Mutagenetix > Incidental Mutation

Incidental Mutation 'R1464:Nphp3'

200970

Institutional Source

Beutler Lab

Gene Symbol

Nphp3

Ensembl Gene

ENSMUSG00000032558

Gene Name

nephronophthisis 3 (adolescent)

Synonyms

pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3

MMRRC Submission

039518-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1464 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

103879743-103921010 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to C at 103909078 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000141596 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000035167] [ENSMUST00000193439] [ENSMUST00000194183] [ENSMUST00000194774]

AlphaFold

Q7TNH6

Predicted Effect

probably benign
Transcript: ENSMUST00000035167

SMART Domains

Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558

Domain	Start	End	E-Value	Type
low complexity region	46	69	N/A	INTRINSIC
coiled coil region	107	203	N/A	INTRINSIC
low complexity region	512	537	N/A	INTRINSIC
low complexity region	613	627	N/A	INTRINSIC
low complexity region	640	650	N/A	INTRINSIC
TPR	938	971	3.16e1	SMART
TPR	980	1013	7.74e-2	SMART
TPR	1022	1055	3.24e1	SMART
low complexity region	1066	1080	N/A	INTRINSIC
TPR	1088	1121	3.67e-3	SMART
TPR	1130	1163	1.3e-3	SMART
TPR	1172	1205	4.38e-1	SMART
TPR	1214	1247	8.69e-5	SMART
TPR	1256	1289	9.03e-3	SMART

Predicted Effect

SMART Domains

Protein: ENSMUSP00000116459
Gene: ENSMUSG00000032558

Domain	Start	End	E-Value	Type
coiled coil region	75	109	N/A	INTRINSIC
low complexity region	418	443	N/A	INTRINSIC
low complexity region	519	532	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000192485

Predicted Effect

probably benign
Transcript: ENSMUST00000193439

SMART Domains

Protein: ENSMUSP00000141540
Gene: ENSMUSG00000032558

Domain	Start	End	E-Value	Type
coiled coil region	75	109	N/A	INTRINSIC
low complexity region	418	443	N/A	INTRINSIC
low complexity region	519	532	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000193642

Predicted Effect

probably benign
Transcript: ENSMUST00000194183

SMART Domains

Protein: ENSMUSP00000142049
Gene: ENSMUSG00000032558

Domain	Start	End	E-Value	Type
Pfam:TPR_10	1	37	3.4e-5	PFAM
Pfam:TPR_12	1	71	1.8e-14	PFAM
Pfam:TPR_10	38	79	6.5e-8	PFAM
Pfam:TPR_1	39	72	6.8e-4	PFAM
Pfam:TPR_10	81	115	9e-3	PFAM
Pfam:TPR_7	83	118	1.6e-2	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000194774

SMART Domains

Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558

Domain	Start	End	E-Value	Type
coiled coil region	49	83	N/A	INTRINSIC
Pfam:NACHT	400	559	2e-6	PFAM
TPR	818	851	3.16e1	SMART
TPR	860	893	7.74e-2	SMART
TPR	902	935	3.24e1	SMART
low complexity region	946	960	N/A	INTRINSIC
TPR	968	1001	3.67e-3	SMART
TPR	1010	1043	1.3e-3	SMART
TPR	1052	1085	4.38e-1	SMART
TPR	1094	1127	8.69e-5	SMART
TPR	1136	1169	9.03e-3	SMART

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.0%
20x: 91.7%

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 containing a coiled-coil (CC) domain, a tubulin-tyrosine ligase (TTL) domain, and a tetratrico peptide repeat (TPR) domain. The encoded protein interacts with nephrocystin, it is required for normal ciliary development, and it functions in renal tubular development. Mutations in this gene are associated with nephronophthisis type 3, and also with renal-hepatic-pancreatic dysplasia, and Meckel syndrome type 7. Naturally occurring read-through transcripts exist between this gene and the downstream ACAD11 (acyl-CoA dehydrogenase family, member 11) gene. [provided by RefSeq, Feb 2011]
PHENOTYPE: Homozygous hypomorphic mice display slowly progressing kidney cysts, enlarged kidneys, increased blood urea nitrogen, kidney inflammation and associated fibrosis, and premature death. Homozygous null mice display mid gestational lethality with partial penetrance of situs inversus. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6030469F06Rik	A	G	12: 31,234,914 (GRCm39)		noncoding transcript	Het
Abca2	T	G	2: 25,337,846 (GRCm39)		probably benign	Het
Adamts8	T	A	9: 30,862,673 (GRCm39)	W86R	probably benign	Het
Adh1	A	G	3: 137,994,508 (GRCm39)		probably null	Het
Adipor2	A	T	6: 119,338,804 (GRCm39)	W150R	probably damaging	Het
Aff4	T	A	11: 53,263,351 (GRCm39)	S124T	probably damaging	Het
Ahnak	G	T	19: 8,982,260 (GRCm39)	K1181N	probably damaging	Het
Ak2	C	A	4: 128,896,152 (GRCm39)		probably benign	Het
Alkbh5	A	G	11: 60,429,873 (GRCm39)	I209V	probably benign	Het
Ankrd11	T	C	8: 123,619,463 (GRCm39)	E1442G	probably damaging	Het
Apba2	T	A	7: 64,345,297 (GRCm39)	D162E	probably benign	Het
Asic3	G	A	5: 24,618,819 (GRCm39)	G37E	probably damaging	Het
AU040320	A	T	4: 126,685,824 (GRCm39)	K133N	possibly damaging	Het
C1qtnf7	A	G	5: 43,766,481 (GRCm39)	S34G	probably benign	Het
Carf	A	G	1: 60,165,065 (GRCm39)		probably benign	Het
Ccdc148	T	A	2: 58,796,374 (GRCm39)	R463*	probably null	Het
Ccdc148	T	C	2: 58,824,455 (GRCm39)	R329G	probably damaging	Het
Ccdc185	A	G	1: 182,576,263 (GRCm39)	I142T	probably benign	Het
Cd274	T	C	19: 29,359,992 (GRCm39)		probably benign	Het
Chrna10	G	A	7: 101,763,454 (GRCm39)	P114S	probably damaging	Het
Chst10	A	G	1: 38,904,772 (GRCm39)	I311T	probably damaging	Het
Cpne9	T	C	6: 113,271,698 (GRCm39)	Y353H	probably damaging	Het
Cubn	G	T	2: 13,330,099 (GRCm39)	A2594E	possibly damaging	Het
Cyp3a13	T	C	5: 137,903,827 (GRCm39)	N277S	possibly damaging	Het
Dctn4	A	G	18: 60,671,478 (GRCm39)	T117A	probably damaging	Het
Ddah1	A	T	3: 145,559,029 (GRCm39)	K96*	probably null	Het
Ddx5	A	C	11: 106,675,711 (GRCm39)	D326E	probably benign	Het
Dlg2	T	C	7: 91,617,406 (GRCm39)	S323P	probably damaging	Het
Dnaaf1	C	T	8: 120,306,049 (GRCm39)	H109Y	probably damaging	Het
Dnah8	C	A	17: 30,914,147 (GRCm39)	R1098S	possibly damaging	Het
Dnajc13	T	C	9: 104,091,366 (GRCm39)	T642A	probably benign	Het
Dnajc18	A	G	18: 35,813,900 (GRCm39)	S290P	possibly damaging	Het
Dscam	T	A	16: 96,602,453 (GRCm39)	H663L	possibly damaging	Het
Eefsec	C	T	6: 88,353,182 (GRCm39)		probably benign	Het
Emc1	A	G	4: 139,098,248 (GRCm39)	N740S	probably damaging	Het
Enpp2	C	T	15: 54,727,208 (GRCm39)	G541D	probably damaging	Het
Fam234b	C	T	6: 135,205,490 (GRCm39)	T485I	probably benign	Het
Fbxl13	A	T	5: 21,688,989 (GRCm39)	I773K	probably benign	Het
Fmo4	A	G	1: 162,621,924 (GRCm39)	F429S	possibly damaging	Het
Fndc3b	A	G	3: 27,494,334 (GRCm39)		probably benign	Het
Frem1	T	C	4: 82,930,116 (GRCm39)	S277G	probably damaging	Het
Gaa	A	G	11: 119,163,810 (GRCm39)	I221V	probably benign	Het
Gnptab	A	G	10: 88,281,616 (GRCm39)		probably benign	Het
Gphn	T	A	12: 78,659,738 (GRCm39)		probably benign	Het
Helz2	T	C	2: 180,881,447 (GRCm39)	E345G	probably damaging	Het
Ifna4	G	T	4: 88,760,237 (GRCm39)	R47I	probably damaging	Het
Igsf21	C	A	4: 139,761,836 (GRCm39)	A281S	probably benign	Het
Ikzf3	T	A	11: 98,407,731 (GRCm39)	I37L	probably benign	Het
Inpp5d	A	T	1: 87,625,827 (GRCm39)		probably benign	Het
Jag1	T	C	2: 136,957,568 (GRCm39)	E48G	probably damaging	Het
Jarid2	G	T	13: 45,001,857 (GRCm39)	V57F	probably damaging	Het
Kcnj4	A	G	15: 79,369,605 (GRCm39)	L125P	probably damaging	Het
Kif21b	A	G	1: 136,083,891 (GRCm39)	K713E	possibly damaging	Het
Layn	T	A	9: 50,968,886 (GRCm39)	S286C	probably damaging	Het
Lepr	T	A	4: 101,592,878 (GRCm39)	D164E	probably benign	Het
Macroh2a1	A	T	13: 56,230,949 (GRCm39)	S310T	probably damaging	Het
Map3k1	T	C	13: 111,892,405 (GRCm39)	H950R	possibly damaging	Het
Map4k5	C	A	12: 69,852,124 (GRCm39)	V801L	possibly damaging	Het
Mapkbp1	T	A	2: 119,851,742 (GRCm39)	S895T	probably benign	Het
Mthfr	T	A	4: 148,138,029 (GRCm39)		probably benign	Het
Naca	T	A	10: 127,884,157 (GRCm39)	M2157K	probably damaging	Het
Nav2	T	C	7: 49,011,952 (GRCm39)	I61T	probably damaging	Het
Nkx2-5	C	A	17: 27,058,253 (GRCm39)	A234S	probably benign	Het
Nol8	G	A	13: 49,830,264 (GRCm39)	S1116N	probably benign	Het
Nppa	T	C	4: 148,085,304 (GRCm39)	S5P	probably benign	Het
Nup210	A	G	6: 91,030,551 (GRCm39)	V123A	possibly damaging	Het
Or13a21	G	T	7: 139,999,286 (GRCm39)	N133K	probably benign	Het
Osbpl11	A	G	16: 33,049,455 (GRCm39)	K604R	probably damaging	Het
Osbpl1a	C	T	18: 13,047,615 (GRCm39)	S113N	probably benign	Het
P2rx4	C	A	5: 122,852,602 (GRCm39)	P92Q	probably damaging	Het
Pde9a	A	T	17: 31,692,136 (GRCm39)	Q148L	probably benign	Het
Phf21b	T	A	15: 84,689,160 (GRCm39)	H122L	probably damaging	Het
Pik3ca	T	A	3: 32,515,990 (GRCm39)	F977I	probably damaging	Het
Pkd1l3	A	G	8: 110,363,059 (GRCm39)		probably benign	Het
Potefam1	A	G	2: 111,055,748 (GRCm39)		probably null	Het
Pp2d1	T	G	17: 53,823,015 (GRCm39)	K17T	possibly damaging	Het
Ppp4r2	A	G	6: 100,843,527 (GRCm39)	E415G	probably damaging	Het
Pramel19	T	A	4: 101,798,503 (GRCm39)	L158Q	probably damaging	Het
Prkg1	A	G	19: 30,556,270 (GRCm39)	S559P	probably damaging	Het
Prss45	A	T	9: 110,670,019 (GRCm39)	Y276F	possibly damaging	Het
Ptk7	G	T	17: 46,883,517 (GRCm39)	N849K	probably damaging	Het
Rnf121	A	G	7: 101,680,782 (GRCm39)	I125T	possibly damaging	Het
Rnf17	A	G	14: 56,699,368 (GRCm39)	N502S	probably damaging	Het
Sap25	T	A	5: 137,640,622 (GRCm39)	Y167*	probably null	Het
Sdk2	G	A	11: 113,720,906 (GRCm39)	T1341I	possibly damaging	Het
Sgcb	A	G	5: 73,792,896 (GRCm39)	V302A	probably benign	Het
Skor1	T	A	9: 63,047,393 (GRCm39)	M865L	possibly damaging	Het
Slc25a45	T	C	19: 5,929,928 (GRCm39)		probably benign	Het
Slc2a3	A	G	6: 122,714,269 (GRCm39)		probably benign	Het
Slc35g1	C	A	19: 38,391,665 (GRCm39)	L316I	probably benign	Het
Slco1a8	C	T	6: 141,938,243 (GRCm39)	W225*	probably null	Het
Spint4	T	A	2: 164,540,568 (GRCm39)	L33H	probably damaging	Het
Sptlc3	A	T	2: 139,389,154 (GRCm39)	D178V	probably benign	Het
Stoml1	A	G	9: 58,167,709 (GRCm39)		probably benign	Het
Tbc1d2	T	A	4: 46,606,491 (GRCm39)	Y818F	possibly damaging	Het
Tbc1d24	A	T	17: 24,400,197 (GRCm39)		probably null	Het
Teddm2	C	T	1: 153,726,277 (GRCm39)	W146*	probably null	Het
Ttn	T	A	2: 76,589,338 (GRCm39)	D12948V	probably damaging	Het
Txndc8	T	C	4: 58,000,274 (GRCm39)	T102A	probably damaging	Het
Uxs1	G	A	1: 43,804,076 (GRCm39)	Q280*	probably null	Het
Vmn1r167	T	C	7: 23,204,681 (GRCm39)	T112A	possibly damaging	Het
Vmn1r195	A	T	13: 22,463,348 (GRCm39)	I273L	probably benign	Het
Vmn1r28	T	A	6: 58,242,217 (GRCm39)	M20K	probably benign	Het
Vmn1r53	G	A	6: 90,200,914 (GRCm39)	L137F	probably benign	Het
Vmn2r105	G	A	17: 20,449,004 (GRCm39)		probably benign	Het
Vps13b	C	T	15: 35,709,630 (GRCm39)	A1859V	probably benign	Het
Vwa5b2	A	G	16: 20,415,019 (GRCm39)	H347R	probably benign	Het
Wnk2	G	A	13: 49,235,451 (GRCm39)	P655S	probably damaging	Het
Zan	T	G	5: 137,418,191 (GRCm39)	D2969A	unknown	Het
Zbtb24	A	G	10: 41,331,075 (GRCm39)	H334R	probably damaging	Het
Zfp108	A	G	7: 23,959,973 (GRCm39)	D188G	probably benign	Het
Zfp784	A	T	7: 5,038,800 (GRCm39)	C253S	possibly damaging	Het
Zfr	T	G	15: 12,146,458 (GRCm39)	C336W	probably damaging	Het

Other mutations in Nphp3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01707:Nphp3	APN	9	103,895,357 (GRCm39)	missense	possibly damaging	0.75
IGL02329:Nphp3	APN	9	103,903,167 (GRCm39)	missense	probably benign	0.19
lithograph	UTSW	9	103,919,189 (GRCm39)	missense	probably damaging	1.00
quartzite	UTSW	9	103,913,376 (GRCm39)	missense	probably damaging	1.00
F5770:Nphp3	UTSW	9	103,913,093 (GRCm39)	critical splice donor site	probably null
FR4548:Nphp3	UTSW	9	103,903,138 (GRCm39)	small deletion	probably benign
FR4589:Nphp3	UTSW	9	103,903,138 (GRCm39)	small deletion	probably benign
R0112:Nphp3	UTSW	9	103,914,547 (GRCm39)	missense	possibly damaging	0.80
R0555:Nphp3	UTSW	9	103,900,633 (GRCm39)	missense	probably damaging	1.00
R0632:Nphp3	UTSW	9	103,895,473 (GRCm39)	missense	probably damaging	1.00
R0674:Nphp3	UTSW	9	103,913,481 (GRCm39)	critical splice donor site	probably null
R0743:Nphp3	UTSW	9	103,899,967 (GRCm39)	small deletion	probably benign
R0853:Nphp3	UTSW	9	103,909,132 (GRCm39)	missense	probably benign	0.03
R0920:Nphp3	UTSW	9	103,909,106 (GRCm39)	missense	probably benign	0.00
R1420:Nphp3	UTSW	9	103,913,092 (GRCm39)	critical splice donor site	probably null
R1476:Nphp3	UTSW	9	103,903,126 (GRCm39)	missense	possibly damaging	0.81
R1585:Nphp3	UTSW	9	103,886,413 (GRCm39)	missense	probably damaging	1.00
R1608:Nphp3	UTSW	9	103,913,039 (GRCm39)	missense	probably benign	0.30
R1688:Nphp3	UTSW	9	103,880,323 (GRCm39)	missense	probably damaging	1.00
R1691:Nphp3	UTSW	9	103,880,010 (GRCm39)	missense	probably benign
R1807:Nphp3	UTSW	9	103,897,940 (GRCm39)	missense	probably benign	0.01
R1857:Nphp3	UTSW	9	103,898,493 (GRCm39)	missense	possibly damaging	0.87
R1962:Nphp3	UTSW	9	103,898,537 (GRCm39)	missense	probably benign	0.00
R2127:Nphp3	UTSW	9	103,885,442 (GRCm39)	missense	probably damaging	0.98
R2138:Nphp3	UTSW	9	103,903,102 (GRCm39)	missense	possibly damaging	0.89
R2233:Nphp3	UTSW	9	103,914,575 (GRCm39)	missense	probably benign	0.02
R2234:Nphp3	UTSW	9	103,914,575 (GRCm39)	missense	probably benign	0.02
R3861:Nphp3	UTSW	9	103,916,525 (GRCm39)	unclassified	probably benign
R3928:Nphp3	UTSW	9	103,888,929 (GRCm39)	missense	probably damaging	0.99
R3961:Nphp3	UTSW	9	103,880,241 (GRCm39)	nonsense	probably null
R4182:Nphp3	UTSW	9	103,915,663 (GRCm39)	missense	probably benign	0.06
R4294:Nphp3	UTSW	9	103,899,916 (GRCm39)	missense	probably damaging	1.00
R4387:Nphp3	UTSW	9	103,907,219 (GRCm39)	missense	possibly damaging	0.94
R4625:Nphp3	UTSW	9	103,913,358 (GRCm39)	missense	possibly damaging	0.66
R4628:Nphp3	UTSW	9	103,880,257 (GRCm39)	missense	probably damaging	0.99
R4696:Nphp3	UTSW	9	103,899,931 (GRCm39)	missense	probably benign	0.01
R4865:Nphp3	UTSW	9	103,909,169 (GRCm39)	missense	probably benign
R4886:Nphp3	UTSW	9	103,880,193 (GRCm39)	missense	probably damaging	1.00
R4973:Nphp3	UTSW	9	103,909,198 (GRCm39)	missense	probably benign
R5445:Nphp3	UTSW	9	103,881,922 (GRCm39)	missense	probably damaging	1.00
R5451:Nphp3	UTSW	9	103,919,221 (GRCm39)	missense	probably benign
R5520:Nphp3	UTSW	9	103,901,872 (GRCm39)	missense	probably benign	0.30
R5641:Nphp3	UTSW	9	103,913,352 (GRCm39)	missense	probably damaging	1.00
R5847:Nphp3	UTSW	9	103,880,236 (GRCm39)	missense	probably damaging	1.00
R5928:Nphp3	UTSW	9	103,912,996 (GRCm39)	missense	probably benign	0.01
R5931:Nphp3	UTSW	9	103,897,945 (GRCm39)	missense	probably damaging	1.00
R6161:Nphp3	UTSW	9	103,909,105 (GRCm39)	missense	probably benign	0.11
R6298:Nphp3	UTSW	9	103,892,640 (GRCm39)	missense	probably damaging	1.00
R6890:Nphp3	UTSW	9	103,919,153 (GRCm39)	missense	probably damaging	0.96
R7009:Nphp3	UTSW	9	103,893,315 (GRCm39)	missense	probably null	0.00
R7065:Nphp3	UTSW	9	103,919,189 (GRCm39)	missense	probably damaging	1.00
R7146:Nphp3	UTSW	9	103,882,036 (GRCm39)	nonsense	probably null
R7198:Nphp3	UTSW	9	103,881,974 (GRCm39)	missense	probably damaging	1.00
R7360:Nphp3	UTSW	9	103,893,277 (GRCm39)	critical splice acceptor site	probably null
R7369:Nphp3	UTSW	9	103,895,449 (GRCm39)	missense	probably damaging	0.99
R7554:Nphp3	UTSW	9	103,919,270 (GRCm39)	missense	probably damaging	0.98
R7591:Nphp3	UTSW	9	103,895,477 (GRCm39)	critical splice donor site	probably null
R7665:Nphp3	UTSW	9	103,882,592 (GRCm39)	splice site	probably null
R7672:Nphp3	UTSW	9	103,909,159 (GRCm39)	missense	probably benign
R7675:Nphp3	UTSW	9	103,893,287 (GRCm39)	missense	probably benign
R8039:Nphp3	UTSW	9	103,909,162 (GRCm39)	missense	probably benign
R8145:Nphp3	UTSW	9	103,913,050 (GRCm39)	missense	probably benign	0.16
R8211:Nphp3	UTSW	9	103,909,096 (GRCm39)	missense	possibly damaging	0.80
R8882:Nphp3	UTSW	9	103,882,793 (GRCm39)	missense	possibly damaging	0.77
R9020:Nphp3	UTSW	9	103,909,150 (GRCm39)	missense	probably benign	0.00
R9132:Nphp3	UTSW	9	103,897,980 (GRCm39)	missense	probably damaging	1.00
R9135:Nphp3	UTSW	9	103,909,214 (GRCm39)	missense	probably damaging	0.99
R9159:Nphp3	UTSW	9	103,897,980 (GRCm39)	missense	probably damaging	1.00
R9204:Nphp3	UTSW	9	103,919,305 (GRCm39)	missense	probably benign
R9226:Nphp3	UTSW	9	103,885,328 (GRCm39)	missense	probably benign	0.00
R9229:Nphp3	UTSW	9	103,913,376 (GRCm39)	missense	probably damaging	1.00
R9526:Nphp3	UTSW	9	103,913,337 (GRCm39)	missense	probably damaging	1.00
R9678:Nphp3	UTSW	9	103,900,686 (GRCm39)	missense	possibly damaging	0.90
R9731:Nphp3	UTSW	9	103,886,369 (GRCm39)	missense	probably damaging	1.00
V7583:Nphp3	UTSW	9	103,913,093 (GRCm39)	critical splice donor site	probably null

Predicted Primers

Posted On

2014-05-23