Mutagenetix > Incidental Mutation

Incidental Mutation 'R7814:Nphp4'

601349

Institutional Source

Beutler Lab

Gene Symbol

Nphp4

Ensembl Gene

ENSMUSG00000039577

Gene Name

nephronophthisis 4 (juvenile) homolog (human)

Synonyms

nmf192, 4930564O18Rik

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.151) question?

Stock #

R7814 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

152476706-152563183 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 152544403 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Tyrosine at position 749 (D749Y)

Ref Sequence

ENSEMBL: ENSMUSP00000049920 (fasta)

Gene Model

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

AlphaFold

P59240

Predicted Effect

probably damaging
Transcript: ENSMUST00000056567
AA Change: D749Y

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

SMART Domains

Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: D749Y

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: D749Y

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

SMART Domains

Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: D749Y

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.2%

Validation Efficiency

100% (90/90)

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110065P20Rik	C	T	4: 124,850,602	G20R	not run	Het
4931409K22Rik	G	T	5: 24,545,422	Q626K	possibly damaging	Het
Adamts13	A	T	2: 26,996,549	M927L	probably benign	Het
Akap6	T	A	12: 53,140,961	N1719K	probably benign	Het
Ank3	G	A	10: 69,986,904	V468M		Het
Aox1	A	G	1: 58,085,467	T956A	probably benign	Het
Ap4m1	T	C	5: 138,174,817	V140A	probably benign	Het
Apc	A	G	18: 34,272,539	T173A	probably damaging	Het
Bclaf1	A	G	10: 20,334,619	T839A	possibly damaging	Het
Btn2a2	T	A	13: 23,482,806	I210F	possibly damaging	Het
Cadps	A	G	14: 12,376,706	W1269R	probably damaging	Het
Capn2	G	C	1: 182,492,146	P159R	probably damaging	Het
Ccdc134	T	G	15: 82,131,523	V68G	probably damaging	Het
Cdh26	A	G	2: 178,470,035	T463A	probably damaging	Het
Cfap206	C	T	4: 34,716,347	V373I	probably benign	Het
Clpx	T	C	9: 65,324,301		probably null	Het
Ctnnd2	A	T	15: 31,020,728	Y1145F	probably benign	Het
Ctr9	T	A	7: 111,033,927	D127E	probably benign	Het
Cyp2f2	G	A	7: 27,129,253	V183I	probably benign	Het
Cyp7b1	G	A	3: 18,097,302	S249L	probably benign	Het
D630023F18Rik	T	A	1: 65,116,691	D125V	possibly damaging	Het
Dbh	A	T	2: 27,174,848	Y357F	probably damaging	Het
Dbp	T	A	7: 45,706,990	L175Q	probably benign	Het
Dmwd	A	T	7: 19,080,843	T473S	probably benign	Het
Dnah9	T	A	11: 66,005,660	Q2446L	probably damaging	Het
Dnmbp	T	C	19: 43,854,176	K498R	probably benign	Het
Dopey2	T	A	16: 93,799,971	I1924N	probably damaging	Het
Dsg1a	T	A	18: 20,338,515		probably null	Het
Dzank1	T	C	2: 144,522,564	T38A	probably damaging	Het
Egfem1	A	G	3: 29,686,791	H538R	probably damaging	Het
Entpd1	T	C	19: 40,727,447	C353R	probably damaging	Het
Ephx2	C	A	14: 66,110,229	C78F	probably benign	Het
Faf2	A	T	13: 54,660,961	H388L	probably benign	Het
Fam186a	G	A	15: 99,944,664	T1233I	possibly damaging	Het
Gfra2	C	A	14: 70,895,970	A80E	probably damaging	Het
Gif	C	A	19: 11,750,187	P125Q	probably benign	Het
Gm17175	T	A	14: 51,574,035		probably benign	Het
Gm8180	T	C	14: 43,783,646	D35G	possibly damaging	Het
Gm884	T	A	11: 103,614,173	H2323L	possibly damaging	Het
Gpr68	C	T	12: 100,879,043	V81M	probably damaging	Het
Hsd3b6	A	G	3: 98,810,943	L35P	probably damaging	Het
Hspd1	A	C	1: 55,078,644	V485G	possibly damaging	Het
Il16	A	G	7: 83,670,140	V381A	possibly damaging	Het
Il17rd	G	A	14: 27,100,117	C600Y	probably benign	Het
Ins2	C	A	7: 142,679,586		probably benign	Het
Itsn2	T	C	12: 4,658,561	I872T	probably benign	Het
Jakmip3	A	T	7: 139,019,129	D219V	probably damaging	Het
Jph4	T	C	14: 55,109,735	T452A	probably damaging	Het
Kazn	T	C	4: 142,210,170	E12G	unknown	Het
Kif20b	A	C	19: 34,950,955	S1206R	possibly damaging	Het
Lca5l	A	G	16: 96,162,557		probably null	Het
Lgals2	A	T	15: 78,851,333	S60R	probably benign	Het
Map10	A	G	8: 125,671,611	E581G	probably benign	Het
Map2k7	G	T	8: 4,243,744	R128L	probably benign	Het
Mapk8	G	C	14: 33,410,877	S34*	probably null	Het
Mcat	A	G	15: 83,547,909	Y253H	probably damaging	Het
Mmp2	T	C	8: 92,850,170	L607P	probably benign	Het
Ncor1	A	T	11: 62,333,926	V836E	probably damaging	Het
Neb	A	G	2: 52,137,380	S7113P	probably damaging	Het
Olfr115	T	A	17: 37,610,656	T32S	probably benign	Het
Olfr1185-ps1	A	G	2: 88,499,072		probably benign	Het
Olfr175-ps1	T	C	16: 58,824,002	K236E	probably damaging	Het
Olfr338	T	C	2: 36,376,809	I11T	possibly damaging	Het
Osbpl11	A	T	16: 33,210,061	R220*	probably null	Het
Plrg1	G	A	3: 83,056,837	V26M	probably damaging	Het
Polr1b	C	A	2: 129,125,544	F952L	probably damaging	Het
Ppfia3	A	C	7: 45,352,262	S560A	probably benign	Het
Ppp3cc	T	A	14: 70,225,015	N391I	possibly damaging	Het
Prdx6b	T	C	2: 80,292,960	S38P	possibly damaging	Het
Psg23	A	T	7: 18,606,914	*472R	probably null	Het
Rapgef4	A	T	2: 72,223,117	M587L	probably benign	Het
Rfx3	T	A	19: 27,826,070	M247L	probably benign	Het
Rgs7	T	A	1: 175,076,069	H463L	probably benign	Het
Riiad1	G	T	3: 94,465,855	S106R	probably benign	Het
Rims4	A	C	2: 163,918,628	I19S	probably benign	Het
Ros1	A	T	10: 52,096,137	M1648K	probably benign	Het
Rrn3	T	C	16: 13,811,589	F590L	probably benign	Het
Samd9l	T	A	6: 3,374,793	T823S	possibly damaging	Het
Sfxn1	C	A	13: 54,091,231	P115Q	possibly damaging	Het
Slc10a7	T	C	8: 78,698,573		probably null	Het
Slc25a16	A	T	10: 62,937,420	M142L	probably benign	Het
Stat2	CGCTGGAGCCAGCCCCACAAGTCCTGCTGGAGCCAGCCCCACAAGTCCTGCTGGAGCCAGCCCCACAAGTCCTGCTGGAGCCAGCCCCACAAGTCCTGCTGGAGCCAGCCCCACAAGTCCAGCTGGAGCCAGCCCCACAAGTCCTGCTGGAGCTAGCCCCACAAGTCCTGCTGGAGCCAGCCCCACAAGTCCTGCTGGAGCTAGCCCCACAAGTCCAGCTGGAGCCAGC	CGCTGGAGCCAGCCCCACAAGTCCTGCTGGAGCCAGCCCCACAAGTCCTGCTGGAGCCAGCCCCACAAGTCCTGCTGGAGCCAGCCCCACAAGTCCAGCTGGAGCCAGCCCCACAAGTCCTGCTGGAGCTAGCCCCACAAGTCCTGCTGGAGCCAGCCCCACAAGTCCTGCTGGAGCTAGCCCCACAAGTCCAGCTGGAGCCAGC	10: 128,290,728		probably benign	Het
Stat5a	T	G	11: 100,875,027	L313R	probably damaging	Het
Strap	A	G	6: 137,741,978	E176G	possibly damaging	Het
Tlr4	T	G	4: 66,841,079	L703R	probably damaging	Het
Trim36	A	T	18: 46,167,624	V660D	possibly damaging	Het
Tspoap1	T	A	11: 87,775,524	D980E	probably damaging	Het
Usp28	T	C	9: 49,003,918	V157A	probably benign	Het
Vmn2r17	A	T	5: 109,427,873	R203S	probably benign	Het
Vmn2r66	T	C	7: 85,007,264	I181M	probably benign	Het
Zan	T	A	5: 137,463,579	T1113S	unknown	Het
Zfp442	C	T	2: 150,409,482	D167N	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
R5890:Nphp4	UTSW	4	152547079	missense	probably benign	0.44
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
R7841:Nphp4	UTSW	4	152496683	missense	probably benign	0.01
R8346:Nphp4	UTSW	4	152561321	missense	probably damaging	1.00
R8479:Nphp4	UTSW	4	152524290	missense	probably benign	0.01
R8847:Nphp4	UTSW	4	152506406	missense	probably damaging	1.00
R8995:Nphp4	UTSW	4	152538888	missense	probably damaging	1.00
R8997:Nphp4	UTSW	4	152538888	missense	probably damaging	1.00
R9075:Nphp4	UTSW	4	152507448	missense	probably damaging	1.00
R9089:Nphp4	UTSW	4	152561216	missense	possibly damaging	0.87
R9191:Nphp4	UTSW	4	152556230	missense	probably damaging	1.00
R9274:Nphp4	UTSW	4	152555599	missense	probably benign	0.05
R9311:Nphp4	UTSW	4	152524257	missense	probably damaging	0.99
R9383:Nphp4	UTSW	4	152544461	critical splice donor site	probably null
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'- GGCAGAAATATCTCCGCATGTAAG -3'
(R):5'- ACACATGGCTGTAGAATCCAG -3'

Sequencing Primer
(F):5'- GGATGATAAATGGCCCTAATTACCTG -3'
(R):5'- AGGGAACACTGTCCTGTTTGTCAC -3'

Posted On

2019-11-26