Mutagenetix > Incidental Mutation

Incidental Mutation 'R2104:Ctns'

230805

Institutional Source

Beutler Lab

Gene Symbol

Ctns

Ensembl Gene

ENSMUSG00000005949

Gene Name

cystinosis, nephropathic

Synonyms

MMRRC Submission

040108-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.116) question?

Stock #

R2104 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

73074422-73089868 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 73083907 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 38 (S38R)

Ref Sequence

ENSEMBL: ENSMUSP00000104116 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006103] [ENSMUST00000108476]

AlphaFold

P57757

Predicted Effect

probably benign
Transcript: ENSMUST00000006103
AA Change: S38R

PolyPhen 2 Score 0.074 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000006103
Gene: ENSMUSG00000005949
AA Change: S38R

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
CTNS	140	171	6.43e-12	SMART
transmembrane domain	206	225	N/A	INTRINSIC
transmembrane domain	238	257	N/A	INTRINSIC
CTNS	279	310	1.47e-6	SMART
transmembrane domain	338	357	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108476
AA Change: S38R

PolyPhen 2 Score 0.074 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000104116
Gene: ENSMUSG00000005949
AA Change: S38R

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
CTNS	140	171	6.43e-12	SMART
transmembrane domain	206	225	N/A	INTRINSIC
transmembrane domain	238	257	N/A	INTRINSIC
CTNS	279	310	1.47e-6	SMART
transmembrane domain	338	357	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130101

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144658

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150468

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.3%

Validation Efficiency

100% (80/80)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a seven-transmembrane domain protein that functions to transport cystine out of lysosomes. Its activity is driven by the H+ electrochemical gradient of the lysosomal membrane. Mutations in this gene cause cystinosis, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2009]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit increased intracellular cystine, progressive accumulation of cystine crystals, occasional muscle impairment, reduced exploratory activity, osteoporosis, and lowered electroretinogram amplitude. [provided by MGI curators]

Allele List at MGI

All alleles(2) : Targeted(2)

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsm3	G	A	7: 119,383,527 (GRCm39)	V563I	probably benign	Het
Amer3	T	C	1: 34,627,759 (GRCm39)	V666A	probably benign	Het
Ankrd16	A	G	2: 11,784,711 (GRCm39)		probably benign	Het
Ankub1	G	T	3: 57,580,296 (GRCm39)	C120*	probably null	Het
Arhgap31	T	C	16: 38,445,941 (GRCm39)	I135V	probably benign	Het
Atp2c2	G	A	8: 120,476,584 (GRCm39)	G633D	probably benign	Het
Camta1	T	A	4: 151,537,751 (GRCm39)	Q143L	probably damaging	Het
Casp8ap2	T	C	4: 32,644,727 (GRCm39)	S1267P	probably benign	Het
Ccn4	A	G	15: 66,791,176 (GRCm39)	E326G	probably benign	Het
Cdh1	T	A	8: 107,380,391 (GRCm39)		probably benign	Het
Cdhr4	C	A	9: 107,873,460 (GRCm39)	D397E	probably damaging	Het
Cdk6	T	G	5: 3,394,387 (GRCm39)	S7R	probably benign	Het
Cert1	T	A	13: 96,771,394 (GRCm39)	N550K	probably damaging	Het
Cilp2	C	A	8: 70,335,442 (GRCm39)	E519*	probably null	Het
Clybl	A	G	14: 122,548,718 (GRCm39)	Y40C	probably damaging	Het
Ctnnal1	T	C	4: 56,812,329 (GRCm39)	*732W	probably null	Het
Cwh43	A	T	5: 73,578,873 (GRCm39)	K293N	possibly damaging	Het
Dcaf5	G	T	12: 80,385,635 (GRCm39)	D830E	probably benign	Het
Dmxl2	A	G	9: 54,322,848 (GRCm39)	V1512A	probably damaging	Het
Dnah9	A	T	11: 65,951,950 (GRCm39)	C1850S	probably damaging	Het
Dpp8	C	T	9: 64,981,849 (GRCm39)		probably null	Het
Enam	A	T	5: 88,649,646 (GRCm39)	Q385L	probably damaging	Het
Etv3	A	G	3: 87,443,369 (GRCm39)	T318A	possibly damaging	Het
Exd2	T	G	12: 80,543,575 (GRCm39)	I586S	probably benign	Het
Fat3	A	G	9: 15,909,813 (GRCm39)	V2063A	possibly damaging	Het
Fezf1	A	G	6: 23,247,331 (GRCm39)	F248S	possibly damaging	Het
Flnc	T	C	6: 29,450,734 (GRCm39)		probably null	Het
Foxc2	A	G	8: 121,844,819 (GRCm39)	Y489C	probably damaging	Het
Gfm2	A	G	13: 97,308,028 (GRCm39)	E540G	probably damaging	Het
Hrg	T	C	16: 22,774,949 (GRCm39)	I193T	probably benign	Het
Ifih1	G	A	2: 62,440,889 (GRCm39)	Q426*	probably null	Het
Ifit1bl2	T	A	19: 34,596,920 (GRCm39)	D232V	probably benign	Het
Igf2bp1	A	G	11: 95,866,122 (GRCm39)	V122A	probably damaging	Het
Inpp1	T	G	1: 52,838,577 (GRCm39)	Q24P	probably damaging	Het
Kifc2	A	G	15: 76,545,454 (GRCm39)	D67G	probably damaging	Het
Lrrc43	G	A	5: 123,639,177 (GRCm39)	G402D	probably benign	Het
Lrrc8c	C	T	5: 105,755,224 (GRCm39)	T333M	possibly damaging	Het
Mab21l3	G	T	3: 101,730,744 (GRCm39)	A165D	probably benign	Het
Mcub	T	A	3: 129,712,337 (GRCm39)	R179S	probably benign	Het
Mdfi	G	C	17: 48,135,562 (GRCm39)	A56G	possibly damaging	Het
Mdn1	A	T	4: 32,743,843 (GRCm39)		probably null	Het
Meox2	A	G	12: 37,217,476 (GRCm39)	T226A	probably damaging	Het
Mipol1	A	G	12: 57,352,842 (GRCm39)		probably null	Het
Mms22l	T	G	4: 24,591,084 (GRCm39)	N1018K	probably benign	Het
Mn1	T	C	5: 111,602,617 (GRCm39)	I1285T	possibly damaging	Het
Muc20	T	G	16: 32,614,547 (GRCm39)	S277R	probably damaging	Het
Muc6	C	A	7: 141,213,991 (GRCm39)	V2845L	probably benign	Het
Mup5	C	A	4: 61,751,962 (GRCm39)	G96C	probably damaging	Het
Neb	T	A	2: 52,146,826 (GRCm39)	M2813L	probably benign	Het
Neb	C	A	2: 52,161,570 (GRCm39)	R2074L	probably damaging	Het
Oasl2	A	T	5: 115,049,063 (GRCm39)	K168*	probably null	Het
Or6c5	T	C	10: 129,074,368 (GRCm39)	S117P	probably damaging	Het
P2rx2	C	T	5: 110,489,007 (GRCm39)	D203N	probably damaging	Het
Ptprg	T	C	14: 11,952,897 (GRCm38)		probably null	Het
Rims4	C	T	2: 163,706,785 (GRCm39)		probably null	Het
Rtn4ip1	T	A	10: 43,808,402 (GRCm39)	W60R	probably benign	Het
Sccpdh	T	C	1: 179,498,162 (GRCm39)	S69P	probably benign	Het
Serpina3b	T	A	12: 104,105,069 (GRCm39)	I415N	probably benign	Het
Slc22a4	T	C	11: 53,874,436 (GRCm39)		probably benign	Het
Slc4a5	G	A	6: 83,274,360 (GRCm39)	A1076T	probably benign	Het
Slit1	T	C	19: 41,590,686 (GRCm39)	K1329E	possibly damaging	Het
Synj2bp	A	C	12: 81,548,826 (GRCm39)	F138V	probably benign	Het
Taar7a	T	C	10: 23,868,959 (GRCm39)	I141V	probably damaging	Het
Tas1r3	T	C	4: 155,946,588 (GRCm39)	E339G	probably benign	Het
Tep1	A	G	14: 51,088,037 (GRCm39)		probably benign	Het
Tgds	A	T	14: 118,359,149 (GRCm39)	Y146*	probably null	Het
Tgm3	G	A	2: 129,879,403 (GRCm39)	V332I	probably benign	Het
Tnnt2	A	G	1: 135,771,547 (GRCm39)		probably benign	Het
Top1	T	A	2: 160,546,739 (GRCm39)	Y340N	probably damaging	Het
Topbp1	T	C	9: 103,195,181 (GRCm39)		probably benign	Het
Tpst1	A	G	5: 130,131,202 (GRCm39)	N224S	probably benign	Het
Traf4	A	G	11: 78,050,840 (GRCm39)	F439L	probably damaging	Het
Trim58	A	G	11: 58,533,964 (GRCm39)		probably benign	Het
Tspan31	T	C	10: 126,904,004 (GRCm39)	N205S	probably damaging	Het
Ube3a	T	A	7: 58,926,225 (GRCm39)	N334K	possibly damaging	Het
Ugt2a3	A	T	5: 87,477,541 (GRCm39)		probably null	Het
Vwf	G	A	6: 125,623,293 (GRCm39)	V1797I	probably benign	Het
Wdr81	G	T	11: 75,343,809 (GRCm39)	P486Q	probably damaging	Het
Whamm	C	T	7: 81,241,519 (GRCm39)	R277*	probably null	Het
Yipf7	T	A	5: 69,678,462 (GRCm39)	N56I	possibly damaging	Het
Zfp523	A	T	17: 28,414,190 (GRCm39)	T75S	probably benign	Het

Other mutations in Ctns

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01448:Ctns	APN	11	73,079,548 (GRCm39)	missense	possibly damaging	0.88
IGL02582:Ctns	APN	11	73,087,478 (GRCm39)	missense	probably benign	0.22
R0103:Ctns	UTSW	11	73,076,137 (GRCm39)	missense	probably damaging	1.00
R1125:Ctns	UTSW	11	73,078,663 (GRCm39)	critical splice acceptor site	probably null
R1333:Ctns	UTSW	11	73,075,823 (GRCm39)	missense	probably benign	0.03
R1422:Ctns	UTSW	11	73,076,072 (GRCm39)	missense	probably damaging	1.00
R1621:Ctns	UTSW	11	73,079,298 (GRCm39)	missense	possibly damaging	0.72
R2427:Ctns	UTSW	11	73,087,512 (GRCm39)	missense	probably damaging	1.00
R4096:Ctns	UTSW	11	73,077,212 (GRCm39)	missense	probably benign	0.11
R4946:Ctns	UTSW	11	73,087,479 (GRCm39)	missense	probably benign
R6220:Ctns	UTSW	11	73,083,954 (GRCm39)	missense	probably benign	0.00
R6307:Ctns	UTSW	11	73,082,559 (GRCm39)	missense	probably benign	0.26
R6744:Ctns	UTSW	11	73,076,111 (GRCm39)	missense	probably damaging	1.00
R7064:Ctns	UTSW	11	73,077,218 (GRCm39)	missense	probably benign	0.19
R7402:Ctns	UTSW	11	73,083,903 (GRCm39)	missense	possibly damaging	0.51
R7583:Ctns	UTSW	11	73,079,296 (GRCm39)	missense	probably benign	0.44
R8071:Ctns	UTSW	11	73,075,760 (GRCm39)	missense	probably damaging	1.00
R8072:Ctns	UTSW	11	73,082,572 (GRCm39)	missense	probably benign	0.00
R8726:Ctns	UTSW	11	73,078,613 (GRCm39)	missense	probably benign	0.18
R9098:Ctns	UTSW	11	73,078,561 (GRCm39)	critical splice donor site	probably null
R9203:Ctns	UTSW	11	73,082,563 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- TTTCTGCTAGACTCTGTGCATG -3'
(R):5'- AGAGCACAATGTAAGCCTGG -3'

Sequencing Primer
(F):5'- CTAGACTCTGTGCATGTTTGAC -3'
(R):5'- CAATGTAAGCCTGGAAATAGACC -3'

Posted On

2014-09-18