Mutagenetix > Incidental Mutation

Incidental Mutation 'R1203:Nphp4'

100250

Institutional Source

Beutler Lab

Gene Symbol

Nphp4

Ensembl Gene

ENSMUSG00000039577

Gene Name

nephronophthisis 4 (juvenile) homolog (human)

Synonyms

nmf192, 4930564O18Rik

MMRRC Submission

039273-MU

Accession Numbers

Essential gene?

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

Stock #

R1203 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

152561163-152647640 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 152573289 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Glutamic Acid at position 76 (K76E)

Ref Sequence

ENSEMBL: ENSMUSP00000080128 (fasta)

Gene Model

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

AlphaFold

P59240

Predicted Effect

probably damaging
Transcript: ENSMUST00000056567
AA Change: K76E

PolyPhen 2 Score 0.962 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: K76E

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 damaging
Transcript: ENSMUST00000081393
AA Change: K76E

PolyPhen 2 Score 0.962 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: K76E

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: ENSMUST00000142027

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146223

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153759

Meta Mutation Damage Score

0.1571

Coding Region Coverage

1x: 99.5%
3x: 98.4%
10x: 95.6%
20x: 89.3%

Validation Efficiency

100% (50/50)

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: 44 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A830018L16Rik	A	T	1: 11,588,818 (GRCm39)	R78S	probably damaging	Het
Aadacl3	T	C	4: 144,190,140 (GRCm39)	T54A	probably benign	Het
Adcy8	A	G	15: 64,618,780 (GRCm39)	I791T	probably damaging	Het
Aldh1b1	A	G	4: 45,803,359 (GRCm39)	D299G	probably damaging	Het
Aoah	A	G	13: 21,000,764 (GRCm39)	E66G	probably damaging	Het
Atl2	G	T	17: 80,160,334 (GRCm39)	H418N	probably damaging	Het
Atp6v1d	A	G	12: 78,908,214 (GRCm39)	I7T	possibly damaging	Het
Calhm3	C	T	19: 47,143,839 (GRCm39)	V155M	probably damaging	Het
Carmil1	A	T	13: 24,282,989 (GRCm39)	I105K	probably damaging	Het
Csrp3	C	A	7: 48,489,278 (GRCm39)	M1I	probably null	Het
Dnah10	T	A	5: 124,837,078 (GRCm39)		probably null	Het
Dnah11	T	C	12: 117,897,547 (GRCm39)	N3561S	possibly damaging	Het
Dzip3	A	T	16: 48,772,180 (GRCm39)	D496E	probably damaging	Het
Eif2ak1	T	C	5: 143,820,797 (GRCm39)	V246A	probably benign	Het
Fam171b	T	A	2: 83,643,313 (GRCm39)	V74E	probably benign	Het
Gm14137	C	T	2: 119,005,605 (GRCm39)	R55W	probably damaging	Het
Gm4950	T	C	18: 51,998,830 (GRCm39)	I42V	probably benign	Het
Gpr35	T	C	1: 92,910,870 (GRCm39)	V194A	probably damaging	Het
Kdm5d	C	T	Y: 941,011 (GRCm39)	S1132F	probably damaging	Het
Muc4	C	A	16: 32,754,529 (GRCm38)	H1468N	probably benign	Het
Ncln	A	G	10: 81,332,027 (GRCm39)	V24A	possibly damaging	Het
Nsf	CAATAATAATAATAATA	CAATAATAATAATAATAATA	11: 103,816,952 (GRCm39)		probably benign	Het
Nup155	A	T	15: 8,187,244 (GRCm39)	H1391L	probably damaging	Het
Or52h2	A	T	7: 103,839,060 (GRCm39)	L118*	probably null	Het
Pabpc1l	G	T	2: 163,879,091 (GRCm39)	V313F	possibly damaging	Het
Pcbd2	G	A	13: 55,880,881 (GRCm39)		probably null	Het
Rapgef6	T	A	11: 54,582,525 (GRCm39)	V1479D	probably benign	Het
Rnf43	T	C	11: 87,618,301 (GRCm39)		probably benign	Het
Robo3	A	G	9: 37,329,978 (GRCm39)	W1113R	probably damaging	Het
Sall1	A	T	8: 89,758,562 (GRCm39)	V514E	probably damaging	Het
Sgpp1	A	G	12: 75,763,056 (GRCm39)	I375T	probably benign	Het
Strc	T	C	2: 121,202,604 (GRCm39)	N1187S	possibly damaging	Het
Tbc1d17	G	A	7: 44,492,895 (GRCm39)	R363W	probably damaging	Het
Tbcd	A	G	11: 121,366,451 (GRCm39)	Q242R	probably benign	Het
Tbcel	A	C	9: 42,362,947 (GRCm39)	V50G	probably damaging	Het
Tead3	C	T	17: 28,560,536 (GRCm39)	A23T	probably benign	Het
Tedc2	T	A	17: 24,435,291 (GRCm39)	E366V	probably damaging	Het
Tedc2	C	A	17: 24,435,292 (GRCm39)	E366*	probably null	Het
Tlcd5	A	G	9: 43,022,775 (GRCm39)	V193A	probably benign	Het
Tmem241	G	T	18: 12,217,035 (GRCm39)		probably benign	Het
Tmtc3	G	T	10: 100,312,606 (GRCm39)	T79K	probably damaging	Het
Utrn	A	G	10: 12,362,281 (GRCm39)	V241A	probably damaging	Het
Vps8	A	T	16: 21,330,307 (GRCm39)	I729F	probably damaging	Het
Zfp407	C	T	18: 84,577,898 (GRCm39)	A1072T	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
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
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
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'- TGTCACAAGGAAGTTGAGTTGCCAG -3'
(R):5'- TGATGCGACAGACACTCTACCTCAC -3'

Sequencing Primer
(F):5'- TGAGTTGCCAGTAGCTGAATG -3'
(R):5'- TTTGGAAACAGAGTGTCCCAC -3'

Posted On

2014-01-15