54	T	C	7: 107,554,469 (GRCm39)	I207T	probably damaging	Het
Pacs2	T	A	12: 113,020,464 (GRCm39)	V279D	possibly damaging	Het
Pdcd2	C	T	17: 15,746,646 (GRCm39)	C171Y	probably benign	Het
Pde11a	T	A	2: 76,168,050 (GRCm39)	D301V	possibly damaging	Het
Pfpl	T	G	19: 12,406,839 (GRCm39)	N363K	probably damaging	Het
Phf14	T	A	6: 11,933,742 (GRCm39)	S201R	probably damaging	Het
Pip4k2c	G	A	10: 127,044,815 (GRCm39)	P66S	probably benign	Het
Pou2f3	G	T	9: 43,038,693 (GRCm39)	H392N	probably benign	Het
Pou3f1	G	T	4: 124,552,697 (GRCm39)	G400C	probably damaging	Het
Ptprg	T	C	14: 12,220,620 (GRCm38)	I1219T	probably damaging	Het
Rfx6	A	G	10: 51,596,124 (GRCm39)	D435G	probably damaging	Het
Rhpn2	T	A	7: 35,084,899 (GRCm39)	S598T	probably benign	Het
Sdccag8	C	A	1: 176,672,387 (GRCm39)		probably null	Het
Sec16b	C	A	1: 157,362,279 (GRCm39)	Y43*	probably null	Het
Sele	T	C	1: 163,876,813 (GRCm39)	Y30H	possibly damaging	Het
Sgsm2	C	T	11: 74,749,016 (GRCm39)		probably null	Het
Slc45a2	T	C	15: 11,025,831 (GRCm39)	Y394H	probably benign	Het
Slc4a10	T	G	2: 62,120,327 (GRCm39)	I788S	probably benign	Het
Slmap	A	T	14: 26,174,749 (GRCm39)	L161*	probably null	Het
Slx4	A	T	16: 3,803,882 (GRCm39)	D977E	probably benign	Het
Spata31e5	A	T	1: 28,816,423 (GRCm39)	Y536*	probably null	Het
Spata31f3	A	G	4: 42,874,013 (GRCm39)		probably benign	Het
Spen	A	T	4: 141,211,069 (GRCm39)	M608K	unknown	Het
St8sia4	G	C	1: 95,519,429 (GRCm39)	T353R	probably damaging	Het
Stab2	G	T	10: 86,679,355 (GRCm39)		probably benign	Het
Stx12	C	T	4: 132,585,741 (GRCm39)	G213D	probably damaging	Het
Synj2	A	T	17: 6,084,123 (GRCm39)	N270Y	probably damaging	Het
Tdrd9	C	T	12: 111,992,015 (GRCm39)	R438*	probably null	Het
Tert	T	C	13: 73,775,200 (GRCm39)	Y18H	probably damaging	Het
Tph1	A	T	7: 46,303,245 (GRCm39)	F244L	probably damaging	Het
Triobp	T	C	15: 78,852,401 (GRCm39)	F852L	possibly damaging	Het
Trpv1	T	C	11: 73,143,834 (GRCm39)		probably benign	Het
Uggt2	A	T	14: 119,312,741 (GRCm39)		probably null	Het
Ulk4	A	G	9: 120,873,885 (GRCm39)	I1182T	probably benign	Het
Uqcc1	A	G	2: 155,752,288 (GRCm39)	Y98H	probably damaging	Het
Usp25	A	G	16: 76,906,105 (GRCm39)	I854V	probably benign	Het
Usp50	T	C	2: 126,603,464 (GRCm39)	S361G	probably damaging	Het
Uspl1	C	A	5: 149,151,625 (GRCm39)	Q743K	probably damaging	Het
Vmn2r3	A	G	3: 64,183,054 (GRCm39)	V215A	possibly damaging	Het
Vmn2r61	A	T	7: 41,915,335 (GRCm39)	H94L	probably benign	Het
Vps37c	T	C	19: 10,690,393 (GRCm39)	V285A	probably benign	Het
Vwa8	T	C	14: 79,300,116 (GRCm39)	V983A	probably damaging	Het
Zcchc9	C	T	13: 91,954,081 (GRCm39)	R58H	probably benign	Het
Zdbf2	T	C	1: 63,345,302 (GRCm39)	V1227A	possibly damaging	Het
Zfp292	T	C	4: 34,839,959 (GRCm39)	K64E	probably damaging	Het
Zfp948	A	G	17: 21,807,764 (GRCm39)	T319A	probably benign	Het
Zp3r	T	G	1: 130,504,870 (GRCm39)		probably benign	Het

Other mutations in Nphp4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00922:Nphp4	APN	4	152,621,766 (GRCm39)	splice site	probably benign
IGL00963:Nphp4	APN	4	152,622,318 (GRCm39)	missense	probably benign	0.01
IGL01571:Nphp4	APN	4	152,640,839 (GRCm39)	missense	probably benign	0.21
IGL01707:Nphp4	APN	4	152,623,440 (GRCm39)	missense	probably benign	0.00
IGL01837:Nphp4	APN	4	152,573,338 (GRCm39)	missense	probably damaging	0.96
IGL02341:Nphp4	APN	4	152,639,926 (GRCm39)	splice site	probably benign
IGL02558:Nphp4	APN	4	152,639,988 (GRCm39)	missense	probably damaging	1.00
IGL02563:Nphp4	APN	4	152,640,677 (GRCm39)	missense	probably benign	0.00
IGL02712:Nphp4	APN	4	152,640,732 (GRCm39)	missense	probably damaging	1.00
IGL03023:Nphp4	APN	4	152,608,692 (GRCm39)	splice site	probably null
R0280:Nphp4	UTSW	4	152,636,393 (GRCm39)	splice site	probably benign
R0317:Nphp4	UTSW	4	152,636,388 (GRCm39)	critical splice donor site	probably null
R0410:Nphp4	UTSW	4	152,641,503 (GRCm39)	missense	probably benign
R0706:Nphp4	UTSW	4	152,640,074 (GRCm39)	missense	probably damaging	0.98
R0785:Nphp4	UTSW	4	152,646,566 (GRCm39)	missense	possibly damaging	0.58
R0890:Nphp4	UTSW	4	152,582,677 (GRCm39)	missense	possibly damaging	0.93
R0930:Nphp4	UTSW	4	152,622,512 (GRCm39)	missense	probably benign	0.01
R1202:Nphp4	UTSW	4	152,573,186 (GRCm39)	splice site	probably null
R1203:Nphp4	UTSW	4	152,573,289 (GRCm39)	missense	probably damaging	0.96
R1366:Nphp4	UTSW	4	152,587,383 (GRCm39)	missense	probably damaging	0.96
R1452:Nphp4	UTSW	4	152,631,475 (GRCm39)	missense	probably damaging	0.99
R1598:Nphp4	UTSW	4	152,646,547 (GRCm39)	missense	probably benign	0.00
R1699:Nphp4	UTSW	4	152,581,121 (GRCm39)	missense	probably damaging	0.99
R2007:Nphp4	UTSW	4	152,639,111 (GRCm39)	missense	probably damaging	0.97
R2082:Nphp4	UTSW	4	152,643,821 (GRCm39)	missense	probably benign	0.38
R2264:Nphp4	UTSW	4	152,587,465 (GRCm39)	splice site	probably benign
R2280:Nphp4	UTSW	4	152,641,500 (GRCm39)	missense	possibly damaging	0.95
R2281:Nphp4	UTSW	4	152,641,500 (GRCm39)	missense	possibly damaging	0.95
R2926:Nphp4	UTSW	4	152,602,596 (GRCm39)	missense	probably damaging	0.99
R3764:Nphp4	UTSW	4	152,622,474 (GRCm39)	splice site	probably benign
R4084:Nphp4	UTSW	4	152,573,248 (GRCm39)	missense	probably damaging	1.00
R4091:Nphp4	UTSW	4	152,631,475 (GRCm39)	missense	probably damaging	0.97
R4240:Nphp4	UTSW	4	152,640,141 (GRCm39)	missense	probably benign	0.07
R4701:Nphp4	UTSW	4	152,581,116 (GRCm39)	missense	probably damaging	1.00
R4778:Nphp4	UTSW	4	152,640,748 (GRCm39)	missense	probably benign	0.44
R4783:Nphp4	UTSW	4	152,639,003 (GRCm39)	missense	probably benign	0.00
R4784:Nphp4	UTSW	4	152,639,003 (GRCm39)	missense	probably benign	0.00
R4974:Nphp4	UTSW	4	152,622,250 (GRCm39)	missense	probably damaging	1.00
R5053:Nphp4	UTSW	4	152,628,919 (GRCm39)	splice site	probably null
R5117:Nphp4	UTSW	4	152,608,689 (GRCm39)	splice site	probably null
R5128:Nphp4	UTSW	4	152,587,448 (GRCm39)	missense	probably benign	0.01
R5665:Nphp4	UTSW	4	152,590,942 (GRCm39)	missense	probably benign	0.25
R5890:Nphp4	UTSW	4	152,631,536 (GRCm39)	missense	probably benign	0.44
R6171:Nphp4	UTSW	4	152,628,906 (GRCm39)	missense	probably damaging	0.99
R6601:Nphp4	UTSW	4	152,587,464 (GRCm39)	splice site	probably null
R6772:Nphp4	UTSW	4	152,628,863 (GRCm39)	missense	probably benign	0.07
R6806:Nphp4	UTSW	4	152,622,558 (GRCm39)	missense	probably benign	0.02
R7006:Nphp4	UTSW	4	152,573,259 (GRCm39)	missense	probably benign	0.12
R7124:Nphp4	UTSW	4	152,640,141 (GRCm39)	missense	probably benign	0.07
R7381:Nphp4	UTSW	4	152,583,460 (GRCm39)	missense	possibly damaging	0.94
R7411:Nphp4	UTSW	4	152,639,174 (GRCm39)	missense	probably benign	0.25
R7638:Nphp4	UTSW	4	152,638,991 (GRCm39)	missense	probably benign	0.08
R7814:Nphp4	UTSW	4	152,628,860 (GRCm39)	missense	probably damaging	1.00
R7814:Nphp4	UTSW	4	152,608,729 (GRCm39)	missense	possibly damaging	0.93
R7841:Nphp4	UTSW	4	152,581,140 (GRCm39)	missense	probably benign	0.01
R8346:Nphp4	UTSW	4	152,645,778 (GRCm39)	missense	probably damaging	1.00
R8479:Nphp4	UTSW	4	152,608,747 (GRCm39)	missense	probably benign	0.01
R8847:Nphp4	UTSW	4	152,590,863 (GRCm39)	missense	probably damaging	1.00
R8995:Nphp4	UTSW	4	152,623,345 (GRCm39)	missense	probably damaging	1.00
R8997:Nphp4	UTSW	4	152,623,345 (GRCm39)	missense	probably damaging	1.00
R9075:Nphp4	UTSW	4	152,591,905 (GRCm39)	missense	probably damaging	1.00
R9089:Nphp4	UTSW	4	152,645,673 (GRCm39)	missense	possibly damaging	0.87
R9191:Nphp4	UTSW	4	152,640,687 (GRCm39)	missense	probably damaging	1.00
R9274:Nphp4	UTSW	4	152,640,056 (GRCm39)	missense	probably benign	0.05
R9311:Nphp4	UTSW	4	152,608,714 (GRCm39)	missense	probably damaging	0.99
R9383:Nphp4	UTSW	4	152,628,918 (GRCm39)	critical splice donor site	probably null
R9628:Nphp4	UTSW	4	152,568,966 (GRCm39)	missense	probably damaging	1.00
R9711:Nphp4	UTSW	4	152,623,434 (GRCm39)	missense	possibly damaging	0.77
R9712:Nphp4	UTSW	4	152,631,521 (GRCm39)	missense	probably benign	0.17
R9752:Nphp4	UTSW	4	152,621,737 (GRCm39)	missense	probably benign	0.00
R9790:Nphp4	UTSW	4	152,646,605 (GRCm39)	missense	probably null	0.64
R9791:Nphp4	UTSW	4	152,646,605 (GRCm39)	missense	probably null	0.64
T0970:Nphp4	UTSW	4	152,640,836 (GRCm39)	missense	probably damaging	1.00
X0058:Nphp4	UTSW	4	152,644,164 (GRCm39)	missense	possibly damaging	0.95
Z1177:Nphp4	UTSW	4	152,602,653 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CCTGCTGCCATGAGTCATAGGAAAC -3'
(R):5'- CGCACGAATGAACTTGCTACAAGC -3'

Sequencing Primer
(F):5'- ATGTGGTGACACATATGCCC -3'
(R):5'- GAACTTGCTACAAGCATCTGAG -3'

Posted On

2013-05-23