Mutagenetix > Incidental Mutation

Incidental Mutation 'R4701:Nphp4'

356010

Institutional Source

Beutler Lab

Gene Symbol

Nphp4

Ensembl Gene

ENSMUSG00000039577

Gene Name

nephronophthisis 4 (juvenile) homolog (human)

Synonyms

nmf192, 4930564O18Rik

MMRRC Submission

041949-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.124) question?

Stock #

R4701 (G1)

Quality Score

216

Status

Validated

Chromosome

Chromosomal Location

152476706-152563183 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 152496659 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 100 (F100S)

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: F100S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: F100S

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: F100S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: F100S

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

Meta Mutation Damage Score

0.9133

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.6%

Validation Efficiency

96% (108/112)

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aarsd1	T	C	11: 101,411,160 (GRCm38)	I196V	probably benign	Het
Aass	T	A	6: 23,075,856 (GRCm38)	K761*	probably null	Het
Abca13	A	G	11: 9,292,306 (GRCm38)	T1390A	possibly damaging	Het
Abhd16a	T	C	17: 35,096,606 (GRCm38)		probably null	Het
Acad11	C	T	9: 104,095,565 (GRCm38)	Q486*	probably null	Het
Actl9	T	C	17: 33,433,935 (GRCm38)	L323P	probably benign	Het
Adam12	T	A	7: 133,916,462 (GRCm38)	I650F	possibly damaging	Het
Adgre4	A	T	17: 55,784,971 (GRCm38)	D77V	probably damaging	Het
Ankrd26	A	G	6: 118,506,485 (GRCm38)	F1586S	possibly damaging	Het
Anpep	T	C	7: 79,839,465 (GRCm38)	T320A	probably benign	Het
Arl15	T	A	13: 113,967,725 (GRCm38)	C133S	probably benign	Het
Ascc3	A	G	10: 50,720,664 (GRCm38)	N1230S	possibly damaging	Het
Atf4	T	A	15: 80,257,417 (GRCm38)	I336K	probably damaging	Het
Atp7b	A	T	8: 22,000,121 (GRCm38)	S1044T	probably benign	Het
Atp8b4	A	G	2: 126,414,293 (GRCm38)	F249L	probably damaging	Het
AU021092	G	T	16: 5,212,193 (GRCm38)	N319K	probably benign	Het
Bbs4	A	G	9: 59,323,519 (GRCm38)	V440A	probably benign	Het
Bpifb4	G	T	2: 153,950,385 (GRCm38)	G450C	probably damaging	Het
Cadm1	G	A	9: 47,818,822 (GRCm38)		probably benign	Het
Ccser2	G	A	14: 36,938,697 (GRCm38)	L500F	probably damaging	Het
Cd22	T	A	7: 30,876,153 (GRCm38)	I155F	probably damaging	Het
Cdkl4	A	T	17: 80,543,652 (GRCm38)	V207E	probably damaging	Het
Cfap65	T	C	1: 74,918,908 (GRCm38)	D947G	probably damaging	Het
Cntn6	T	C	6: 104,804,360 (GRCm38)	V397A	probably benign	Het
Cpox	T	A	16: 58,677,969 (GRCm38)	Y388*	probably null	Het
Dab1	C	T	4: 104,731,751 (GRCm38)	A524V	probably benign	Het
Dda1	T	A	8: 71,473,810 (GRCm38)	Y58N	probably damaging	Het
Dennd4a	C	T	9: 64,897,357 (GRCm38)	T1326I	possibly damaging	Het
Eps8l2	A	T	7: 141,357,260 (GRCm38)	I338F	probably damaging	Het
Fbxo42	A	G	4: 141,199,809 (GRCm38)	T467A	probably benign	Het
Flt4	T	C	11: 49,626,808 (GRCm38)	F319S	possibly damaging	Het
Fmn1	A	T	2: 113,584,071 (GRCm38)	Y895F	possibly damaging	Het
Gm6887	C	A	7: 42,465,093 (GRCm38)		noncoding transcript	Het
Grid2	A	G	6: 64,665,915 (GRCm38)	D887G	probably benign	Het
Grm6	C	T	11: 50,863,010 (GRCm38)	P714S	probably damaging	Het
Gsto2	A	G	19: 47,884,656 (GRCm38)	I157V	probably benign	Het
Il15ra	A	G	2: 11,718,345 (GRCm38)		probably null	Het
Impg1	A	G	9: 80,314,400 (GRCm38)	F713L	probably benign	Het
Jag1	T	A	2: 137,094,456 (GRCm38)	T373S	probably benign	Het
Kcnh3	T	A	15: 99,241,945 (GRCm38)	L904Q	probably benign	Het
Kctd19	C	A	8: 105,390,429 (GRCm38)	G356V	possibly damaging	Het
Kdm5b	T	A	1: 134,606,012 (GRCm38)		probably benign	Het
Kif1a	T	C	1: 93,078,835 (GRCm38)	I37V	probably damaging	Het
Lama5	G	A	2: 180,191,696 (GRCm38)	R1508C	probably damaging	Het
Lamb1	T	A	12: 31,266,848 (GRCm38)	C65*	probably null	Het
Lingo1	A	G	9: 56,620,258 (GRCm38)	F349S	probably damaging	Het
Loxl4	G	A	19: 42,607,613 (GRCm38)	H147Y	probably benign	Het
Lrrn4cl	T	A	19: 8,852,055 (GRCm38)	N132K	probably damaging	Het
Med17	A	T	9: 15,270,360 (GRCm38)	H31Q	probably damaging	Het
Med23	A	T	10: 24,893,648 (GRCm38)	L476F	probably damaging	Het
Mgst1	A	T	6: 138,150,838 (GRCm38)	D66V	probably damaging	Het
Mroh2a	T	C	1: 88,234,612 (GRCm38)		probably null	Het
Mroh2a	A	C	1: 88,241,618 (GRCm38)	I672L	probably benign	Het
Muc4	A	T	16: 32,755,846 (GRCm38)		probably benign	Het
Myo18a	C	T	11: 77,817,665 (GRCm38)	T30M	probably damaging	Het
Ncapg2	G	T	12: 116,440,618 (GRCm38)	R903L	probably benign	Het
Nme1	A	G	11: 93,965,908 (GRCm38)	I9T	probably damaging	Het
Nmt2	T	A	2: 3,322,641 (GRCm38)	I357N	probably benign	Het
Oca2	C	A	7: 56,255,002 (GRCm38)	T72K	probably benign	Het
Olfr1411	C	A	1: 92,597,438 (GRCm38)	D306E	probably benign	Het
Olfr625-ps1	G	A	7: 103,683,062 (GRCm38)	V105M	probably damaging	Het
Olfr676	A	T	7: 105,035,591 (GRCm38)	D131V	probably damaging	Het
Olfr677	A	T	7: 105,056,879 (GRCm38)	D211V	probably damaging	Het
Olfr871	T	C	9: 20,212,625 (GRCm38)	I92T	probably damaging	Het
Plce1	A	T	19: 38,725,007 (GRCm38)	T1240S	probably benign	Het
Plch1	A	T	3: 63,699,496 (GRCm38)		probably null	Het
Plxna4	T	C	6: 32,516,688 (GRCm38)	D331G	probably damaging	Het
Ppp1r3a	T	C	6: 14,718,993 (GRCm38)	T641A	probably benign	Het
Rab32	A	G	10: 10,550,854 (GRCm38)	L116P	probably benign	Het
Recql4	C	T	15: 76,708,585 (GRCm38)	C302Y	probably damaging	Het
Rorc	G	C	3: 94,391,710 (GRCm38)	E391Q	probably null	Het
Saa4	A	T	7: 46,731,627 (GRCm38)	F24I	possibly damaging	Het
Sall1	T	A	8: 89,031,160 (GRCm38)	K772M	probably damaging	Het
Sdk1	T	G	5: 142,185,231 (GRCm38)	L1950V	probably damaging	Het
Sil1	T	C	18: 35,266,896 (GRCm38)	E352G	probably benign	Het
Slc26a3	C	T	12: 31,447,774 (GRCm38)	P59L	probably damaging	Het
Smco2	T	C	6: 146,861,942 (GRCm38)		probably benign	Het
Sppl3	A	G	5: 115,103,313 (GRCm38)		probably null	Het
St6gal2	T	A	17: 55,496,344 (GRCm38)	V360D	probably damaging	Het
Stard9	G	A	2: 120,705,713 (GRCm38)	R345Q	possibly damaging	Het
Susd4	T	A	1: 182,892,061 (GRCm38)	Y414N	probably damaging	Het
Tenm4	T	C	7: 96,895,349 (GRCm38)	Y2191H	probably damaging	Het
Tln2	A	G	9: 67,346,527 (GRCm38)	V754A	probably benign	Het
Tmem132c	T	A	5: 127,564,496 (GRCm38)		probably benign	Het
Tnn	A	T	1: 160,147,768 (GRCm38)	S30T	possibly damaging	Het
Trpd52l3	G	T	19: 30,004,495 (GRCm38)	V217F	probably damaging	Het
Trpm1	G	T	7: 64,243,500 (GRCm38)	L1033F	probably damaging	Het
Tulp2	A	G	7: 45,517,924 (GRCm38)	E182G	probably damaging	Het
Ubr4	A	G	4: 139,471,336 (GRCm38)	K4490R	possibly damaging	Het
Usp17la	A	T	7: 104,860,649 (GRCm38)	R154*	probably null	Het
Vmn2r17	T	G	5: 109,427,983 (GRCm38)	M240R	probably damaging	Het
Vmn2r22	T	A	6: 123,650,469 (GRCm38)	N56I	probably benign	Het
Wdr66	A	G	5: 123,322,613 (GRCm38)	K1213E	probably benign	Het
Zdhhc21	A	T	4: 82,820,334 (GRCm38)	I206N	possibly damaging	Het
Zfp148	T	A	16: 33,456,908 (GRCm38)	D122E	probably benign	Het
Zfp804a	A	T	2: 82,256,582 (GRCm38)	S252C	probably damaging	Het
Zgrf1	C	T	3: 127,598,704 (GRCm38)	T1291I	probably benign	Het

Other mutations in Nphp4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00922:Nphp4	APN	4	152,537,309 (GRCm38)	splice site	probably benign
IGL00963:Nphp4	APN	4	152,537,861 (GRCm38)	missense	probably benign	0.01
IGL01571:Nphp4	APN	4	152,556,382 (GRCm38)	missense	probably benign	0.21
IGL01707:Nphp4	APN	4	152,538,983 (GRCm38)	missense	probably benign	0.00
IGL01837:Nphp4	APN	4	152,488,881 (GRCm38)	missense	probably damaging	0.96
IGL02341:Nphp4	APN	4	152,555,469 (GRCm38)	splice site	probably benign
IGL02558:Nphp4	APN	4	152,555,531 (GRCm38)	missense	probably damaging	1.00
IGL02563:Nphp4	APN	4	152,556,220 (GRCm38)	missense	probably benign	0.00
IGL02712:Nphp4	APN	4	152,556,275 (GRCm38)	missense	probably damaging	1.00
IGL03023:Nphp4	APN	4	152,524,235 (GRCm38)	splice site	probably null
R0280:Nphp4	UTSW	4	152,551,936 (GRCm38)	splice site	probably benign
R0317:Nphp4	UTSW	4	152,551,931 (GRCm38)	critical splice donor site	probably null
R0410:Nphp4	UTSW	4	152,557,046 (GRCm38)	missense	probably benign
R0433:Nphp4	UTSW	4	152,518,172 (GRCm38)	missense	probably benign	0.00
R0706:Nphp4	UTSW	4	152,555,617 (GRCm38)	missense	probably damaging	0.98
R0785:Nphp4	UTSW	4	152,562,109 (GRCm38)	missense	possibly damaging	0.58
R0890:Nphp4	UTSW	4	152,498,220 (GRCm38)	missense	possibly damaging	0.93
R0930:Nphp4	UTSW	4	152,538,055 (GRCm38)	missense	probably benign	0.01
R1202:Nphp4	UTSW	4	152,488,729 (GRCm38)	splice site	probably null
R1203:Nphp4	UTSW	4	152,488,832 (GRCm38)	missense	probably damaging	0.96
R1366:Nphp4	UTSW	4	152,502,926 (GRCm38)	missense	probably damaging	0.96
R1452:Nphp4	UTSW	4	152,547,018 (GRCm38)	missense	probably damaging	0.99
R1598:Nphp4	UTSW	4	152,562,090 (GRCm38)	missense	probably benign	0.00
R1699:Nphp4	UTSW	4	152,496,664 (GRCm38)	missense	probably damaging	0.99
R2007:Nphp4	UTSW	4	152,554,654 (GRCm38)	missense	probably damaging	0.97
R2082:Nphp4	UTSW	4	152,559,364 (GRCm38)	missense	probably benign	0.38
R2264:Nphp4	UTSW	4	152,503,008 (GRCm38)	splice site	probably benign
R2280:Nphp4	UTSW	4	152,557,043 (GRCm38)	missense	possibly damaging	0.95
R2281:Nphp4	UTSW	4	152,557,043 (GRCm38)	missense	possibly damaging	0.95
R2926:Nphp4	UTSW	4	152,518,139 (GRCm38)	missense	probably damaging	0.99
R3764:Nphp4	UTSW	4	152,538,017 (GRCm38)	splice site	probably benign
R4084:Nphp4	UTSW	4	152,488,791 (GRCm38)	missense	probably damaging	1.00
R4091:Nphp4	UTSW	4	152,547,018 (GRCm38)	missense	probably damaging	0.97
R4240:Nphp4	UTSW	4	152,555,684 (GRCm38)	missense	probably benign	0.07
R4778:Nphp4	UTSW	4	152,556,291 (GRCm38)	missense	probably benign	0.44
R4783:Nphp4	UTSW	4	152,554,546 (GRCm38)	missense	probably benign	0.00
R4784:Nphp4	UTSW	4	152,554,546 (GRCm38)	missense	probably benign	0.00
R4974:Nphp4	UTSW	4	152,537,793 (GRCm38)	missense	probably damaging	1.00
R5053:Nphp4	UTSW	4	152,544,462 (GRCm38)	splice site	probably null
R5117:Nphp4	UTSW	4	152,524,232 (GRCm38)	splice site	probably null
R5128:Nphp4	UTSW	4	152,502,991 (GRCm38)	missense	probably benign	0.01
R5665:Nphp4	UTSW	4	152,506,485 (GRCm38)	missense	probably benign	0.25
R5890:Nphp4	UTSW	4	152,547,079 (GRCm38)	missense	probably benign	0.44
R6171:Nphp4	UTSW	4	152,544,449 (GRCm38)	missense	probably damaging	0.99
R6601:Nphp4	UTSW	4	152,503,007 (GRCm38)	splice site	probably null
R6772:Nphp4	UTSW	4	152,544,406 (GRCm38)	missense	probably benign	0.07
R6806:Nphp4	UTSW	4	152,538,101 (GRCm38)	missense	probably benign	0.02
R7006:Nphp4	UTSW	4	152,488,802 (GRCm38)	missense	probably benign	0.12
R7124:Nphp4	UTSW	4	152,555,684 (GRCm38)	missense	probably benign	0.07
R7381:Nphp4	UTSW	4	152,499,003 (GRCm38)	missense	possibly damaging	0.94
R7411:Nphp4	UTSW	4	152,554,717 (GRCm38)	missense	probably benign	0.25
R7638:Nphp4	UTSW	4	152,554,534 (GRCm38)	missense	probably benign	0.08
R7814:Nphp4	UTSW	4	152,544,403 (GRCm38)	missense	probably damaging	1.00
R7814:Nphp4	UTSW	4	152,524,272 (GRCm38)	missense	possibly damaging	0.93
R7841:Nphp4	UTSW	4	152,496,683 (GRCm38)	missense	probably benign	0.01
R8346:Nphp4	UTSW	4	152,561,321 (GRCm38)	missense	probably damaging	1.00
R8479:Nphp4	UTSW	4	152,524,290 (GRCm38)	missense	probably benign	0.01
R8847:Nphp4	UTSW	4	152,506,406 (GRCm38)	missense	probably damaging	1.00
R8995:Nphp4	UTSW	4	152,538,888 (GRCm38)	missense	probably damaging	1.00
R8997:Nphp4	UTSW	4	152,538,888 (GRCm38)	missense	probably damaging	1.00
R9075:Nphp4	UTSW	4	152,507,448 (GRCm38)	missense	probably damaging	1.00
R9089:Nphp4	UTSW	4	152,561,216 (GRCm38)	missense	possibly damaging	0.87
R9191:Nphp4	UTSW	4	152,556,230 (GRCm38)	missense	probably damaging	1.00
R9274:Nphp4	UTSW	4	152,555,599 (GRCm38)	missense	probably benign	0.05
R9311:Nphp4	UTSW	4	152,524,257 (GRCm38)	missense	probably damaging	0.99
R9383:Nphp4	UTSW	4	152,544,461 (GRCm38)	critical splice donor site	probably null
R9628:Nphp4	UTSW	4	152,484,509 (GRCm38)	missense	probably damaging	1.00
R9711:Nphp4	UTSW	4	152,538,977 (GRCm38)	missense	possibly damaging	0.77
R9712:Nphp4	UTSW	4	152,547,064 (GRCm38)	missense	probably benign	0.17
R9752:Nphp4	UTSW	4	152,537,280 (GRCm38)	missense	probably benign	0.00
R9790:Nphp4	UTSW	4	152,562,148 (GRCm38)	missense	probably null	0.64
R9791:Nphp4	UTSW	4	152,562,148 (GRCm38)	missense	probably null	0.64
T0970:Nphp4	UTSW	4	152,556,379 (GRCm38)	missense	probably damaging	1.00
X0058:Nphp4	UTSW	4	152,559,707 (GRCm38)	missense	possibly damaging	0.95
Z1177:Nphp4	UTSW	4	152,518,196 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCGTGTTGAACTGAACTAGGC -3'
(R):5'- GAGTACTGTTTACCGTTTGTCC -3'

Sequencing Primer
(F):5'- GTATGAACTCCAGCTCCTGAG -3'
(R):5'- TGTCCTGGGCTGCAGAG -3'

Posted On

2015-10-21