Mutagenetix > Incidental Mutation

Incidental Mutation 'R0890:Nphp4'

83460

Institutional Source

Beutler Lab

Gene Symbol

Nphp4

Ensembl Gene

ENSMUSG00000039577

Gene Name

nephronophthisis 4 (juvenile) homolog (human)

Synonyms

nmf192, 4930564O18Rik

MMRRC Submission

039053-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.133) question?

Stock #

R0890 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

152561163-152647640 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 152582677 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Isoleucine at position 169 (L169I)

Ref Sequence

ENSEMBL: ENSMUSP00000080128 (fasta)

Gene Model

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

AlphaFold

P59240

Predicted Effect

possibly damaging
Transcript: ENSMUST00000056567
AA Change: L169I

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

SMART Domains

Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: L169I

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

possibly damaging
Transcript: ENSMUST00000081393
AA Change: L169I

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

SMART Domains

Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: L169I

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146223

Coding Region Coverage

1x: 99.4%
3x: 98.7%
10x: 97.1%
20x: 94.0%

Validation Efficiency

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: 32 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca15	T	C	7: 119,972,936 (GRCm39)	S837P	probably benign	Het
Cdh24	A	G	14: 54,870,051 (GRCm39)	V240A	probably benign	Het
Clcn4	T	C	7: 7,291,964 (GRCm39)	T556A	possibly damaging	Het
Coa7	G	A	4: 108,195,583 (GRCm39)	A171T	probably damaging	Het
Col12a1	A	T	9: 79,607,684 (GRCm39)	S381R	probably damaging	Het
Col9a3	C	T	2: 180,251,856 (GRCm39)	P335L	probably benign	Het
Dcxr	T	A	11: 120,617,297 (GRCm39)	N82I	probably damaging	Het
Dhdh	T	C	7: 45,131,395 (GRCm39)	D146G	possibly damaging	Het
Dhrs13	T	A	11: 77,925,176 (GRCm39)	L99Q	probably null	Het
Dnai1	C	T	4: 41,604,253 (GRCm39)	T220M	possibly damaging	Het
Gapvd1	T	A	2: 34,602,329 (GRCm39)	D606V	probably damaging	Het
Gcn1	T	G	5: 115,717,852 (GRCm39)	C246G	possibly damaging	Het
Gdf10	A	G	14: 33,654,113 (GRCm39)	K207E	possibly damaging	Het
Gucy2d	T	C	7: 98,122,472 (GRCm39)	V1046A	probably benign	Het
Itpr3	C	A	17: 27,307,985 (GRCm39)	Y257*	probably null	Het
Kifc5b	C	T	17: 27,141,996 (GRCm39)	T158M	possibly damaging	Het
Klra7	C	T	6: 130,195,916 (GRCm39)	D251N	probably benign	Het
Mesp1	T	C	7: 79,442,683 (GRCm39)	D198G	probably benign	Het
Mrgprb8	T	A	7: 48,038,777 (GRCm39)	C149*	probably null	Het
Or1j1	T	A	2: 36,702,586 (GRCm39)	T173S	probably benign	Het
Or52p2	C	A	7: 102,237,408 (GRCm39)	E181*	probably null	Het
Or5h17	T	A	16: 58,820,150 (GRCm39)	I34K	possibly damaging	Het
Pcgf5	A	T	19: 36,389,544 (GRCm39)	H7L	probably benign	Het
Polr3b	A	C	10: 84,550,200 (GRCm39)	K970T	probably benign	Het
Pomgnt1	A	G	4: 116,009,382 (GRCm39)	D93G	probably benign	Het
Rnf213	A	G	11: 119,321,312 (GRCm39)	K1256E	possibly damaging	Het
Scn9a	T	C	2: 66,314,079 (GRCm39)	T1869A	probably damaging	Het
Setdb2	A	G	14: 59,656,669 (GRCm39)	V232A	possibly damaging	Het
Sh3d21	T	C	4: 126,044,945 (GRCm39)	E578G	probably damaging	Het
Tmem168	A	T	6: 13,603,271 (GRCm39)	S32T	probably damaging	Het
Vmn1r38	T	G	6: 66,753,514 (GRCm39)	I201L	probably benign	Het
Wfs1	C	A	5: 37,132,888 (GRCm39)	W130C	probably damaging	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
R0433:Nphp4	UTSW	4	152,602,629 (GRCm39)	missense	probably benign	0.00
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
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'- TGAGAACTGTGCTCCAGTGATGC -3'
(R):5'- TCAGATACACGTCAGAGTCAGAGGC -3'

Sequencing Primer
(F):5'- ggagttagaggtggttgtgag -3'
(R):5'- CAGAGTCAGAGGCAGGTTCC -3'

Posted On

2013-11-08