Mutagenetix > Incidental Mutations

Incidental Mutation 'R9135:Nphp3'

693944

Institutional Source

Beutler Lab

Gene Symbol

Nphp3

Ensembl Gene

ENSMUSG00000032558

Gene Name

nephronophthisis 3 (adolescent)

Synonyms

3632410F03Rik, D330020E01Rik, pcy, nephrocystin 3

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R9135 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

104002544-104043818 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 104032015 bp (GRCm38)

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
1110008L16Rik	T	A	12: 55,379,404	L513Q	probably damaging	Het
Abcb9	T	C	5: 124,090,113	T22A	possibly damaging	Het
Abi3bp	A	G	16: 56,596,810	D419G	probably benign	Het
Acoxl	A	T	2: 127,854,771		probably benign	Het
Acvr1	T	C	2: 58,462,971	T326A	possibly damaging	Het
Adgra2	T	C	8: 27,120,951	L976P	probably damaging	Het
Adora2b	A	G	11: 62,265,060		probably null	Het
Ak1	A	T	2: 32,631,170	Q117L	probably damaging	Het
Akr1c14	T	A	13: 4,078,029	D143E	probably damaging	Het
Ap4e1	A	T	2: 127,019,322	H127L	probably damaging	Het
Asxl3	T	A	18: 22,516,613	I553N	probably damaging	Het
Asxl3	T	A	18: 22,524,424	N1830K	possibly damaging	Het
Atp11a	G	A	8: 12,813,144	A108T	probably damaging	Het
Bag6	A	G	17: 35,143,461	T582A	unknown	Het
Bbs9	T	C	9: 22,578,709	S259P	probably damaging	Het
Bean1	CT	C	8: 104,182,032		probably null	Het
Blvrb	T	C	7: 27,465,785	S177P	probably damaging	Het
C1s2	T	A	6: 124,625,683	D523V	probably benign	Het
Cacna2d1	C	T	5: 16,353,852	T736I	probably damaging	Het
Card9	T	C	2: 26,352,385	N513S	probably benign	Het
Casp2	A	G	6: 42,268,948	T180A	probably benign	Het
Cenpf	A	T	1: 189,672,549	L361Q	probably damaging	Het
Cnbd2	T	C	2: 156,375,568	I659T	probably damaging	Het
Cped1	A	T	6: 21,987,013	D68V	probably damaging	Het
Cxcr1	T	C	1: 74,191,940	I308V	probably benign	Het
Dad1	A	G	14: 54,253,706	L46P	probably damaging	Het
Defb23	G	A	2: 152,459,502	A50V	probably benign	Het
Dhx33	C	T	11: 70,987,166	A684T	probably damaging	Het
Epb41l4a	T	A	18: 33,832,676	N366I	probably benign	Het
Erich3	A	G	3: 154,762,275	E788G		Het
Fam241b	T	C	10: 62,109,113	N35S	probably benign	Het
Fbxo24	T	A	5: 137,624,264	Q80L	probably benign	Het
Foxk1	T	G	5: 142,448,742	F254V	probably benign	Het
Gm10801	C	CGTG	2: 98,663,807		probably null	Het
Gm12886	T	C	4: 121,417,546	I46V	probably benign	Het
Gm20834	G	T	Y: 10,323,354	H27Q	probably damaging	Het
Gm2888	A	G	14: 3,032,106	N138S	probably damaging	Het
Gm5773	T	C	3: 93,773,872	C284R	possibly damaging	Het
Gprin3	A	T	6: 59,353,288	M678K	probably benign	Het
Grm7	T	C	6: 111,495,768	V856A	probably benign	Het
Il18rap	C	T	1: 40,543,017	T366M	probably benign	Het
Immt	C	T	6: 71,874,419	T588I	probably damaging	Het
Ints1	G	C	5: 139,751,946	N2145K	possibly damaging	Het
Jade2	T	C	11: 51,825,124	D418G	probably benign	Het
Kdf1	T	C	4: 133,528,829	Y286H	probably damaging	Het
Kif18a	A	G	2: 109,341,161	Y861C	possibly damaging	Het
Lama2	T	A	10: 27,422,519	I194F	probably damaging	Het
Lhx8	A	G	3: 154,328,426	S33P	probably benign	Het
Lmo7	T	C	14: 101,880,861	I174T	probably damaging	Het
Lrfn2	A	T	17: 49,069,948	D19V	possibly damaging	Het
Lrrk1	A	T	7: 66,278,609	I1257N	probably damaging	Het
Malrd1	T	A	2: 15,797,705	H1076Q	unknown	Het
Map3k14	A	C	11: 103,237,538	M419R	probably damaging	Het
Mcm10	G	A	2: 5,006,561	R200C	probably benign	Het
Mertk	A	G	2: 128,762,115	N390D	probably benign	Het
Mitf	T	A	6: 98,013,719	I361N	probably damaging	Het
Mrgprb1	T	A	7: 48,447,298	I289F	possibly damaging	Het
Muc5ac	A	T	7: 141,798,481	D659V	probably damaging	Het
Nox4	G	A	7: 87,376,240	R525Q	probably benign	Het
Olfr1434	T	A	19: 12,283,444	L132Q	probably damaging	Het
Olfr1467	T	A	19: 13,365,391	S254R	possibly damaging	Het
Olfr20	T	C	11: 73,354,490	S246P	probably damaging	Het
Olfr296-ps1	G	A	7: 86,561,948	C72Y	unknown	Het
Pagr1a	T	C	7: 127,016,782	E47G	probably benign	Het
Papss2	G	T	19: 32,641,364	R274L	probably damaging	Het
Pcdhga10	C	A	18: 37,747,907	F240L	probably damaging	Het
Pcsk5	T	G	19: 17,586,108	E555A		Het
Peg10	C	CTCA	6: 4,756,453		probably benign	Het
Pgrmc2	T	A	3: 41,068,664	D206V	probably damaging	Het
Pkd1	T	C	17: 24,572,002	V1057A		Het
Plekha5	T	C	6: 140,534,513	I113T	probably damaging	Het
Prss32	C	T	17: 23,859,225	T295I	possibly damaging	Het
Ptprk	G	T	10: 28,580,417	V1072F	probably damaging	Het
Rasd2	T	A	8: 75,218,546	M1K	probably null	Het
Rhag	T	A	17: 40,828,411	M79K	probably damaging	Het
Rnf19a	C	A	15: 36,253,164		probably null	Het
Rnf213	G	T	11: 119,408,747	G101C		Het
Sap130	T	A	18: 31,647,063	D45E	probably benign	Het
Scel	T	A	14: 103,602,190	F510I	probably benign	Het
Sertad2	A	T	11: 20,648,425	E207V	probably benign	Het
Shoc2	T	A	19: 53,987,879	S67T	probably benign	Het
Slc22a3	T	C	17: 12,426,732	I441V	possibly damaging	Het
Slfn5	A	G	11: 82,960,677	D600G	probably benign	Het
Smim7	G	A	8: 72,570,913	T10M	probably damaging	Het
Sntb2	A	T	8: 106,936,199	Q133L	possibly damaging	Het
Steap3	A	C	1: 120,234,318	M408R	probably benign	Het
Supt4a	T	C	11: 87,742,798	I60T	probably benign	Het
Swt1	A	C	1: 151,368,488	C899G	possibly damaging	Het
Taok3	A	G	5: 117,206,679	E157G	probably damaging	Het
Taok3	T	C	5: 117,241,103	V401A	probably benign	Het
Taok3	C	T	5: 117,241,180	L427F	possibly damaging	Het
Tcf25	A	G	8: 123,381,443	E79G	probably benign	Het
Tigit	G	A	16: 43,659,513	L140F	possibly damaging	Het
Tmem143	G	T	7: 45,897,378		probably benign	Het
Tmem151b	C	T	17: 45,545,429	V362M	possibly damaging	Het
Tmem230	A	G	2: 132,244,069	F58L	probably benign	Het
Trim25	T	C	11: 89,009,162	M245T	probably benign	Het
Trim36	A	C	18: 46,169,343	V546G	probably benign	Het
Triml1	T	C	8: 43,130,587	N326D	probably damaging	Het
Trp53bp2	T	C	1: 182,458,763	V1056A	probably damaging	Het
Trpa1	C	A	1: 14,882,211	M865I	probably damaging	Het
Ttbk1	A	T	17: 46,479,206	Y104*	probably null	Het
Tubg1	T	A	11: 101,123,431	H139Q	probably damaging	Het
Ufsp2	A	G	8: 45,994,013		probably null	Het
Uhrf1bp1	T	A	17: 27,885,928	L532*	probably null	Het
Usp47	A	T	7: 112,053,224	N36I	probably benign	Het
Vmn1r32	G	A	6: 66,553,136	R219*	probably null	Het
Vmn2r59	G	A	7: 42,043,701	P492S	probably benign	Het
Vmn2r59	G	C	7: 42,043,703	A491G		Het
Wdr63	T	C	3: 146,066,834	T486A	probably benign	Het
Wdr76	T	C	2: 121,534,111	Y299H	probably damaging	Het
Wnt5a	C	T	14: 28,518,352	A153V	probably benign	Het
Zfp202	T	C	9: 40,208,941	V226A	possibly damaging	Het
Zfp219	C	T	14: 52,007,141	R527H	probably damaging	Het
Zfp408	A	T	2: 91,645,183	L542H	probably damaging	Het
Zfyve9	A	T	4: 108,682,189	C271*	probably null	Het

Other mutations in Nphp3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01707:Nphp3	APN	9	104018158	missense	possibly damaging	0.75
IGL02329:Nphp3	APN	9	104025968	missense	probably benign	0.19
lithograph	UTSW	9	104041990	missense	probably damaging	1.00
F5770:Nphp3	UTSW	9	104035894	critical splice donor site	probably null
FR4548:Nphp3	UTSW	9	104025939	small deletion	probably benign
FR4589:Nphp3	UTSW	9	104025939	small deletion	probably benign
R0112:Nphp3	UTSW	9	104037348	missense	possibly damaging	0.80
R0555:Nphp3	UTSW	9	104023434	missense	probably damaging	1.00
R0632:Nphp3	UTSW	9	104018274	missense	probably damaging	1.00
R0674:Nphp3	UTSW	9	104036282	critical splice donor site	probably null
R0743:Nphp3	UTSW	9	104022768	small deletion	probably benign
R0853:Nphp3	UTSW	9	104031933	missense	probably benign	0.03
R0920:Nphp3	UTSW	9	104031907	missense	probably benign	0.00
R1420:Nphp3	UTSW	9	104035893	critical splice donor site	probably null
R1464:Nphp3	UTSW	9	104031879	splice site	probably benign
R1476:Nphp3	UTSW	9	104025927	missense	possibly damaging	0.81
R1585:Nphp3	UTSW	9	104009214	missense	probably damaging	1.00
R1608:Nphp3	UTSW	9	104035840	missense	probably benign	0.30
R1688:Nphp3	UTSW	9	104003124	missense	probably damaging	1.00
R1691:Nphp3	UTSW	9	104002811	missense	probably benign
R1807:Nphp3	UTSW	9	104020741	missense	probably benign	0.01
R1857:Nphp3	UTSW	9	104021294	missense	possibly damaging	0.87
R1962:Nphp3	UTSW	9	104021338	missense	probably benign	0.00
R2127:Nphp3	UTSW	9	104008243	missense	probably damaging	0.98
R2138:Nphp3	UTSW	9	104025903	missense	possibly damaging	0.89
R2233:Nphp3	UTSW	9	104037376	missense	probably benign	0.02
R2234:Nphp3	UTSW	9	104037376	missense	probably benign	0.02
R3861:Nphp3	UTSW	9	104039326	unclassified	probably benign
R3928:Nphp3	UTSW	9	104011730	missense	probably damaging	0.99
R3961:Nphp3	UTSW	9	104003042	nonsense	probably null
R4182:Nphp3	UTSW	9	104038464	missense	probably benign	0.06
R4294:Nphp3	UTSW	9	104022717	missense	probably damaging	1.00
R4387:Nphp3	UTSW	9	104030020	missense	possibly damaging	0.94
R4625:Nphp3	UTSW	9	104036159	missense	possibly damaging	0.66
R4628:Nphp3	UTSW	9	104003058	missense	probably damaging	0.99
R4696:Nphp3	UTSW	9	104022732	missense	probably benign	0.01
R4865:Nphp3	UTSW	9	104031970	missense	probably benign
R4886:Nphp3	UTSW	9	104002994	missense	probably damaging	1.00
R4973:Nphp3	UTSW	9	104031999	missense	probably benign
R5445:Nphp3	UTSW	9	104004723	missense	probably damaging	1.00
R5451:Nphp3	UTSW	9	104042022	missense	probably benign
R5520:Nphp3	UTSW	9	104024673	missense	probably benign	0.30
R5641:Nphp3	UTSW	9	104036153	missense	probably damaging	1.00
R5847:Nphp3	UTSW	9	104003037	missense	probably damaging	1.00
R5928:Nphp3	UTSW	9	104035797	missense	probably benign	0.01
R5931:Nphp3	UTSW	9	104020746	missense	probably damaging	1.00
R6161:Nphp3	UTSW	9	104031906	missense	probably benign	0.11
R6298:Nphp3	UTSW	9	104015441	missense	probably damaging	1.00
R6890:Nphp3	UTSW	9	104041954	missense	probably damaging	0.96
R7009:Nphp3	UTSW	9	104016116	missense	probably null	0.00
R7065:Nphp3	UTSW	9	104041990	missense	probably damaging	1.00
R7146:Nphp3	UTSW	9	104004837	nonsense	probably null
R7198:Nphp3	UTSW	9	104004775	missense	probably damaging	1.00
R7360:Nphp3	UTSW	9	104016078	critical splice acceptor site	probably null
R7369:Nphp3	UTSW	9	104018250	missense	probably damaging	0.99
R7554:Nphp3	UTSW	9	104042071	missense	probably damaging	0.98
R7591:Nphp3	UTSW	9	104018278	critical splice donor site	probably null
R7665:Nphp3	UTSW	9	104005393	splice site	probably null
R7672:Nphp3	UTSW	9	104031960	missense	probably benign
R7675:Nphp3	UTSW	9	104016088	missense	probably benign
R8039:Nphp3	UTSW	9	104031963	missense	probably benign
R8145:Nphp3	UTSW	9	104035851	missense	probably benign	0.16
R8211:Nphp3	UTSW	9	104031897	missense	possibly damaging	0.80
R8882:Nphp3	UTSW	9	104005594	missense	possibly damaging	0.77
R9020:Nphp3	UTSW	9	104031951	missense	probably benign	0.00
R9132:Nphp3	UTSW	9	104020781	missense	probably damaging	1.00
R9159:Nphp3	UTSW	9	104020781	missense	probably damaging	1.00
R9204:Nphp3	UTSW	9	104042106	missense	probably benign
R9226:Nphp3	UTSW	9	104008129	missense	probably benign	0.00
R9229:Nphp3	UTSW	9	104036177	missense	probably damaging	1.00
V7583:Nphp3	UTSW	9	104035894	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