Mutagenetix > Incidental Mutation

Incidental Mutation 'R1857:Nphp1'

206203

Institutional Source

Beutler Lab

Gene Symbol

Nphp1

Ensembl Gene

ENSMUSG00000027378

Gene Name

nephronophthisis 1 (juvenile) homolog (human)

Synonyms

nephrocystin

MMRRC Submission

039881-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1857 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

127582652-127630817 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 127612296 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 217 (D217V)

Ref Sequence

ENSEMBL: ENSMUSP00000105986 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000028857
AA Change: D217V

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000028857
Gene: ENSMUSG00000027378
AA Change: D217V

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 benign
Transcript: ENSMUST00000110357
AA Change: D217V

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000105986
Gene: ENSMUSG00000027378
AA Change: D217V

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

Coding Region Coverage

1x: 97.4%
3x: 96.9%
10x: 95.3%
20x: 92.2%

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 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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aars1	T	A	8: 111,766,789 (GRCm39)	I57N	probably damaging	Het
Abca15	T	C	7: 119,960,592 (GRCm39)	S685P	probably damaging	Het
Adpgk	G	T	9: 59,222,248 (GRCm39)	V392L	probably benign	Het
Akap14	C	T	X: 36,420,779 (GRCm39)	A476T	probably damaging	Het
Amdhd1	A	T	10: 93,367,416 (GRCm39)	I246N	probably damaging	Het
Amhr2	T	A	15: 102,355,212 (GRCm39)	L165*	probably null	Het
Atr	T	A	9: 95,747,150 (GRCm39)	I144N	probably damaging	Het
Ccdc33	T	C	9: 57,939,991 (GRCm39)	N750S	possibly damaging	Het
Cdh23	A	G	10: 60,159,076 (GRCm39)	I2233T	probably damaging	Het
Cfap46	C	A	7: 139,233,324 (GRCm39)	V774F	probably damaging	Het
Cfap69	G	T	5: 5,632,518 (GRCm39)	T362K	possibly damaging	Het
Cnih3	A	G	1: 181,277,638 (GRCm39)	H101R	probably damaging	Het
Crebrf	T	A	17: 26,961,937 (GRCm39)	Y345N	probably benign	Het
Cyb5r4	C	T	9: 86,923,332 (GRCm39)	S185L	probably benign	Het
Cyp2j5	T	C	4: 96,547,723 (GRCm39)	E173G	possibly damaging	Het
Cyp3a41b	T	A	5: 145,503,660 (GRCm39)	I296F	probably benign	Het
Dse	T	C	10: 34,029,225 (GRCm39)	T622A	probably benign	Het
Duxf4	A	G	10: 58,071,602 (GRCm39)	V204A	probably benign	Het
Dync1h1	T	A	12: 110,629,059 (GRCm39)	F4205L	probably damaging	Het
Eif3a	A	C	19: 60,770,635 (GRCm39)	L71V	probably damaging	Het
Eif3h	T	C	15: 51,662,674 (GRCm39)	Y124C	probably damaging	Het
Eif4g3	A	T	4: 137,903,187 (GRCm39)	Q1169L	possibly damaging	Het
Endod1	T	A	9: 14,268,405 (GRCm39)	H360L	probably benign	Het
Fbxo38	A	G	18: 62,648,489 (GRCm39)	I683T	probably damaging	Het
Frem2	T	A	3: 53,562,294 (GRCm39)	T738S	probably benign	Het
Gm1527	A	T	3: 28,957,539 (GRCm39)	T148S	probably damaging	Het
Gm4894	T	C	9: 49,189,976 (GRCm39)	S84P	unknown	Het
Hsh2d	G	A	8: 72,954,304 (GRCm39)	D229N	probably benign	Het
Il1f10	A	T	2: 24,182,817 (GRCm39)	D31V	possibly damaging	Het
Lrrc56	A	G	7: 140,787,421 (GRCm39)	M353V	probably benign	Het
Meiob	T	C	17: 25,042,544 (GRCm39)	V124A	probably damaging	Het
Mmp11	A	T	10: 75,764,191 (GRCm39)	D91E	probably benign	Het
Mpped2	T	C	2: 106,613,989 (GRCm39)	Y108H	probably damaging	Het
Mroh9	A	G	1: 162,866,714 (GRCm39)	V674A	probably damaging	Het
Mtor	G	T	4: 148,565,336 (GRCm39)	Q1015H	probably damaging	Het
Mylk3	G	A	8: 86,055,223 (GRCm39)	T711I	probably damaging	Het
Ndufaf6	G	T	4: 11,053,474 (GRCm39)	H277Q	probably benign	Het
Neurl4	G	T	11: 69,796,361 (GRCm39)	G435V	probably damaging	Het
Nipal2	A	G	15: 34,678,779 (GRCm39)	S21P	possibly damaging	Het
Nphp3	T	C	9: 103,898,493 (GRCm39)	I432T	possibly damaging	Het
Oprd1	T	G	4: 131,840,992 (GRCm39)	D322A	probably damaging	Het
Or10ag2	T	C	2: 87,248,992 (GRCm39)	L198P	probably damaging	Het
Or2b28	A	G	13: 21,531,346 (GRCm39)	M83V	possibly damaging	Het
Or56a3b	T	G	7: 104,770,751 (GRCm39)	L29R	probably benign	Het
Pcdh10	C	A	3: 45,334,372 (GRCm39)	Q229K	possibly damaging	Het
Pdlim7	G	A	13: 55,653,858 (GRCm39)	T253M	probably damaging	Het
Pfdn1	C	A	18: 36,584,153 (GRCm39)	M60I	probably benign	Het
Pigc	T	G	1: 161,798,446 (GRCm39)	S143A	possibly damaging	Het
Pkd1l2	T	C	8: 117,767,408 (GRCm39)	D1294G	possibly damaging	Het
Ppp2r1a	T	C	17: 21,181,951 (GRCm39)	S490P	possibly damaging	Het
Ppp2r3d	T	A	9: 101,090,092 (GRCm39)	N77I	probably damaging	Het
Pramel17	T	C	4: 101,692,770 (GRCm39)	Y410C	probably damaging	Het
Pramel29	C	T	4: 143,935,091 (GRCm39)	V217I	possibly damaging	Het
Prl7a2	A	T	13: 27,843,163 (GRCm39)	C213*	probably null	Het
Prpf8	T	A	11: 75,386,249 (GRCm39)		probably null	Het
Psmd7	A	T	8: 108,311,525 (GRCm39)	N109K	probably damaging	Het
Ptprn	T	C	1: 75,224,549 (GRCm39)	K936E	possibly damaging	Het
Ro60	T	C	1: 143,646,488 (GRCm39)	T86A	probably benign	Het
Ror1	A	T	4: 100,298,700 (GRCm39)	Q691L	probably damaging	Het
Sars2	A	G	7: 28,449,437 (GRCm39)	M322V	probably benign	Het
Scfd2	C	A	5: 74,372,962 (GRCm39)	E638*	probably null	Het
Scgb3a2	A	G	18: 43,899,900 (GRCm39)	T63A	probably benign	Het
Slc5a4a	T	C	10: 76,002,569 (GRCm39)	S242P	probably benign	Het
Smarcd1	A	G	15: 99,607,295 (GRCm39)	K382E	probably damaging	Het
Sox5	T	A	6: 143,906,541 (GRCm39)	S305C	probably damaging	Het
Sp5	C	A	2: 70,307,213 (GRCm39)	H299Q	possibly damaging	Het
Stard13	T	C	5: 151,018,903 (GRCm39)	Y60C	probably damaging	Het
Tmprss6	A	G	15: 78,336,752 (GRCm39)	F383L	probably damaging	Het
Ttc23	T	C	7: 67,328,821 (GRCm39)		probably null	Het
Ugt2b34	T	C	5: 87,052,241 (GRCm39)	T252A	possibly damaging	Het
Vangl2	A	T	1: 171,837,464 (GRCm39)	L115Q	probably damaging	Het
Vmn1r42	A	G	6: 89,821,597 (GRCm39)	I324T	probably benign	Het
Vwa5b1	A	G	4: 138,296,413 (GRCm39)	F1205L	probably damaging	Het
Zfp951	G	C	5: 104,962,723 (GRCm39)	T281R	probably damaging	Het
Zscan30	A	G	18: 24,104,524 (GRCm39)		noncoding transcript	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
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
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'- TTGCACATGCCTGCACATAC -3'
(R):5'- CAAGTTGTAGAATTACCGTGCC -3'

Sequencing Primer
(F):5'- TGCCTGCACATACAACCC -3'
(R):5'- GTAGAATTACCGTGCCTGTCTATC -3'

Posted On

2014-06-23