Mutagenetix > Incidental Mutation

Incidental Mutation 'R4783:Nphp4'

404217

Institutional Source

Beutler Lab

Gene Symbol

Nphp4

Ensembl Gene

ENSMUSG00000039577

Gene Name

nephronophthisis 4 (juvenile) homolog (human)

Synonyms

nmf192, 4930564O18Rik

MMRRC Submission

042416-MU

Accession Numbers

Essential gene?

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

Stock #

R4783 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

152476706-152563183 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 152554546 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Lysine at position 878 (R878K)

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: R878K

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

SMART Domains

Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: R878K

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: R878K

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

SMART Domains

Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: R878K

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

0.0898

Coding Region Coverage

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

Validation Efficiency

100% (99/99)

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: 95 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110082J24Rik	G	A	5: 30,105,200 (GRCm38)	R54*	probably null	Het
Acsl6	A	T	11: 54,336,993 (GRCm38)	M350L	probably damaging	Het
Adgrv1	T	C	13: 81,095,445 (GRCm38)	T6279A	probably damaging	Het
Ago3	A	T	4: 126,368,503 (GRCm38)	M418K	probably benign	Het
Ascc2	G	A	11: 4,646,653 (GRCm38)	R58H	probably benign	Het
Brinp3	A	G	1: 146,727,640 (GRCm38)		probably benign	Het
Carmil3	T	C	14: 55,501,321 (GRCm38)		probably null	Het
Ccdc47	T	A	11: 106,203,604 (GRCm38)	H7L	probably benign	Het
Ccndbp1	A	T	2: 121,008,522 (GRCm38)	T5S	probably benign	Het
Cdr2	A	T	7: 120,958,421 (GRCm38)	F294I	probably benign	Het
Chd8	C	A	14: 52,205,368 (GRCm38)	C575F	probably damaging	Het
Ctsll3	G	A	13: 60,800,395 (GRCm38)	T156I	probably damaging	Het
Dgcr8	G	A	16: 18,258,310 (GRCm38)	R4*	probably null	Het
Dnah1	T	A	14: 31,263,479 (GRCm38)	K3818N	probably damaging	Het
Dok2	C	T	14: 70,777,874 (GRCm38)	P347L	probably benign	Het
Elf1	T	A	14: 79,580,743 (GRCm38)	N567K	probably benign	Het
Emsy	T	C	7: 98,646,479 (GRCm38)	N72S	possibly damaging	Het
Fam76a	A	T	4: 132,902,117 (GRCm38)		probably null	Het
Fam76a	A	G	4: 132,916,190 (GRCm38)	Y78H	probably damaging	Het
Fbn1	A	T	2: 125,324,919 (GRCm38)	C2026S	probably damaging	Het
Fbxo4	T	C	15: 3,969,041 (GRCm38)	T312A	probably benign	Het
Fhip1a	G	T	3: 85,688,570 (GRCm38)	T115K	probably damaging	Het
Flnb	A	T	14: 7,905,701 (GRCm38)	E1150D	probably benign	Het
Galt	T	C	4: 41,758,189 (GRCm38)	V318A	probably damaging	Het
Git1	T	G	11: 77,499,837 (GRCm38)	L133R	probably damaging	Het
Gm11168	G	A	9: 3,006,915 (GRCm38)	M213I	probably benign	Het
Gm7233	A	G	14: 43,179,966 (GRCm38)	E25G	probably benign	Het
Golga2	T	A	2: 32,297,156 (GRCm38)	N89K	probably damaging	Het
Grin1	T	A	2: 25,292,381 (GRCm38)	H956L	possibly damaging	Het
Hlcs	C	T	16: 94,268,539 (GRCm38)	V164I	possibly damaging	Het
Hmgcr	G	A	13: 96,666,193 (GRCm38)	T66M	probably damaging	Het
Ifi206	A	T	1: 173,480,866 (GRCm38)	H521Q	probably benign	Het
Lgals3bp	G	A	11: 118,393,514 (GRCm38)	T413I	probably damaging	Het
Lrrc7	A	G	3: 158,127,213 (GRCm38)		probably null	Het
Mapk11	T	C	15: 89,149,488 (GRCm38)	Y9C	probably damaging	Het
Mccc1	C	A	3: 35,975,873 (GRCm38)	M429I	probably damaging	Het
Metrnl	A	G	11: 121,707,924 (GRCm38)	E40G	probably benign	Het
Mrgpra1	A	G	7: 47,335,470 (GRCm38)	S154P	probably damaging	Het
Myh13	A	T	11: 67,341,270 (GRCm38)	I459F	probably damaging	Het
Nalf1	T	C	8: 9,208,026 (GRCm38)	Y374C	probably damaging	Het
Nedd4l	C	A	18: 65,172,927 (GRCm38)	D424E	probably damaging	Het
Nid1	C	T	13: 13,499,741 (GRCm38)	R902W	probably damaging	Het
Numa1	A	G	7: 102,013,566 (GRCm38)	T1997A	probably damaging	Het
Nutm1	G	A	2: 112,248,936 (GRCm38)	A878V	probably benign	Het
Nxf1	G	A	19: 8,766,798 (GRCm38)	A339T	probably benign	Het
Oas1b	C	A	5: 120,814,513 (GRCm38)	Q90K	probably benign	Het
Olfr1175-ps	A	G	2: 88,323,156 (GRCm38)	I183T	probably damaging	Het
Olfr721-ps1	A	C	14: 14,407,729 (GRCm38)	Y167S	possibly damaging	Het
Optn	T	C	2: 5,054,627 (GRCm38)	M27V	probably benign	Het
Or1r1	A	G	11: 73,984,008 (GRCm38)	F200S	probably damaging	Het
Or4f56	A	T	2: 111,873,050 (GRCm38)	D268E	possibly damaging	Het
Or5ac17	G	T	16: 59,215,859 (GRCm38)	F251L	probably damaging	Het
Or5g29	A	G	2: 85,590,938 (GRCm38)	T133A	probably benign	Het
Or5h18	G	T	16: 59,027,897 (GRCm38)	D3E	probably benign	Het
Oxgr1	T	C	14: 120,022,364 (GRCm38)	I144V	probably benign	Het
Pax5	T	A	4: 44,570,086 (GRCm38)	T127S	probably damaging	Het
Pcsk2	T	C	2: 143,687,679 (GRCm38)		probably null	Het
Pdxk	A	G	10: 78,464,792 (GRCm38)	V19A	possibly damaging	Het
Pik3c2a	A	T	7: 116,417,825 (GRCm38)	S232R	probably damaging	Het
Ppip5k1	T	C	2: 121,340,848 (GRCm38)	D620G	possibly damaging	Het
Ppp4r4	T	A	12: 103,590,858 (GRCm38)		probably null	Het
Psmd1	A	G	1: 86,078,712 (GRCm38)	N267D	probably damaging	Het
Pudp	A	G	18: 50,568,065 (GRCm38)	V199A	probably damaging	Het
Rasal3	T	A	17: 32,396,781 (GRCm38)	D361V	probably damaging	Het
Rbm12	T	C	2: 156,096,564 (GRCm38)	D596G	possibly damaging	Het
Rbm6	T	C	9: 107,852,903 (GRCm38)	D182G	probably damaging	Het
Rif1	T	C	2: 52,112,747 (GRCm38)	V2071A	probably damaging	Het
Rilp	C	T	11: 75,510,641 (GRCm38)	A110V	possibly damaging	Het
Rprd2	A	G	3: 95,774,333 (GRCm38)	V332A	probably benign	Het
Sbpl	T	A	17: 23,953,330 (GRCm38)	D205V	unknown	Het
Scn9a	T	C	2: 66,540,623 (GRCm38)	I538V	probably benign	Het
Serpina1d	T	C	12: 103,767,824 (GRCm38)	S74G	possibly damaging	Het
Serpina3n	T	C	12: 104,409,110 (GRCm38)	I147T	possibly damaging	Het
Serpinb8	A	G	1: 107,604,742 (GRCm38)	N188S	probably benign	Het
Sipa1l3	A	G	7: 29,377,641 (GRCm38)	V902A	probably damaging	Het
Slc25a47	T	A	12: 108,855,334 (GRCm38)	L123Q	probably damaging	Het
Slc30a2	A	T	4: 134,344,006 (GRCm38)		probably null	Het
Slc66a1	G	T	4: 139,300,001 (GRCm38)	H343Q	probably benign	Het
Snx13	T	A	12: 35,098,286 (GRCm38)	D271E	probably damaging	Het
Tbc1d9b	A	G	11: 50,171,298 (GRCm38)	N1211S	probably benign	Het
Tdrd3	T	A	14: 87,472,101 (GRCm38)	I67N	probably damaging	Het
Thbs1	T	C	2: 118,114,792 (GRCm38)	V282A	probably benign	Het
Tmc8	A	G	11: 117,791,605 (GRCm38)		probably null	Het
Trim11	T	A	11: 58,988,924 (GRCm38)	F284Y	probably null	Het
Ttn	A	G	2: 76,769,603 (GRCm38)	Y19076H	probably damaging	Het
Ttn	G	T	2: 76,721,797 (GRCm38)	Y29419*	probably null	Het
Ubr4	T	C	4: 139,421,733 (GRCm38)	S448P	possibly damaging	Het
Ugt2b34	T	C	5: 86,891,473 (GRCm38)	E443G	probably damaging	Het
Usp29	A	G	7: 6,961,391 (GRCm38)	T78A	probably damaging	Het
Vmn1r227	A	G	17: 20,735,134 (GRCm38)		noncoding transcript	Het
Vmn1r85	A	T	7: 13,084,861 (GRCm38)	W119R	probably damaging	Het
Vmn2r12	A	T	5: 109,086,513 (GRCm38)	V611E	probably damaging	Het
Vmn2r97	A	T	17: 18,929,288 (GRCm38)	M313L	probably benign	Het
Zap70	T	C	1: 36,779,173 (GRCm38)	Y314H	probably damaging	Het
Zfp667	T	A	7: 6,305,685 (GRCm38)	F451I	possibly damaging	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
R4701:Nphp4	UTSW	4	152,496,659 (GRCm38)	missense	probably damaging	1.00
R4778:Nphp4	UTSW	4	152,556,291 (GRCm38)	missense	probably benign	0.44
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'- CTACTGGTGTTAGCTAAGGATTACG -3'
(R):5'- AAGCTGATCCTGCGACTGTC -3'

Sequencing Primer
(F):5'- CTAAGGATTACGGTCAGAGGTCCTC -3'
(R):5'- TGATCCTGCGACTGTCAGAGTC -3'

Posted On

2016-07-22