Mutagenetix > Incidental Mutation

Incidental Mutation 'R4546:Nphp1'

333754

Institutional Source

Beutler Lab

Gene Symbol

Nphp1

Ensembl Gene

ENSMUSG00000027378

Gene Name

nephronophthisis 1 (juvenile) homolog (human)

Synonyms

nephrocystin

MMRRC Submission

041780-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4546 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

127582652-127630817 bp(-) (GRCm39)

Type of Mutation

splice site (5 bp from exon)

DNA Base Change (assembly)

C to T at 127607939 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000105986 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028857] [ENSMUST00000110357]

AlphaFold

no structure available at present

Predicted Effect

probably null
Transcript: ENSMUST00000028857

SMART Domains

Protein: ENSMUSP00000028857
Gene: ENSMUSG00000027378

Domain	Start	End	E-Value	Type
low complexity region	118	143	N/A	INTRINSIC
SH3	158	214	5.91e-19	SMART
low complexity region	220	246	N/A	INTRINSIC
Blast:14_3_3	391	491	3e-55	BLAST
low complexity region	634	641	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000110357

SMART Domains

Protein: ENSMUSP00000105986
Gene: ENSMUSG00000027378

Domain	Start	End	E-Value	Type
low complexity region	118	143	N/A	INTRINSIC
SH3	158	214	5.91e-19	SMART
low complexity region	220	246	N/A	INTRINSIC
Blast:14_3_3	390	490	3e-55	BLAST
low complexity region	633	640	N/A	INTRINSIC

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.0%

Validation Efficiency

97% (65/67)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with src homology domain 3 (SH3) patterns. This protein interacts with Crk-associated substrate, and it appears to function in the control of cell division, as well as in cell-cell and cell-matrix adhesion signaling, likely as part of a multifunctional complex localized in actin- and microtubule-based structures. Mutations in this gene cause familial juvenile nephronophthisis type 1, a kidney disorder involving both tubules and glomeruli. Defects in this gene are also associated with Senior-Loken syndrome type 1, also referred to as juvenile nephronophthisis with Leber amaurosis, which is characterized by kidney and eye disease, and with Joubert syndrome type 4, which is characterized by cerebellar ataxia, oculomotor apraxia, psychomotor delay and neonatal breathing abnormalities, sometimes including retinal dystrophy and renal disease. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit male infertility due to defects in sperm maturation. Mice homozygous for another knock-out allele exhibit absent photoreceptor outer segment and photoreceptor degeneration. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 56 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9930012K11Rik	G	A	14: 70,393,927 (GRCm39)	S236L	probably benign	Het
Ahcyl	C	T	16: 45,974,330 (GRCm39)	C349Y	possibly damaging	Het
Alg9	C	T	9: 50,716,654 (GRCm39)	T409M	possibly damaging	Het
Alpi	T	A	1: 87,026,839 (GRCm39)	Y413F	probably damaging	Het
Asmt	T	C	X: 169,110,230 (GRCm39)		probably null	Het
Atf7	A	G	15: 102,442,762 (GRCm39)	V449A	probably benign	Het
Bnc2	A	G	4: 84,210,213 (GRCm39)	F744L	probably benign	Het
Ccnyl1	G	T	1: 64,762,735 (GRCm39)	M347I	probably benign	Het
Cdk13	T	C	13: 17,941,159 (GRCm39)	K21R	probably damaging	Het
Cenpf	A	C	1: 189,386,847 (GRCm39)	L1811R	probably damaging	Het
Cfap91	C	T	16: 38,155,885 (GRCm39)	V113I	probably benign	Het
Cr2	A	G	1: 194,853,349 (GRCm39)	I43T	possibly damaging	Het
Cspg4	T	A	9: 56,795,913 (GRCm39)	L1216Q	possibly damaging	Het
Cylc2	A	T	4: 51,229,840 (GRCm39)	D394V	unknown	Het
Cylc2	C	G	4: 51,229,651 (GRCm39)	T331R	unknown	Het
Dcaf8	T	C	1: 172,007,460 (GRCm39)		probably benign	Het
Dlec1	A	T	9: 118,957,146 (GRCm39)	I796F	probably damaging	Het
Dnah12	A	T	14: 26,494,971 (GRCm39)	Q1343L	probably damaging	Het
Dnajc21	T	C	15: 10,447,183 (GRCm39)	R522G	probably benign	Het
F2rl3	C	T	8: 73,489,211 (GRCm39)	A146V	probably benign	Het
Fastkd1	C	T	2: 69,542,655 (GRCm39)	E51K	probably damaging	Het
Glrb	T	C	3: 80,786,993 (GRCm39)	S57G	probably damaging	Het
Gm5507	T	A	18: 54,117,409 (GRCm39)		noncoding transcript	Het
Golga4	A	G	9: 118,385,913 (GRCm39)	K22E	probably damaging	Het
Hdac1-ps	A	T	17: 78,800,388 (GRCm39)	T460S	probably benign	Het
Ift122	T	A	6: 115,867,549 (GRCm39)	L433Q	probably damaging	Het
Il21r	A	G	7: 125,228,071 (GRCm39)	R181G	probably damaging	Het
Il5ra	G	T	6: 106,715,459 (GRCm39)	S125*	probably null	Het
Kdm7a	T	C	6: 39,152,406 (GRCm39)	R97G	probably benign	Het
Lepr	T	A	4: 101,671,838 (GRCm39)	I954N	probably benign	Het
Lims1	T	C	10: 58,254,612 (GRCm39)		probably benign	Het
Mest	T	C	6: 30,740,679 (GRCm39)	W13R	probably damaging	Het
Mfn2	A	G	4: 147,971,909 (GRCm39)	V224A	probably benign	Het
Muc15	T	C	2: 110,567,844 (GRCm39)	S330P	probably damaging	Het
Ncapg	T	C	5: 45,828,554 (GRCm39)	F102L	probably damaging	Het
Nkd2	T	C	13: 73,971,475 (GRCm39)	D187G	probably benign	Het
Or10ag59	T	C	2: 87,405,530 (GRCm39)	F34S	probably benign	Het
Or1e19	T	C	11: 73,316,012 (GRCm39)	N266D	probably benign	Het
Or2a12	C	T	6: 42,904,348 (GRCm39)	S61L	probably damaging	Het
Osbpl6	T	C	2: 76,414,836 (GRCm39)	V409A	possibly damaging	Het
Pdhx	A	T	2: 102,903,742 (GRCm39)	L18Q	probably null	Het
Pear1	C	T	3: 87,661,968 (GRCm39)	G469D	probably damaging	Het
Plec	T	C	15: 76,065,757 (GRCm39)	T1506A	probably benign	Het
Plod3	T	A	5: 137,017,801 (GRCm39)	D192E	possibly damaging	Het
Rbks	T	C	5: 31,781,912 (GRCm39)	N296S	probably benign	Het
Sema3c	G	A	5: 17,899,770 (GRCm39)	V421I	probably benign	Het
Slc15a4	A	G	5: 127,681,600 (GRCm39)		probably null	Het
Slc7a8	C	G	14: 54,973,247 (GRCm39)	G240A	possibly damaging	Het
Tmem200c	A	G	17: 69,149,166 (GRCm39)	D583G	probably benign	Het
Trpm6	A	G	19: 18,809,841 (GRCm39)	Y1079C	probably damaging	Het
Ttn	T	C	2: 76,652,932 (GRCm39)		probably null	Het
Vcp	T	C	4: 42,988,813 (GRCm39)		probably benign	Het
Vmn2r78	T	C	7: 86,603,811 (GRCm39)	V663A	probably damaging	Het
Vmn2r9	T	G	5: 108,995,551 (GRCm39)	M366L	probably benign	Het
Wdr11	A	G	7: 129,230,729 (GRCm39)	E878G	probably damaging	Het
Zan	C	G	5: 137,382,096 (GRCm39)	M5150I	unknown	Het

Other mutations in Nphp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00570:Nphp1	APN	2	127,605,805 (GRCm39)	missense	probably damaging	0.99
IGL00589:Nphp1	APN	2	127,605,769 (GRCm39)	missense	probably damaging	1.00
IGL01143:Nphp1	APN	2	127,622,056 (GRCm39)	missense	probably benign	0.06
IGL01893:Nphp1	APN	2	127,611,564 (GRCm39)	missense	probably damaging	1.00
IGL01922:Nphp1	APN	2	127,621,989 (GRCm39)	missense	possibly damaging	0.95
IGL02123:Nphp1	APN	2	127,595,969 (GRCm39)	missense	probably benign	0.03
IGL02340:Nphp1	APN	2	127,621,987 (GRCm39)	nonsense	probably null
IGL02836:Nphp1	APN	2	127,611,543 (GRCm39)	missense	probably benign	0.00
IGL03109:Nphp1	APN	2	127,610,089 (GRCm39)	critical splice donor site	probably benign
R1632:Nphp1	UTSW	2	127,612,312 (GRCm39)	missense	probably benign	0.32
R1857:Nphp1	UTSW	2	127,612,296 (GRCm39)	missense	probably benign	0.00
R4425:Nphp1	UTSW	2	127,630,719 (GRCm39)	missense	possibly damaging	0.82
R4514:Nphp1	UTSW	2	127,590,007 (GRCm39)	missense	probably benign	0.26
R4580:Nphp1	UTSW	2	127,610,089 (GRCm39)	critical splice donor site	probably null
R5634:Nphp1	UTSW	2	127,601,570 (GRCm39)	missense	possibly damaging	0.81
R7152:Nphp1	UTSW	2	127,595,899 (GRCm39)	missense	probably benign
R7326:Nphp1	UTSW	2	127,603,137 (GRCm39)	missense	possibly damaging	0.76
R7985:Nphp1	UTSW	2	127,587,829 (GRCm39)	missense	probably damaging	0.97
R8029:Nphp1	UTSW	2	127,583,036 (GRCm39)	missense	probably benign	0.00
R8715:Nphp1	UTSW	2	127,605,729 (GRCm39)	missense	possibly damaging	0.91
R8967:Nphp1	UTSW	2	127,582,897 (GRCm39)	missense	probably damaging	1.00
R8997:Nphp1	UTSW	2	127,595,982 (GRCm39)	missense	possibly damaging	0.88
R9328:Nphp1	UTSW	2	127,582,892 (GRCm39)	missense	possibly damaging	0.77
R9450:Nphp1	UTSW	2	127,616,008 (GRCm39)	missense
R9755:Nphp1	UTSW	2	127,595,951 (GRCm39)	nonsense	probably null
X0022:Nphp1	UTSW	2	127,603,134 (GRCm39)	missense	probably damaging	1.00
X0025:Nphp1	UTSW	2	127,621,047 (GRCm39)	missense	probably benign	0.16

Predicted Primers

PCR Primer
(F):5'- GATAGTTGGGGTTACATAGTAAGACC -3'
(R):5'- CGTGGAACGATATCAATTTAGGG -3'

Sequencing Primer
(F):5'- GGGTTACATAGTAAGACCTTGTCTC -3'
(R):5'- TGGAACGATATCAATTTAGGGTTTTG -3'

Posted On

2015-08-18