Mutagenetix > Incidental Mutations

Incidental Mutation 'R1476:Nphp3'

164081

Institutional Source

Beutler Lab

Gene Symbol

Nphp3

Ensembl Gene

ENSMUSG00000032558

Gene Name

nephronophthisis 3 (adolescent)

Synonyms

3632410F03Rik, D330020E01Rik, pcy, nephrocystin 3

MMRRC Submission

039529-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R1476 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

104002544-104043818 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 104025927 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 701 (R701L)

Ref Sequence

ENSEMBL: ENSMUSP00000035167 (fasta)

Gene Model

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

AlphaFold

Q7TNH6

Predicted Effect

possibly damaging
Transcript: ENSMUST00000035167
AA Change: R701L

PolyPhen 2 Score 0.805 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: R701L

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

unknown
Transcript: ENSMUST00000129819
AA Change: R581L

SMART Domains

Protein: ENSMUSP00000116459
Gene: ENSMUSG00000032558
AA Change: R581L

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: 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

unknown
Transcript: ENSMUST00000194774
AA Change: R581L

SMART Domains

Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: R581L

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

Meta Mutation Damage Score

0.1046

Coding Region Coverage

1x: 99.3%
3x: 98.4%
10x: 96.5%
20x: 93.1%

Validation Efficiency

95% (80/84)

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310033P09Rik	A	G	11: 59,208,702		probably benign	Het
4932431P20Rik	A	G	7: 29,534,890		noncoding transcript	Het
A730015C16Rik	G	A	4: 108,848,008	V40M	probably damaging	Het
Abcg2	A	G	6: 58,678,337	D419G	probably benign	Het
Adamts17	A	C	7: 67,075,343	E777A	probably damaging	Het
Ak1	A	G	2: 32,633,466	K166R	probably benign	Het
Ankrd12	T	C	17: 65,986,305	K711R	probably damaging	Het
Ate1	A	T	7: 130,418,571		probably null	Het
Atp5a1	A	G	18: 77,781,925	H519R	probably benign	Het
Best1	G	T	19: 9,990,489	Y284*	probably null	Het
C2cd6	A	G	1: 59,076,728		probably benign	Het
Casz1	G	T	4: 148,946,171	V1216L	probably benign	Het
Cdc42bpg	A	G	19: 6,313,782	D493G	probably damaging	Het
Ces2f	A	G	8: 104,952,502	D317G	possibly damaging	Het
Chst15	A	T	7: 132,270,273	M93K	possibly damaging	Het
Cntnap5a	T	C	1: 115,901,020	L58P	probably damaging	Het
Crip3	T	C	17: 46,430,776		probably benign	Het
Csmd2	G	A	4: 128,487,001	E2117K	probably benign	Het
Cstf3	A	G	2: 104,648,219	D212G	possibly damaging	Het
Cttnbp2	T	C	6: 18,434,221	K546R	probably damaging	Het
Cubn	A	G	2: 13,476,120	I308T	probably benign	Het
Cxcl9	T	A	5: 92,325,113	D75V	probably damaging	Het
Dcdc5	C	T	2: 106,358,632		noncoding transcript	Het
Defa30	C	A	8: 21,134,736	T25K	possibly damaging	Het
Dock7	A	T	4: 99,079,435	H239Q	possibly damaging	Het
Dpp4	A	G	2: 62,347,901	V629A	possibly damaging	Het
Fam83a	T	C	15: 58,009,945	M390T	probably benign	Het
Fem1c	A	G	18: 46,524,485	L54P	probably damaging	Het
Fntb	T	A	12: 76,910,233	M282K	probably benign	Het
Gm11099	G	A	2: 58,859,470		probably benign	Het
Gm1527	T	C	3: 28,926,556	S602P	probably benign	Het
Gm20388	A	G	8: 122,269,584		probably benign	Het
Gm5478	T	A	15: 101,644,645	I331F	probably damaging	Het
Gm7853	C	A	14: 36,089,583		noncoding transcript	Het
Gsta2	A	T	9: 78,341,865	C18S	probably benign	Het
H1foo	T	C	6: 115,947,740	V69A	possibly damaging	Het
Hecw1	T	C	13: 14,306,086	E465G	probably damaging	Het
Herc1	A	G	9: 66,508,266	D4841G	probably damaging	Het
Hus1b	A	G	13: 30,947,001	V225A	probably benign	Het
Keg1	A	T	19: 12,716,023	M137L	probably benign	Het
Kmt2a	C	T	9: 44,824,635		probably benign	Het
Megf6	G	T	4: 154,177,121	V68L	probably benign	Het
Mga	T	A	2: 119,941,675	V1672E	probably damaging	Het
Mios	T	C	6: 8,234,237	S803P	probably benign	Het
Mkl1	T	C	15: 81,018,208		probably benign	Het
Msh4	A	T	3: 153,863,384	Y851N	probably damaging	Het
Mybl1	A	C	1: 9,672,661		probably null	Het
Myo5c	A	G	9: 75,275,939	Y865C	probably damaging	Het
Naip1	T	C	13: 100,426,870	S596G	probably benign	Het
Nek5	G	T	8: 22,096,731	Q355K	possibly damaging	Het
Olfr1006	T	A	2: 85,674,918	T78S	possibly damaging	Het
Olfr1023	T	A	2: 85,887,248	Y149*	probably null	Het
Olfr1052	T	C	2: 86,298,479	I221T	probably damaging	Het
Olfr1094	T	C	2: 86,829,198	S149P	probably benign	Het
Olfr666	A	T	7: 104,893,237	Y130*	probably null	Het
Palm	A	G	10: 79,815,187	N149D	possibly damaging	Het
Pot1b	T	C	17: 55,653,451	I626M	possibly damaging	Het
Ptprt	T	A	2: 161,927,484	D487V	probably damaging	Het
Qpct	A	G	17: 79,070,772	I124V	probably benign	Het
Rbm12b1	T	A	4: 12,145,817	D596E	possibly damaging	Het
Rnf157	A	G	11: 116,354,759	C277R	probably damaging	Het
Rnf169	A	G	7: 99,925,328	S687P	possibly damaging	Het
Sfxn1	T	A	13: 54,092,450		probably null	Het
Slc6a21	T	C	7: 45,272,628	V649A	probably benign	Het
Slit3	A	T	11: 35,686,299	T1120S	probably damaging	Het
Spem2	A	T	11: 69,818,070	M58K	probably benign	Het
Sprr2k	T	A	3: 92,433,396		probably benign	Het
Sspo	T	C	6: 48,463,400		probably null	Het
Sv2b	A	T	7: 75,120,043	F584I	possibly damaging	Het
Tkfc	A	T	19: 10,595,326	M317K	probably null	Het
Tnni3k	C	T	3: 155,030,305	G134S	probably benign	Het
Ttn	C	T	2: 76,739,780	R26923H	probably damaging	Het
Tuba3b	T	C	6: 145,618,453	V75A	possibly damaging	Het
Unc79	T	C	12: 103,183,525	L2626P	probably damaging	Het
Usp24	A	T	4: 106,361,933	I491F	probably damaging	Het
V1ra8	A	T	6: 90,203,150	I112F	probably damaging	Het
Vmn1r29	T	G	6: 58,307,678	F128V	probably benign	Het
Zfp157	T	A	5: 138,455,095		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
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
R9135:Nphp3	UTSW	9	104032015	missense	probably damaging	0.99
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'- CTTCCCTTCTGCAACTGGAAGTCTG -3'
(R):5'- TTCAGCAGTGAGCCACATTCTCC -3'

Sequencing Primer
(F):5'- GCCATAGCCAGGCACCC -3'
(R):5'- GAACTCTGAGACCTGTTAAACTGG -3'

Posted On

2014-03-28