Mutagenetix > Incidental Mutation

Incidental Mutation 'R9135:Nphp3'

693944

Institutional Source

Beutler Lab

Gene Symbol

Nphp3

Ensembl Gene

ENSMUSG00000032558

Gene Name

nephronophthisis 3 (adolescent)

Synonyms

pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9135 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

103879743-103921010 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 103909214 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Arginine at position 808 (L808R)

Ref Sequence

ENSEMBL: ENSMUSP00000035167 (fasta)

Gene Model

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

AlphaFold

Q7TNH6

Predicted Effect

probably damaging
Transcript: ENSMUST00000035167
AA Change: L808R

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: L808R

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

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

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

unknown
Transcript: ENSMUST00000194774
AA Change: L688R

SMART Domains

Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: L688R

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: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

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: 116 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb9	T	C	5: 124,228,176 (GRCm39)	T22A	possibly damaging	Het
Abi3bp	A	G	16: 56,417,173 (GRCm39)	D419G	probably benign	Het
Acoxl	A	T	2: 127,696,691 (GRCm39)		probably benign	Het
Acvr1	T	C	2: 58,352,983 (GRCm39)	T326A	possibly damaging	Het
Adgra2	T	C	8: 27,610,979 (GRCm39)	L976P	probably damaging	Het
Adora2b	A	G	11: 62,155,886 (GRCm39)		probably null	Het
Ak1	A	T	2: 32,521,182 (GRCm39)	Q117L	probably damaging	Het
Akr1c14	T	A	13: 4,128,029 (GRCm39)	D143E	probably damaging	Het
Ap4e1	A	T	2: 126,861,242 (GRCm39)	H127L	probably damaging	Het
Asxl3	T	A	18: 22,649,670 (GRCm39)	I553N	probably damaging	Het
Asxl3	T	A	18: 22,657,481 (GRCm39)	N1830K	possibly damaging	Het
Atp11a	G	A	8: 12,863,144 (GRCm39)	A108T	probably damaging	Het
Bag6	A	G	17: 35,362,437 (GRCm39)	T582A	unknown	Het
Bbs9	T	C	9: 22,490,005 (GRCm39)	S259P	probably damaging	Het
Bean1	CT	C	8: 104,908,664 (GRCm39)		probably null	Het
Bltp3a	T	A	17: 28,104,902 (GRCm39)	L532*	probably null	Het
Blvrb	T	C	7: 27,165,210 (GRCm39)	S177P	probably damaging	Het
C1s2	T	A	6: 124,602,642 (GRCm39)	D523V	probably benign	Het
Cacna2d1	C	T	5: 16,558,850 (GRCm39)	T736I	probably damaging	Het
Card9	T	C	2: 26,242,397 (GRCm39)	N513S	probably benign	Het
Casp2	A	G	6: 42,245,882 (GRCm39)	T180A	probably benign	Het
Cenpf	A	T	1: 189,404,746 (GRCm39)	L361Q	probably damaging	Het
Cnbd2	T	C	2: 156,217,488 (GRCm39)	I659T	probably damaging	Het
Cped1	A	T	6: 21,987,012 (GRCm39)	D68V	probably damaging	Het
Cxcr1	T	C	1: 74,231,099 (GRCm39)	I308V	probably benign	Het
Dad1	A	G	14: 54,491,163 (GRCm39)	L46P	probably damaging	Het
Defb23	G	A	2: 152,301,422 (GRCm39)	A50V	probably benign	Het
Dhx33	C	T	11: 70,877,992 (GRCm39)	A684T	probably damaging	Het
Dnai3	T	C	3: 145,772,589 (GRCm39)	T486A	probably benign	Het
Epb41l4a	T	A	18: 33,965,729 (GRCm39)	N366I	probably benign	Het
Erich3	A	G	3: 154,467,912 (GRCm39)	E788G		Het
Fam241b	T	C	10: 61,944,892 (GRCm39)	N35S	probably benign	Het
Fbxo24	T	A	5: 137,622,526 (GRCm39)	Q80L	probably benign	Het
Foxk1	T	G	5: 142,434,497 (GRCm39)	F254V	probably benign	Het
Gm10801	C	CGTG	2: 98,494,152 (GRCm39)		probably null	Het
Gm12886	T	C	4: 121,274,743 (GRCm39)	I46V	probably benign	Het
Gm20834	G	T	Y: 10,323,354 (GRCm39)	H27Q	probably damaging	Het
Gm2888	A	G	14: 3,032,106 (GRCm38)	N138S	probably damaging	Het
Gm5773	T	C	3: 93,681,179 (GRCm39)	C284R	possibly damaging	Het
Gprin3	A	T	6: 59,330,273 (GRCm39)	M678K	probably benign	Het
Grm7	T	C	6: 111,472,729 (GRCm39)	V856A	probably benign	Het
Il18rap	C	T	1: 40,582,177 (GRCm39)	T366M	probably benign	Het
Immt	C	T	6: 71,851,403 (GRCm39)	T588I	probably damaging	Het
Ints1	G	C	5: 139,737,701 (GRCm39)	N2145K	possibly damaging	Het
Jade2	T	C	11: 51,715,951 (GRCm39)	D418G	probably benign	Het
Kdf1	T	C	4: 133,256,140 (GRCm39)	Y286H	probably damaging	Het
Kif18a	A	G	2: 109,171,506 (GRCm39)	Y861C	possibly damaging	Het
Lama2	T	A	10: 27,298,515 (GRCm39)	I194F	probably damaging	Het
Lhx8	A	G	3: 154,034,063 (GRCm39)	S33P	probably benign	Het
Lmo7	T	C	14: 102,118,297 (GRCm39)	I174T	probably damaging	Het
Lrfn2	A	T	17: 49,376,976 (GRCm39)	D19V	possibly damaging	Het
Lrrk1	A	T	7: 65,928,357 (GRCm39)	I1257N	probably damaging	Het
Malrd1	T	A	2: 15,802,516 (GRCm39)	H1076Q	unknown	Het
Map3k14	A	C	11: 103,128,364 (GRCm39)	M419R	probably damaging	Het
Mcm10	G	A	2: 5,011,372 (GRCm39)	R200C	probably benign	Het
Mertk	A	G	2: 128,604,035 (GRCm39)	N390D	probably benign	Het
Mitf	T	A	6: 97,990,680 (GRCm39)	I361N	probably damaging	Het
Mrgprb1	T	A	7: 48,097,046 (GRCm39)	I289F	possibly damaging	Het
Muc5ac	A	T	7: 141,352,218 (GRCm39)	D659V	probably damaging	Het
Nox4	G	A	7: 87,025,448 (GRCm39)	R525Q	probably benign	Het
Or14c42-ps1	G	A	7: 86,211,156 (GRCm39)	C72Y	unknown	Het
Or1e1	T	C	11: 73,245,316 (GRCm39)	S246P	probably damaging	Het
Or5an1	T	A	19: 12,260,808 (GRCm39)	L132Q	probably damaging	Het
Or5b113	T	A	19: 13,342,755 (GRCm39)	S254R	possibly damaging	Het
Pagr1a	T	C	7: 126,615,954 (GRCm39)	E47G	probably benign	Het
Papss2	G	T	19: 32,618,764 (GRCm39)	R274L	probably damaging	Het
Pcdhga10	C	A	18: 37,880,960 (GRCm39)	F240L	probably damaging	Het
Pcsk5	T	G	19: 17,563,472 (GRCm39)	E555A		Het
Peg10	C	CTCA	6: 4,756,453 (GRCm39)		probably benign	Het
Pgrmc2	T	A	3: 41,023,099 (GRCm39)	D206V	probably damaging	Het
Pkd1	T	C	17: 24,790,976 (GRCm39)	V1057A		Het
Plekha5	T	C	6: 140,480,239 (GRCm39)	I113T	probably damaging	Het
Prorp	T	A	12: 55,426,189 (GRCm39)	L513Q	probably damaging	Het
Prss32	C	T	17: 24,078,199 (GRCm39)	T295I	possibly damaging	Het
Ptprk	G	T	10: 28,456,413 (GRCm39)	V1072F	probably damaging	Het
Rasd2	T	A	8: 75,945,174 (GRCm39)	M1K	probably null	Het
Rhag	T	A	17: 41,139,302 (GRCm39)	M79K	probably damaging	Het
Rnf19a	C	A	15: 36,253,310 (GRCm39)		probably null	Het
Rnf213	G	T	11: 119,299,573 (GRCm39)	G101C		Het
Sap130	T	A	18: 31,780,116 (GRCm39)	D45E	probably benign	Het
Scel	T	A	14: 103,839,626 (GRCm39)	F510I	probably benign	Het
Sertad2	A	T	11: 20,598,425 (GRCm39)	E207V	probably benign	Het
Shoc2	T	A	19: 53,976,310 (GRCm39)	S67T	probably benign	Het
Slc22a3	T	C	17: 12,645,619 (GRCm39)	I441V	possibly damaging	Het
Slfn5	A	G	11: 82,851,503 (GRCm39)	D600G	probably benign	Het
Smim7	G	A	8: 73,324,757 (GRCm39)	T10M	probably damaging	Het
Sntb2	A	T	8: 107,662,831 (GRCm39)	Q133L	possibly damaging	Het
Steap3	A	C	1: 120,162,048 (GRCm39)	M408R	probably benign	Het
Supt4a	T	C	11: 87,633,624 (GRCm39)	I60T	probably benign	Het
Swt1	A	C	1: 151,244,239 (GRCm39)	C899G	possibly damaging	Het
Taok3	A	G	5: 117,344,744 (GRCm39)	E157G	probably damaging	Het
Taok3	C	T	5: 117,379,245 (GRCm39)	L427F	possibly damaging	Het
Taok3	T	C	5: 117,379,168 (GRCm39)	V401A	probably benign	Het
Tcf25	A	G	8: 124,108,182 (GRCm39)	E79G	probably benign	Het
Tigit	G	A	16: 43,479,876 (GRCm39)	L140F	possibly damaging	Het
Tmem143	G	T	7: 45,546,802 (GRCm39)		probably benign	Het
Tmem151b	C	T	17: 45,856,355 (GRCm39)	V362M	possibly damaging	Het
Tmem230	A	G	2: 132,085,989 (GRCm39)	F58L	probably benign	Het
Trim25	T	C	11: 88,899,988 (GRCm39)	M245T	probably benign	Het
Trim36	A	C	18: 46,302,410 (GRCm39)	V546G	probably benign	Het
Triml1	T	C	8: 43,583,624 (GRCm39)	N326D	probably damaging	Het
Trp53bp2	T	C	1: 182,286,328 (GRCm39)	V1056A	probably damaging	Het
Trpa1	C	A	1: 14,952,435 (GRCm39)	M865I	probably damaging	Het
Ttbk1	A	T	17: 46,790,132 (GRCm39)	Y104*	probably null	Het
Tubg1	T	A	11: 101,014,257 (GRCm39)	H139Q	probably damaging	Het
Ufsp2	A	G	8: 46,447,050 (GRCm39)		probably null	Het
Usp47	A	T	7: 111,652,431 (GRCm39)	N36I	probably benign	Het
Vmn1r32	G	A	6: 66,530,120 (GRCm39)	R219*	probably null	Het
Vmn2r59	G	A	7: 41,693,125 (GRCm39)	P492S	probably benign	Het
Vmn2r59	G	C	7: 41,693,127 (GRCm39)	A491G		Het
Wdr76	T	C	2: 121,364,592 (GRCm39)	Y299H	probably damaging	Het
Wnt5a	C	T	14: 28,240,309 (GRCm39)	A153V	probably benign	Het
Zfp202	T	C	9: 40,120,237 (GRCm39)	V226A	possibly damaging	Het
Zfp219	C	T	14: 52,244,598 (GRCm39)	R527H	probably damaging	Het
Zfp408	A	T	2: 91,475,528 (GRCm39)	L542H	probably damaging	Het
Zfyve9	A	T	4: 108,539,386 (GRCm39)	C271*	probably null	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
R1464:Nphp3	UTSW	9	103,909,078 (GRCm39)	splice site	probably benign
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
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

PCR Primer
(F):5'- AGAAATTCTTGGCCATGGTTTC -3'
(R):5'- GTTGGACAGGTTTCACATGC -3'

Sequencing Primer
(F):5'- CCATGGTTTCTGGGGTAGCC -3'
(R):5'- GGACAGGTTTCACATGCAATTTAAAG -3'

Posted On

2022-01-20