Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01707:Nphp3'

104642

Institutional Source

Australian Phenomics Network (link to record)

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 #

IGL01707

Quality Score

Status

Chromosome

Chromosomal Location

103879743-103921010 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 103895357 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 371 (D371V)

Ref Sequence

ENSEMBL: ENSMUSP00000141540 (fasta)

Gene Model

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

AlphaFold

Q7TNH6

Predicted Effect

probably benign
Transcript: ENSMUST00000035167
AA Change: D465V

PolyPhen 2 Score 0.315 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: D465V

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
AA Change: D345V

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: ENSMUST00000191919

Predicted Effect

possibly damaging
Transcript: ENSMUST00000193439
AA Change: D371V

PolyPhen 2 Score 0.748 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000141540
Gene: ENSMUSG00000032558
AA Change: D371V

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

possibly damaging
Transcript: ENSMUST00000194774
AA Change: D345V

PolyPhen 2 Score 0.615 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: D345V

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

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: 33 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ablim1	C	A	19: 57,027,879 (GRCm39)	R404L	probably damaging	Het
Acot6	C	A	12: 84,147,763 (GRCm39)	S6R	probably benign	Het
Adamtsl4	T	A	3: 95,591,301 (GRCm39)	Q222L	probably benign	Het
Adgre5	T	A	8: 84,450,976 (GRCm39)	T725S	probably damaging	Het
Agbl3	A	T	6: 34,816,389 (GRCm39)	K766N	possibly damaging	Het
Ankrd12	A	G	17: 66,291,273 (GRCm39)	S1387P	probably damaging	Het
Camk2a	G	A	18: 61,093,122 (GRCm39)		probably null	Het
Cd209d	T	C	8: 3,928,296 (GRCm39)	I30V	probably benign	Het
Ces1d	A	T	8: 93,916,178 (GRCm39)	S150T	possibly damaging	Het
Cox4i2	T	C	2: 152,598,956 (GRCm39)	Y38H	probably damaging	Het
Csmd2	T	C	4: 128,276,798 (GRCm39)	Y867H	possibly damaging	Het
Dbh	G	A	2: 27,055,556 (GRCm39)	C10Y	probably benign	Het
Dnajc13	A	G	9: 104,106,178 (GRCm39)	V332A	probably damaging	Het
Gnb3	G	T	6: 124,816,652 (GRCm39)	A11E	possibly damaging	Het
Herc2	A	G	7: 55,814,935 (GRCm39)	R2725G	probably damaging	Het
Kdm4c	C	T	4: 74,255,164 (GRCm39)	L573F	probably damaging	Het
Kmt2c	T	A	5: 25,505,096 (GRCm39)	Q3404L	probably damaging	Het
Mmp9	A	G	2: 164,791,909 (GRCm39)	H231R	probably benign	Het
Nphp4	A	G	4: 152,623,440 (GRCm39)	I705V	probably benign	Het
Nutm2	A	T	13: 50,623,753 (GRCm39)	N150I	probably damaging	Het
Or51a7	T	C	7: 102,615,126 (GRCm39)	I273T	probably damaging	Het
Or51aa5	A	T	7: 103,167,141 (GRCm39)	I150N	probably damaging	Het
Phb2	A	G	6: 124,690,998 (GRCm39)	Q52R	probably benign	Het
Plekhh1	T	A	12: 79,125,738 (GRCm39)	V1258E	probably benign	Het
Pou2f1	A	T	1: 165,742,685 (GRCm39)	N69K	probably damaging	Het
Rapsn	T	A	2: 90,873,585 (GRCm39)	M297K	probably benign	Het
Senp5	A	C	16: 31,808,588 (GRCm39)	V195G	probably damaging	Het
Trim25	T	C	11: 88,890,517 (GRCm39)	V68A	probably damaging	Het
Ttc41	A	T	10: 86,612,631 (GRCm39)	R1301S	probably damaging	Het
Vcan	T	C	13: 89,837,864 (GRCm39)	Y1600C	probably damaging	Het
Washc5	A	G	15: 59,213,864 (GRCm39)	I864T	possibly damaging	Het
Wif1	T	A	10: 120,919,890 (GRCm39)		probably null	Het
Zdhhc15	G	A	X: 103,609,422 (GRCm39)	R208C	probably damaging	Het

Other mutations in Nphp3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
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

Posted On

2014-01-21