Mutagenetix > Incidental Mutation

Incidental Mutation 'R7675:Nphp3'

592422

Institutional Source

Beutler Lab

Gene Symbol

Nphp3

Ensembl Gene

ENSMUSG00000032558

Gene Name

nephronophthisis 3 (adolescent)

Synonyms

3632410F03Rik, D330020E01Rik, pcy, nephrocystin 3

MMRRC Submission

045706-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7675 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

104002544-104043818 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 104016088 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Aspartic acid at position 424 (E424D)

Ref Sequence

ENSEMBL: ENSMUSP00000035167 (fasta)

Gene Model

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

AlphaFold

Q7TNH6

Predicted Effect

probably benign
Transcript: ENSMUST00000035167
AA Change: E424D

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: E424D

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
AA Change: E330D

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000141540
Gene: ENSMUSG00000032558
AA Change: E330D

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

SMART Domains

Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: E304D

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

0.0898

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

97% (28/29)

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: 31 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010109A12Rik	T	C	5: 93,213,374	S96P	unknown	Het
5730559C18Rik	G	T	1: 136,216,003	A565E	probably benign	Het
Acaca	A	G	11: 84,315,916	E1534G	probably benign	Het
Adam7	A	T	14: 68,499,853	D773E	probably benign	Het
C130026I21Rik	C	T	1: 85,247,015	M266I	probably benign	Het
Cacna1s	T	A	1: 136,110,874	I1398N	probably damaging	Het
Calu	C	T	6: 29,356,517	T14I	probably benign	Het
Casp8	A	G	1: 58,823,947	D2G	possibly damaging	Het
Cldn1	T	C	16: 26,371,511	N39S	probably benign	Het
Clspn	T	C	4: 126,566,320	S447P	probably benign	Het
Eef2k	A	G	7: 120,858,504	T29A	probably benign	Het
Elmsan1	G	T	12: 84,173,800	P127T	probably damaging	Het
Fam205c	TCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGTCATTCAACACTTTGG	TCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGTCATTCAACACTTTGG	4: 42,871,823		probably benign	Het
Gm5519	G	C	19: 33,825,028	G157A	probably benign	Het
Gm9844	A	T	7: 24,862,359	T28S	probably benign	Het
Gucy2c	A	G	6: 136,716,032	V723A	possibly damaging	Het
Ighv1-69	A	T	12: 115,623,589	W3R	probably damaging	Het
Krtap16-1	A	G	11: 99,985,433	C382R	possibly damaging	Het
Lrrc8a	G	A	2: 30,255,668	D165N	probably damaging	Het
Naaladl2	T	A	3: 24,551,652	M148L	probably benign	Het
Prpf40a	T	C	2: 53,145,636	K714R	possibly damaging	Het
Ptpn23	A	T	9: 110,387,026	L1254*	probably null	Het
Sap30l	A	G	11: 57,810,041	K174E	probably damaging	Het
Serpinb9d	C	T	13: 33,202,776	Q276*	probably null	Het
Tex14	A	G	11: 87,509,678	D432G	probably damaging	Het
Unc119	G	A	11: 78,343,597	G11R	probably damaging	Het
Usp36	A	G	11: 118,263,696	V965A	probably benign	Het
Vmn2r4	A	T	3: 64,415,236	Y21N	probably benign	Het
Zbtb38	G	T	9: 96,685,541	D1163E	probably benign	Het
Zfp62	A	G	11: 49,216,020	I313V	possibly damaging	Het
Zfp980	C	T	4: 145,701,594	Q298*	probably null	Het

Other mutations in Nphp3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01707:Nphp3	APN	9	104,018,158 (GRCm38)	missense	possibly damaging	0.75
IGL02329:Nphp3	APN	9	104,025,968 (GRCm38)	missense	probably benign	0.19
lithograph	UTSW	9	104,041,990 (GRCm38)	missense	probably damaging	1.00
quartzite	UTSW	9	104,036,177 (GRCm38)	missense	probably damaging	1.00
F5770:Nphp3	UTSW	9	104,035,894 (GRCm38)	critical splice donor site	probably null
FR4548:Nphp3	UTSW	9	104,025,939 (GRCm38)	small deletion	probably benign
FR4589:Nphp3	UTSW	9	104,025,939 (GRCm38)	small deletion	probably benign
R0112:Nphp3	UTSW	9	104,037,348 (GRCm38)	missense	possibly damaging	0.80
R0555:Nphp3	UTSW	9	104,023,434 (GRCm38)	missense	probably damaging	1.00
R0632:Nphp3	UTSW	9	104,018,274 (GRCm38)	missense	probably damaging	1.00
R0674:Nphp3	UTSW	9	104,036,282 (GRCm38)	critical splice donor site	probably null
R0743:Nphp3	UTSW	9	104,022,768 (GRCm38)	small deletion	probably benign
R0853:Nphp3	UTSW	9	104,031,933 (GRCm38)	missense	probably benign	0.03
R0920:Nphp3	UTSW	9	104,031,907 (GRCm38)	missense	probably benign	0.00
R1420:Nphp3	UTSW	9	104,035,893 (GRCm38)	critical splice donor site	probably null
R1464:Nphp3	UTSW	9	104,031,879 (GRCm38)	splice site	probably benign
R1476:Nphp3	UTSW	9	104,025,927 (GRCm38)	missense	possibly damaging	0.81
R1585:Nphp3	UTSW	9	104,009,214 (GRCm38)	missense	probably damaging	1.00
R1608:Nphp3	UTSW	9	104,035,840 (GRCm38)	missense	probably benign	0.30
R1688:Nphp3	UTSW	9	104,003,124 (GRCm38)	missense	probably damaging	1.00
R1691:Nphp3	UTSW	9	104,002,811 (GRCm38)	missense	probably benign
R1807:Nphp3	UTSW	9	104,020,741 (GRCm38)	missense	probably benign	0.01
R1857:Nphp3	UTSW	9	104,021,294 (GRCm38)	missense	possibly damaging	0.87
R1962:Nphp3	UTSW	9	104,021,338 (GRCm38)	missense	probably benign	0.00
R2127:Nphp3	UTSW	9	104,008,243 (GRCm38)	missense	probably damaging	0.98
R2138:Nphp3	UTSW	9	104,025,903 (GRCm38)	missense	possibly damaging	0.89
R2233:Nphp3	UTSW	9	104,037,376 (GRCm38)	missense	probably benign	0.02
R2234:Nphp3	UTSW	9	104,037,376 (GRCm38)	missense	probably benign	0.02
R3861:Nphp3	UTSW	9	104,039,326 (GRCm38)	unclassified	probably benign
R3928:Nphp3	UTSW	9	104,011,730 (GRCm38)	missense	probably damaging	0.99
R3961:Nphp3	UTSW	9	104,003,042 (GRCm38)	nonsense	probably null
R4182:Nphp3	UTSW	9	104,038,464 (GRCm38)	missense	probably benign	0.06
R4294:Nphp3	UTSW	9	104,022,717 (GRCm38)	missense	probably damaging	1.00
R4387:Nphp3	UTSW	9	104,030,020 (GRCm38)	missense	possibly damaging	0.94
R4625:Nphp3	UTSW	9	104,036,159 (GRCm38)	missense	possibly damaging	0.66
R4628:Nphp3	UTSW	9	104,003,058 (GRCm38)	missense	probably damaging	0.99
R4696:Nphp3	UTSW	9	104,022,732 (GRCm38)	missense	probably benign	0.01
R4865:Nphp3	UTSW	9	104,031,970 (GRCm38)	missense	probably benign
R4886:Nphp3	UTSW	9	104,002,994 (GRCm38)	missense	probably damaging	1.00
R4973:Nphp3	UTSW	9	104,031,999 (GRCm38)	missense	probably benign
R5445:Nphp3	UTSW	9	104,004,723 (GRCm38)	missense	probably damaging	1.00
R5451:Nphp3	UTSW	9	104,042,022 (GRCm38)	missense	probably benign
R5520:Nphp3	UTSW	9	104,024,673 (GRCm38)	missense	probably benign	0.30
R5641:Nphp3	UTSW	9	104,036,153 (GRCm38)	missense	probably damaging	1.00
R5847:Nphp3	UTSW	9	104,003,037 (GRCm38)	missense	probably damaging	1.00
R5928:Nphp3	UTSW	9	104,035,797 (GRCm38)	missense	probably benign	0.01
R5931:Nphp3	UTSW	9	104,020,746 (GRCm38)	missense	probably damaging	1.00
R6161:Nphp3	UTSW	9	104,031,906 (GRCm38)	missense	probably benign	0.11
R6298:Nphp3	UTSW	9	104,015,441 (GRCm38)	missense	probably damaging	1.00
R6890:Nphp3	UTSW	9	104,041,954 (GRCm38)	missense	probably damaging	0.96
R7009:Nphp3	UTSW	9	104,016,116 (GRCm38)	missense	probably null	0.00
R7065:Nphp3	UTSW	9	104,041,990 (GRCm38)	missense	probably damaging	1.00
R7146:Nphp3	UTSW	9	104,004,837 (GRCm38)	nonsense	probably null
R7198:Nphp3	UTSW	9	104,004,775 (GRCm38)	missense	probably damaging	1.00
R7360:Nphp3	UTSW	9	104,016,078 (GRCm38)	critical splice acceptor site	probably null
R7369:Nphp3	UTSW	9	104,018,250 (GRCm38)	missense	probably damaging	0.99
R7554:Nphp3	UTSW	9	104,042,071 (GRCm38)	missense	probably damaging	0.98
R7591:Nphp3	UTSW	9	104,018,278 (GRCm38)	critical splice donor site	probably null
R7665:Nphp3	UTSW	9	104,005,393 (GRCm38)	splice site	probably null
R7672:Nphp3	UTSW	9	104,031,960 (GRCm38)	missense	probably benign
R8039:Nphp3	UTSW	9	104,031,963 (GRCm38)	missense	probably benign
R8145:Nphp3	UTSW	9	104,035,851 (GRCm38)	missense	probably benign	0.16
R8211:Nphp3	UTSW	9	104,031,897 (GRCm38)	missense	possibly damaging	0.80
R8882:Nphp3	UTSW	9	104,005,594 (GRCm38)	missense	possibly damaging	0.77
R9020:Nphp3	UTSW	9	104,031,951 (GRCm38)	missense	probably benign	0.00
R9132:Nphp3	UTSW	9	104,020,781 (GRCm38)	missense	probably damaging	1.00
R9135:Nphp3	UTSW	9	104,032,015 (GRCm38)	missense	probably damaging	0.99
R9159:Nphp3	UTSW	9	104,020,781 (GRCm38)	missense	probably damaging	1.00
R9204:Nphp3	UTSW	9	104,042,106 (GRCm38)	missense	probably benign
R9226:Nphp3	UTSW	9	104,008,129 (GRCm38)	missense	probably benign	0.00
R9229:Nphp3	UTSW	9	104,036,177 (GRCm38)	missense	probably damaging	1.00
R9526:Nphp3	UTSW	9	104,036,138 (GRCm38)	missense	probably damaging	1.00
R9678:Nphp3	UTSW	9	104,023,487 (GRCm38)	missense	possibly damaging	0.90
R9731:Nphp3	UTSW	9	104,009,170 (GRCm38)	missense	probably damaging	1.00
V7583:Nphp3	UTSW	9	104,035,894 (GRCm38)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- ATCTCTGTGTGACCTGAGGC -3'
(R):5'- CAACAGAAAGATGGCGCTC -3'

Sequencing Primer
(F):5'- ACCTGAGGCAAGTTTCGG -3'
(R):5'- CCTGGGGTACTGTTCTCAAAAATGAC -3'

Posted On

2019-11-12