Mutagenetix > Incidental Mutations

Incidental Mutation 'R5890:Nphp4'

457078

Institutional Source

Beutler Lab

Gene Symbol

Nphp4

Ensembl Gene

ENSMUSG00000039577

Gene Name

nephronophthisis 4 (juvenile) homolog (human)

Synonyms

nmf192, 4930564O18Rik

MMRRC Submission

044091-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.195) question?

Stock #

R5890 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

152476706-152563183 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 152547079 bp

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 812 (V812A)

Ref Sequence

ENSEMBL: ENSMUSP00000080128 (fasta)

Gene Model

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

Predicted Effect

probably benign
Transcript: ENSMUST00000056567
AA Change: V812A

PolyPhen 2 Score 0.441 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: V812A

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: V812A

PolyPhen 2 Score 0.441 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: V812A

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

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.6%
20x: 92.9%

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610507B11Rik	C	T	11: 78,273,270	Q40*	probably null	Het
Abcc9	A	G	6: 142,604,828		probably null	Het
Acsm3	C	A	7: 119,775,234	T303N	probably benign	Het
Adamts13	A	T	2: 26,986,591	R506W	probably damaging	Het
Adck5	C	T	15: 76,593,585	T166M	probably damaging	Het
Adcy8	T	A	15: 64,815,417	I413F	probably damaging	Het
Adgrl2	A	T	3: 148,859,175	D252E	probably damaging	Het
Aldh16a1	T	A	7: 45,144,545	T636S	probably benign	Het
Ampd1	C	A	3: 103,090,075	F264L	probably damaging	Het
Arhgap17	T	C	7: 123,286,758		probably benign	Het
Babam2	A	G	5: 32,064,807		probably benign	Het
Bod1l	T	A	5: 41,820,578	E1131V	probably benign	Het
Cbs	C	T	17: 31,613,219	V553M	probably damaging	Het
Cd72	T	C	4: 43,454,475	K18R	probably damaging	Het
Cep89	A	G	7: 35,429,162	Y580C	probably damaging	Het
Chrnb1	T	A	11: 69,792,729	I264F	possibly damaging	Het
Cntf	A	G	19: 12,763,993	W168R	probably damaging	Het
Cxxc1	T	A	18: 74,221,166	D648E	possibly damaging	Het
Cyp2c68	A	T	19: 39,712,492	L294Q	probably damaging	Het
Dab2ip	T	C	2: 35,715,402	S532P	probably damaging	Het
Defb3	G	A	8: 19,295,184	C52Y	probably damaging	Het
Dennd5a	T	G	7: 109,934,221	E114A	probably benign	Het
Dnah12	T	C	14: 26,706,884	F222L	probably benign	Het
Dock9	A	C	14: 121,668,408		probably null	Het
Fras1	A	T	5: 96,645,948	H1043L	probably benign	Het
Gamt	C	A	10: 80,259,907	R63L	possibly damaging	Het
Gm1527	A	G	3: 28,915,395	H298R	probably benign	Het
Gphb5	C	T	12: 75,415,822		probably null	Het
Greb1	A	T	12: 16,733,421	V104D	possibly damaging	Het
Hck	A	G	2: 153,129,076	D86G	probably damaging	Het
Jhy	T	A	9: 40,922,662	K321*	probably null	Het
Kcna5	C	T	6: 126,534,736	R143H	probably damaging	Het
Kif19a	G	T	11: 114,789,438	W867L	possibly damaging	Het
Map3k4	G	A	17: 12,271,416	A376V	probably damaging	Het
Mars	A	T	10: 127,298,045	M661K	probably benign	Het
Mecp2	C	T	X: 74,035,437	V496M	probably damaging	Het
Mfsd2b	A	T	12: 4,867,651	C132S	probably damaging	Het
Mfsd4a	T	C	1: 132,038,928	Y356C	probably damaging	Het
Mif4gd	G	T	11: 115,609,362	A89E	probably benign	Het
Mkln1	A	T	6: 31,490,547	E593D	probably benign	Het
Mlh1	G	T	9: 111,228,495	N749K	possibly damaging	Het
Mrgprb2	T	A	7: 48,551,959	*339C	probably null	Het
Nrcam	G	T	12: 44,576,771	V1048L	probably benign	Het
Obsl1	G	A	1: 75,493,859	A856V	probably damaging	Het
Osgepl1	T	A	1: 53,318,167	F163I	probably damaging	Het
Pcdha6	C	A	18: 36,969,068	T438K	possibly damaging	Het
Pcdhb20	A	T	18: 37,505,233	M271L	probably benign	Het
Phip	T	C	9: 82,906,952	T770A	probably benign	Het
Ppm1d	A	G	11: 85,326,908	T166A	probably damaging	Het
Ptprf	A	T	4: 118,224,735	I1102K	probably benign	Het
Sbsn	T	C	7: 30,753,267	V569A	possibly damaging	Het
Skida1	T	A	2: 18,046,003		probably benign	Het
Smg1	T	A	7: 118,190,586		probably benign	Het
Sorcs2	A	G	5: 36,229,191	Y168H	probably damaging	Het
Sufu	A	T	19: 46,454,733		probably null	Het
Tbc1d24	A	T	17: 24,185,526	W215R	probably damaging	Het
Tenm4	T	C	7: 96,902,860	L2502P	probably damaging	Het
Tgm4	A	T	9: 123,061,638	E10V	probably damaging	Het
Trip11	T	C	12: 101,885,972	E611G	probably damaging	Het
Ttn	C	A	2: 76,709,899	A34248S	possibly damaging	Het
Ube3a	T	A	7: 59,272,028	N49K	probably damaging	Het
Ube3c	A	G	5: 29,658,292	D855G	possibly damaging	Het
Ugt8a	A	G	3: 125,875,553	S301P	probably benign	Het
Wdfy4	T	A	14: 33,102,577	N1295I	possibly damaging	Het
Wdr47	G	T	3: 108,610,012	G43C	probably damaging	Het
Wdtc1	A	C	4: 133,294,362	L601W	unknown	Het
Zfp236	A	G	18: 82,640,151	F614S	possibly damaging	Het
Zfp637	T	A	6: 117,845,086	D58E	possibly damaging	Het

Other mutations in Nphp4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00922:Nphp4	APN	4	152537309	splice site	probably benign
IGL00963:Nphp4	APN	4	152537861	missense	probably benign	0.01
IGL01571:Nphp4	APN	4	152556382	missense	probably benign	0.21
IGL01707:Nphp4	APN	4	152538983	missense	probably benign	0.00
IGL01837:Nphp4	APN	4	152488881	missense	probably damaging	0.96
IGL02341:Nphp4	APN	4	152555469	splice site	probably benign
IGL02558:Nphp4	APN	4	152555531	missense	probably damaging	1.00
IGL02563:Nphp4	APN	4	152556220	missense	probably benign	0.00
IGL02712:Nphp4	APN	4	152556275	missense	probably damaging	1.00
IGL03023:Nphp4	APN	4	152524235	splice site	probably null
R0280:Nphp4	UTSW	4	152551936	splice site	probably benign
R0317:Nphp4	UTSW	4	152551931	critical splice donor site	probably null
R0410:Nphp4	UTSW	4	152557046	missense	probably benign
R0433:Nphp4	UTSW	4	152518172	missense	probably benign	0.00
R0706:Nphp4	UTSW	4	152555617	missense	probably damaging	0.98
R0785:Nphp4	UTSW	4	152562109	missense	possibly damaging	0.58
R0890:Nphp4	UTSW	4	152498220	missense	possibly damaging	0.93
R0930:Nphp4	UTSW	4	152538055	missense	probably benign	0.01
R1202:Nphp4	UTSW	4	152488729	splice site	probably null
R1203:Nphp4	UTSW	4	152488832	missense	probably damaging	0.96
R1366:Nphp4	UTSW	4	152502926	missense	probably damaging	0.96
R1452:Nphp4	UTSW	4	152547018	missense	probably damaging	0.99
R1598:Nphp4	UTSW	4	152562090	missense	probably benign	0.00
R1699:Nphp4	UTSW	4	152496664	missense	probably damaging	0.99
R2007:Nphp4	UTSW	4	152554654	missense	probably damaging	0.97
R2082:Nphp4	UTSW	4	152559364	missense	probably benign	0.38
R2264:Nphp4	UTSW	4	152503008	splice site	probably benign
R2280:Nphp4	UTSW	4	152557043	missense	possibly damaging	0.95
R2281:Nphp4	UTSW	4	152557043	missense	possibly damaging	0.95
R2926:Nphp4	UTSW	4	152518139	missense	probably damaging	0.99
R3764:Nphp4	UTSW	4	152538017	splice site	probably benign
R4084:Nphp4	UTSW	4	152488791	missense	probably damaging	1.00
R4091:Nphp4	UTSW	4	152547018	missense	probably damaging	0.97
R4240:Nphp4	UTSW	4	152555684	missense	probably benign	0.07
R4701:Nphp4	UTSW	4	152496659	missense	probably damaging	1.00
R4778:Nphp4	UTSW	4	152556291	missense	probably benign	0.44
R4783:Nphp4	UTSW	4	152554546	missense	probably benign	0.00
R4784:Nphp4	UTSW	4	152554546	missense	probably benign	0.00
R4974:Nphp4	UTSW	4	152537793	missense	probably damaging	1.00
R5053:Nphp4	UTSW	4	152544462	splice site	probably null
R5117:Nphp4	UTSW	4	152524232	splice site	probably null
R5128:Nphp4	UTSW	4	152502991	missense	probably benign	0.01
R5665:Nphp4	UTSW	4	152506485	missense	probably benign	0.25
R6171:Nphp4	UTSW	4	152544449	missense	probably damaging	0.99
R6601:Nphp4	UTSW	4	152503007	splice site	probably null
R6772:Nphp4	UTSW	4	152544406	missense	probably benign	0.07
R6806:Nphp4	UTSW	4	152538101	missense	probably benign	0.02
R7006:Nphp4	UTSW	4	152488802	missense	probably benign	0.12
R7124:Nphp4	UTSW	4	152555684	missense	probably benign	0.07
R7381:Nphp4	UTSW	4	152499003	missense	possibly damaging	0.94
R7411:Nphp4	UTSW	4	152554717	missense	probably benign	0.25
R7638:Nphp4	UTSW	4	152554534	missense	probably benign	0.08
R7814:Nphp4	UTSW	4	152524272	missense	possibly damaging	0.93
R7814:Nphp4	UTSW	4	152544403	missense	probably damaging	1.00
R7841:Nphp4	UTSW	4	152496683	missense	probably benign	0.01
T0970:Nphp4	UTSW	4	152556379	missense	probably damaging	1.00
X0058:Nphp4	UTSW	4	152559707	missense	possibly damaging	0.95
Z1177:Nphp4	UTSW	4	152518196	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TAACCCTCAGGAGTCTGCTG -3'
(R):5'- AGAAGGGTGATTCCAAGCTC -3'

Sequencing Primer
(F):5'- TGTCCGTGGTTAGACCCCAG -3'
(R):5'- AAGGGTGATTCCAAGCTCCTGTC -3'

Posted On

2017-02-15