Mutagenetix > Incidental Mutation

Incidental Mutation 'R0785:Nphp4'

76811

Institutional Source

Beutler Lab

Gene Symbol

Nphp4

Ensembl Gene

ENSMUSG00000039577

Gene Name

nephronophthisis 4 (juvenile) homolog (human)

Synonyms

nmf192, 4930564O18Rik

MMRRC Submission

038965-MU

Accession Numbers

Essential gene?

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

Stock #

R0785 (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 152646566 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 1366 (D1366G)

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: D1366G

PolyPhen 2 Score 0.580 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: D1366G

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: D1366G

PolyPhen 2 Score 0.580 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: D1366G

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

Meta Mutation Damage Score

0.0758

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 95.1%
20x: 87.1%

Validation Efficiency

100% (36/36)

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: 33 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca14	G	A	7: 119,893,380 (GRCm39)	G1277R	probably damaging	Het
Adam10	A	G	9: 70,675,170 (GRCm39)	E593G	possibly damaging	Het
Adh6a	T	C	3: 138,034,829 (GRCm39)		probably benign	Het
Akap6	T	A	12: 52,933,405 (GRCm39)	I299N	probably benign	Het
Bltp1	T	C	3: 37,013,483 (GRCm39)		probably benign	Het
Bod1l	A	T	5: 41,977,359 (GRCm39)	N1318K	probably benign	Het
Ccdc121rt2	A	G	5: 112,598,434 (GRCm39)	D327G	probably benign	Het
Eif2b2	C	A	12: 85,268,335 (GRCm39)	T170K	probably damaging	Het
Ermard	T	A	17: 15,242,239 (GRCm39)	H138Q	probably damaging	Het
Ern2	A	T	7: 121,770,884 (GRCm39)		probably null	Het
Fkbp11	T	C	15: 98,624,430 (GRCm39)	K108R	probably damaging	Het
Golgb1	A	G	16: 36,719,152 (GRCm39)	K353E	possibly damaging	Het
Hipk1	G	T	3: 103,661,641 (GRCm39)		probably null	Het
Itga4	A	G	2: 79,119,649 (GRCm39)	D485G	possibly damaging	Het
Krt1c	C	A	15: 101,726,356 (GRCm39)	G61C	unknown	Het
Med12l	T	A	3: 59,168,253 (GRCm39)	L1561Q	probably damaging	Het
Mtmr14	T	C	6: 113,254,908 (GRCm39)		probably null	Het
Myorg	A	G	4: 41,497,539 (GRCm39)	V697A	probably benign	Het
Naip1	A	G	13: 100,559,584 (GRCm39)	M1140T	probably benign	Het
Naip1	C	T	13: 100,559,593 (GRCm39)	R1137Q	probably benign	Het
Nav2	T	A	7: 49,070,081 (GRCm39)	H251Q	probably benign	Het
Or2b7	A	G	13: 21,739,958 (GRCm39)	V78A	probably benign	Het
Or6c75	A	G	10: 129,336,750 (GRCm39)		probably null	Het
Pde6c	A	C	19: 38,121,628 (GRCm39)	M79L	probably benign	Het
Pld5	C	T	1: 175,803,018 (GRCm39)		probably benign	Het
Polr1g	G	C	7: 19,091,210 (GRCm39)	S299C	probably benign	Het
Rps6kc1	A	G	1: 190,541,142 (GRCm39)	V387A	probably damaging	Het
Tas2r136	T	C	6: 132,754,890 (GRCm39)	D79G	probably benign	Het
Tmem243	A	T	5: 9,168,488 (GRCm39)	K90I	probably damaging	Het
Topbp1	A	G	9: 103,192,289 (GRCm39)	H260R	probably damaging	Het
Trappc1	A	G	11: 69,215,636 (GRCm39)		probably benign	Het
Vmn2r125	C	A	4: 156,703,396 (GRCm39)	A258D	probably benign	Het
Zfp300	T	C	X: 20,949,164 (GRCm39)	Y200C	possibly 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
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'- TGTCTCATGGAAGCCAGCATCAC -3'
(R):5'- TCTCTCAGGCACCACTCTGCAAAG -3'

Sequencing Primer
(F):5'- ATCACCTGGCCTTGGGAC -3'
(R):5'- TTTCTCAGAGGAAATCCACCTG -3'

Posted On

2013-10-16