Mutagenetix > Incidental Mutation

Incidental Mutation 'R9678:Nphp3'

735776

Institutional Source

Beutler Lab

Gene Symbol

Nphp3

Ensembl Gene

ENSMUSG00000032558

Gene Name

nephronophthisis 3 (adolescent)

Synonyms

pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9678 (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 C at 103900686 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 648 (V648A)

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: V648A

PolyPhen 2 Score 0.902 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: V648A

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

SMART Domains

Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: V528A

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: 99.8%
3x: 99.7%
10x: 99.3%
20x: 98.6%

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: 39 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgre1	A	G	17: 57,750,997 (GRCm39)	N557S	probably damaging	Het
Atr	C	T	9: 95,792,610 (GRCm39)	A1644V	possibly damaging	Het
C4b	A	G	17: 34,960,763 (GRCm39)		probably null	Het
Cdca2	A	T	14: 67,937,778 (GRCm39)	C292S	unknown	Het
Cdkn1c	T	C	7: 143,014,383 (GRCm39)	D21G	probably benign	Het
Clec12a	C	A	6: 129,330,628 (GRCm39)	T70K	probably benign	Het
Crnkl1	A	T	2: 145,761,875 (GRCm39)	S561T	probably benign	Het
Dock4	TGTGCCGGTGCCGGTGCCGGTGCCGGTGCC	TGTGCCGGTGCCGGTGCCGGTGCCGGTGCCGGTGCC	12: 40,894,379 (GRCm39)		probably benign	Het
Dock4	CGGTGC	CGGTGCGGGTGC	12: 40,894,396 (GRCm39)		probably benign	Het
Dock4	TGCCGG	TGCCGGCGCCGG	12: 40,894,387 (GRCm39)		probably benign	Het
Ehbp1	T	C	11: 22,101,108 (GRCm39)	D274G	possibly damaging	Het
Fsd2	T	C	7: 81,209,449 (GRCm39)	Y131C	probably damaging	Het
Gm10153	C	A	7: 141,743,723 (GRCm39)	C115F	unknown	Het
Gm10376	A	T	14: 42,873,024 (GRCm39)	M1K	probably null	Het
Gm10837	A	T	14: 122,728,438 (GRCm39)	K105*	probably null	Het
H3f3a	A	G	1: 180,637,680 (GRCm39)		probably null	Het
Igkv10-96	T	A	6: 68,609,224 (GRCm39)	M24L	probably benign	Het
Inpp4a	T	C	1: 37,405,952 (GRCm39)	S157P	probably damaging	Het
Meaf6	A	G	4: 124,996,689 (GRCm39)	N133S	possibly damaging	Het
Or1i2	C	T	10: 78,447,717 (GRCm39)	G253R	probably damaging	Het
Or5k17	A	G	16: 58,746,640 (GRCm39)	M98T	probably benign	Het
Parm1	A	G	5: 91,742,144 (GRCm39)	T171A	possibly damaging	Het
Pik3r1	G	T	13: 101,839,289 (GRCm39)	R188S	probably damaging	Het
Rbsn	T	C	6: 92,188,619 (GRCm39)	H32R	probably damaging	Het
Sdk2	G	T	11: 113,685,789 (GRCm39)	Y1910*	probably null	Het
Slfn8	T	C	11: 82,907,723 (GRCm39)	I273M	probably damaging	Het
Sult1a1	C	T	7: 126,273,536 (GRCm39)	V132I	probably benign	Het
Tagln3	T	A	16: 45,544,605 (GRCm39)	Y22F	probably damaging	Het
Tenm4	A	G	7: 96,386,619 (GRCm39)	E575G	possibly damaging	Het
Trim24	T	C	6: 37,942,449 (GRCm39)	V987A	probably damaging	Het
Trpm7	C	A	2: 126,686,290 (GRCm39)	V313F	probably damaging	Het
Trub1	A	T	19: 57,446,549 (GRCm39)	N93I	probably benign	Het
Ugdh	A	G	5: 65,581,470 (GRCm39)	V60A	possibly damaging	Het
Ugt2b5	A	C	5: 87,273,186 (GRCm39)	D493E	probably damaging	Het
Utrn	G	T	10: 12,615,159 (GRCm39)	D337E	probably benign	Het
Vmn2r14	A	G	5: 109,364,041 (GRCm39)	L625P	probably damaging	Het
Vmn2r89	A	G	14: 51,693,511 (GRCm39)	D287G	probably benign	Het
Xirp2	A	T	2: 67,339,788 (GRCm39)	E676D	possibly damaging	Het
Zbbx	A	G	3: 75,046,841 (GRCm39)	L26P	probably damaging	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
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
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'- TTCCAACCTAGGATTAAACCATTCC -3'
(R):5'- TTTCATTTCTAGGTCCGGAGAG -3'

Sequencing Primer
(F):5'- GGATTAAACCATTCCCAAATAAGGTC -3'
(R):5'- CCAAGCCTTACAGATGGTGC -3'

Posted On

2022-11-14