Mutagenetix > Incidental Mutation

Incidental Mutation 'R5634:Nphp1'

440018

Institutional Source

Beutler Lab

Gene Symbol

Nphp1

Ensembl Gene

ENSMUSG00000027378

Gene Name

nephronophthisis 1 (juvenile) homolog (human)

Synonyms

nephrocystin

MMRRC Submission

043285-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5634 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

127582652-127630817 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 127601570 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 412 (C412S)

Ref Sequence

ENSEMBL: ENSMUSP00000105986 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000028857
AA Change: C413S

PolyPhen 2 Score 0.471 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000028857
Gene: ENSMUSG00000027378
AA Change: C413S

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

possibly damaging
Transcript: ENSMUST00000110357
AA Change: C412S

PolyPhen 2 Score 0.815 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000105986
Gene: ENSMUSG00000027378
AA Change: C412S

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

0.2537

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.7%

Validation Efficiency

98% (60/61)

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acat1	T	C	9: 53,494,921 (GRCm39)		probably benign	Het
Aen	A	T	7: 78,552,255 (GRCm39)	T34S	probably benign	Het
Apoh	T	A	11: 108,302,875 (GRCm39)	V280E	probably damaging	Het
Ccdc87	A	G	19: 4,890,693 (GRCm39)	H395R	probably benign	Het
Ccrl2	T	A	9: 110,885,055 (GRCm39)		probably null	Het
Cdh20	T	C	1: 104,902,800 (GRCm39)	F497S	probably damaging	Het
Cfap54	C	A	10: 92,740,125 (GRCm39)		probably benign	Het
Cimap1b	T	A	15: 89,262,410 (GRCm39)	T70S	probably benign	Het
Cipc	T	A	12: 86,999,749 (GRCm39)		probably null	Het
Col14a1	T	A	15: 55,381,694 (GRCm39)	Y1756N	probably damaging	Het
Cyp2c54	G	A	19: 40,060,858 (GRCm39)	A95V	possibly damaging	Het
Dcdc5	A	G	2: 106,234,325 (GRCm39)		noncoding transcript	Het
Dnah17	T	C	11: 117,943,752 (GRCm39)		probably null	Het
Eepd1	A	T	9: 25,514,849 (GRCm39)	N552I	probably benign	Het
Eif2ak4	A	T	2: 118,292,792 (GRCm39)	R1218W	probably damaging	Het
Fbxw18	T	A	9: 109,505,871 (GRCm39)	I467F	possibly damaging	Het
Ffar4	GCTTCTT	GCTT	19: 38,102,373 (GRCm39)		probably benign	Het
Gm4787	G	C	12: 81,424,604 (GRCm39)	T518S	probably benign	Het
Gpha2	A	G	19: 6,276,890 (GRCm39)	T25A	probably benign	Het
Grin3a	T	A	4: 49,792,843 (GRCm39)	I297F	probably damaging	Het
Herc2	G	A	7: 55,856,531 (GRCm39)	G3924R	probably damaging	Het
Hmcn2	G	T	2: 31,223,893 (GRCm39)	D97Y	probably damaging	Het
Igdcc4	G	A	9: 65,041,828 (GRCm39)	G1131D	probably benign	Het
Il18rap	T	C	1: 40,578,536 (GRCm39)		probably benign	Het
Ino80d	C	A	1: 63,101,442 (GRCm39)		probably benign	Het
Klhl1	T	C	14: 96,477,707 (GRCm39)	T454A	probably damaging	Het
Krt84	C	A	15: 101,437,084 (GRCm39)	V360L	probably benign	Het
Lin9	T	A	1: 180,496,763 (GRCm39)	L351I	probably benign	Het
Lrrc37	T	C	11: 103,432,840 (GRCm39)	N1267S	possibly damaging	Het
Mapkbp1	A	G	2: 119,803,576 (GRCm39)	N15S	probably damaging	Het
Med13l	T	C	5: 118,698,915 (GRCm39)	F22S	possibly damaging	Het
Mrc2	T	A	11: 105,227,040 (GRCm39)	C548*	probably null	Het
Nacad	T	C	11: 6,552,387 (GRCm39)	E268G	possibly damaging	Het
Nfxl1	A	G	5: 72,686,833 (GRCm39)	C527R	probably damaging	Het
Or1e16	AGCGGTCGTAGGC	AGC	11: 73,286,480 (GRCm39)		probably null	Het
Or4g16	A	G	2: 111,137,437 (GRCm39)	I296V	probably benign	Het
Per2	C	T	1: 91,372,429 (GRCm39)	C215Y	probably benign	Het
Pias1	T	C	9: 62,803,255 (GRCm39)	T343A	probably benign	Het
Pja2	C	T	17: 64,599,862 (GRCm39)	V541M	probably damaging	Het
Plxna4	G	A	6: 32,214,658 (GRCm39)	Q608*	probably null	Het
Ppil4	T	A	10: 7,690,542 (GRCm39)	D398E	probably benign	Het
Ppp4r3a	T	A	12: 101,009,780 (GRCm39)	D8V	probably damaging	Het
Pstk	A	C	7: 130,973,072 (GRCm39)	D57A	probably damaging	Het
Ptprd	T	C	4: 75,990,255 (GRCm39)	I53V	probably benign	Het
Pyroxd2	A	G	19: 42,728,924 (GRCm39)	F159L	probably benign	Het
Rnf103	A	G	6: 71,486,601 (GRCm39)	M411V	probably benign	Het
Scn4a	T	C	11: 106,220,830 (GRCm39)	D943G	probably benign	Het
Sdk2	T	C	11: 113,742,540 (GRCm39)	T790A	probably damaging	Het
Sfr1	T	C	19: 47,722,310 (GRCm39)	L242P	probably damaging	Het
Snx25	T	C	8: 46,494,428 (GRCm39)	D819G	possibly damaging	Het
Sult2b1	A	G	7: 45,383,506 (GRCm39)	V183A	probably damaging	Het
Tcf4	C	A	18: 69,769,918 (GRCm39)	S8R	possibly damaging	Het
Ttc7	A	G	17: 87,649,515 (GRCm39)	D531G	probably benign	Het
Uap1l1	A	C	2: 25,254,145 (GRCm39)	C271G	probably damaging	Het
Ubtf	T	C	11: 102,201,150 (GRCm39)	Y268C	probably damaging	Het
Vinac1	A	T	2: 128,881,406 (GRCm39)	D173E	probably benign	Het
Zfp951	A	T	5: 104,963,155 (GRCm39)	M137K	probably benign	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
R4546:Nphp1	UTSW	2	127,607,939 (GRCm39)	splice site	probably null
R4580:Nphp1	UTSW	2	127,610,089 (GRCm39)	critical splice donor site	probably null
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'- TCTGGTTCCTTCAGAGTTAATTTCTG -3'
(R):5'- TGGTCCATCTACTTTCAAGAACATTT -3'

Sequencing Primer
(F):5'- TCAGGGCGTTTTACCAGAAC -3'
(R):5'- GGGATCAAACTCAAGTCTTCAGGC -3'

Posted On

2016-11-08