Mutagenetix > Incidental Mutation

Incidental Mutation 'R5027:Cln6'

391436

Institutional Source

Beutler Lab

Gene Symbol

Cln6

Ensembl Gene

ENSMUSG00000032245

Gene Name

ceroid-lipofuscinosis, neuronal 6

Synonyms

D9Bwg1455e, 1810065L06Rik

MMRRC Submission

042618-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5027 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

62746067-62759288 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 62754375 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 139 (Y139C)

Ref Sequence

ENSEMBL: ENSMUSP00000034776 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034776] [ENSMUST00000141821]

AlphaFold

Q3U466

Predicted Effect

probably damaging
Transcript: ENSMUST00000034776
AA Change: Y139C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000034776
Gene: ENSMUSG00000032245
AA Change: Y139C

Domain	Start	End	E-Value	Type
Pfam:CLN6	27	306	1.3e-167	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000124984
AA Change: Y20C

SMART Domains

Protein: ENSMUSP00000115675
Gene: ENSMUSG00000032245
AA Change: Y20C

Domain	Start	End	E-Value	Type
Pfam:CLN6	1	64	1.3e-34	PFAM
Pfam:CLN6	68	189	2.7e-53	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132250

Predicted Effect

probably benign
Transcript: ENSMUST00000138276

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139570

Predicted Effect

probably benign
Transcript: ENSMUST00000141821

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156423

Meta Mutation Damage Score

0.9687

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.4%
20x: 92.6%

Validation Efficiency

97% (97/100)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is one of eight which have been associated with neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten disease, NCL comprises a class of autosomal recessive, neurodegenerative disorders affecting children. The genes responsible likely encode proteins involved in the degradation of post-translationally modified proteins in lysosomes. The primary defect in NCL disorders is thought to be associated with lysosomal storage function. [provided by RefSeq, Oct 2008]
PHENOTYPE: Homozygous mutants have progressive retinal atrophy, limb paralysis, and seizures that lead to early death. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca14	T	G	7: 119,911,505 (GRCm39)	I1363R	probably benign	Het
Abcc1	T	C	16: 14,221,917 (GRCm39)		probably null	Het
Adgrf1	T	A	17: 43,614,638 (GRCm39)	F241I	probably damaging	Het
Afg3l1	T	C	8: 124,216,553 (GRCm39)	M264T	probably benign	Het
Ankle1	T	C	8: 71,861,623 (GRCm39)	S434P	probably damaging	Het
Apoe	C	T	7: 19,430,940 (GRCm39)	A101T	probably damaging	Het
Apol11a	G	T	15: 77,401,153 (GRCm39)	K213N	probably damaging	Het
Asap2	A	G	12: 21,254,082 (GRCm39)	M198V	probably damaging	Het
Atg4b	C	T	1: 93,714,297 (GRCm39)	A360V	probably benign	Het
B3gnt5	T	A	16: 19,588,444 (GRCm39)	V221D	probably damaging	Het
Baz2b	A	T	2: 59,928,988 (GRCm39)		probably benign	Het
Cep350	C	A	1: 155,809,100 (GRCm39)	W492L	probably benign	Het
Col16a1	C	T	4: 129,972,988 (GRCm39)	T643M	probably benign	Het
Cul9	C	T	17: 46,811,708 (GRCm39)	E2507K	probably damaging	Het
Dgkz	A	T	2: 91,775,888 (GRCm39)	V125D	probably benign	Het
Dnah17	T	C	11: 117,993,365 (GRCm39)	M1127V	probably benign	Het
Dnajb1	C	A	8: 84,336,732 (GRCm39)	D67E	probably benign	Het
Dync1li1	A	G	9: 114,542,612 (GRCm39)	D258G	probably damaging	Het
Egflam	G	T	15: 7,283,125 (GRCm39)	P311T	probably benign	Het
Fbxw11	T	A	11: 32,602,811 (GRCm39)		probably benign	Het
Fn3krp	T	G	11: 121,320,274 (GRCm39)	D206E	probably benign	Het
Fsip2	A	G	2: 82,819,477 (GRCm39)	H5070R	possibly damaging	Het
Gm6605	T	C	7: 38,149,683 (GRCm39)		noncoding transcript	Het
Gna14	C	A	19: 16,580,636 (GRCm39)	T158K	probably benign	Het
Gstt2	A	T	10: 75,667,726 (GRCm39)	I243N	probably damaging	Het
Haus6	C	T	4: 86,523,933 (GRCm39)	D50N	possibly damaging	Het
Hcrtr2	A	G	9: 76,230,578 (GRCm39)	I70T	probably benign	Het
Herc1	G	A	9: 66,380,811 (GRCm39)	V3563I	probably benign	Het
Herc1	A	T	9: 66,411,900 (GRCm39)	I4707F	probably damaging	Het
Hic2	C	T	16: 17,076,611 (GRCm39)	A480V	possibly damaging	Het
Hsd17b3	A	G	13: 64,210,720 (GRCm39)	Y212H	probably damaging	Het
Hspa5	A	G	2: 34,665,827 (GRCm39)	K557R	probably damaging	Het
Iqch	T	C	9: 63,432,294 (GRCm39)	E367G	possibly damaging	Het
Itgb4	C	T	11: 115,874,983 (GRCm39)	R447W	probably benign	Het
Lars2	A	G	9: 123,270,560 (GRCm39)	M551V	probably benign	Het
Lbp	T	C	2: 158,150,646 (GRCm39)	I57T	possibly damaging	Het
Liat1	A	G	11: 75,891,047 (GRCm39)	K54E	probably damaging	Het
Litaf	T	C	16: 10,778,868 (GRCm39)	Q142R	possibly damaging	Het
Lpar5	G	C	6: 125,059,110 (GRCm39)	R277P	possibly damaging	Het
Muc6	T	A	7: 141,216,349 (GRCm39)	I2710F	probably benign	Het
Myo7b	T	A	18: 32,108,265 (GRCm39)	I1199F	probably benign	Het
Naca	A	C	10: 127,883,990 (GRCm39)	E2140D	possibly damaging	Het
Nup214	G	T	2: 31,881,329 (GRCm39)	G396C	probably damaging	Het
Or2v1	A	T	11: 49,025,451 (GRCm39)	Q144L	probably benign	Het
Or5aq7	T	A	2: 86,938,150 (GRCm39)	I194F	probably benign	Het
Or5j3	G	A	2: 86,128,540 (GRCm39)	V127I	possibly damaging	Het
Or7g33	A	G	9: 19,448,573 (GRCm39)	Y218H	probably damaging	Het
Or8b57	A	T	9: 40,003,690 (GRCm39)	S187T	probably damaging	Het
P4htm	A	G	9: 108,456,492 (GRCm39)	V436A	probably benign	Het
Pfkm	A	G	15: 98,017,307 (GRCm39)	I117V	possibly damaging	Het
Phlpp1	T	G	1: 106,209,201 (GRCm39)	V518G	probably damaging	Het
Piwil4	G	A	9: 14,621,240 (GRCm39)	L598F	probably damaging	Het
Polr1b	T	G	2: 128,965,803 (GRCm39)	I815R	possibly damaging	Het
Ppef2	T	C	5: 92,382,150 (GRCm39)	N515S	probably damaging	Het
Prp2rt	A	G	13: 97,235,648 (GRCm39)	I33T	probably benign	Het
Prpsap2	G	T	11: 61,631,830 (GRCm39)		probably null	Het
Rab27a	A	G	9: 73,002,695 (GRCm39)	D208G	probably benign	Het
Ralgds	A	G	2: 28,442,102 (GRCm39)		probably null	Het
Raph1	C	A	1: 60,535,436 (GRCm39)	C540F	probably damaging	Het
Rbsn	A	G	6: 92,175,231 (GRCm39)	L281P	probably damaging	Het
Rigi	T	A	4: 40,208,845 (GRCm39)	M756L	probably benign	Het
Rmdn1	G	T	4: 19,588,533 (GRCm39)	G110*	probably null	Het
Rph3a	T	A	5: 121,092,512 (GRCm39)	E363V	possibly damaging	Het
Serpina16	G	T	12: 103,641,262 (GRCm39)	Y154*	probably null	Het
Sh2d3c	G	A	2: 32,634,814 (GRCm39)	E198K	possibly damaging	Het
Shank2	C	A	7: 143,812,842 (GRCm39)	Y663*	probably null	Het
Sharpin	T	C	15: 76,234,225 (GRCm39)		probably benign	Het
Slitrk1	G	A	14: 109,149,740 (GRCm39)	P324S	probably benign	Het
Sorbs2	T	A	8: 46,199,571 (GRCm39)		probably null	Het
Spag16	C	T	1: 69,962,963 (GRCm39)		probably benign	Het
Sycp2l	A	T	13: 41,283,247 (GRCm39)		probably null	Het
Synj1	A	T	16: 90,737,407 (GRCm39)		probably null	Het
Sytl1	T	C	4: 132,983,530 (GRCm39)		probably benign	Het
Tkfc	A	T	19: 10,570,023 (GRCm39)		probably null	Het
Tnn	T	C	1: 159,972,781 (GRCm39)	T274A	probably damaging	Het
Trav14-2	T	A	14: 53,878,505 (GRCm39)	W35R	probably damaging	Het
Trim72	T	C	7: 127,607,137 (GRCm39)	M222T	probably damaging	Het
Trim9	A	G	12: 70,393,482 (GRCm39)	V154A	probably damaging	Het
Ttc7b	T	C	12: 100,268,001 (GRCm39)	Y266C	probably damaging	Het
Uchl3	T	A	14: 101,903,982 (GRCm39)	I43K	possibly damaging	Het
Vdac1	T	A	11: 52,279,305 (GRCm39)	N269K	possibly damaging	Het
Wdr72	T	A	9: 74,053,258 (GRCm39)	W187R	probably damaging	Het
Zfp30	T	A	7: 29,492,491 (GRCm39)	C248*	probably null	Het
Zfp940	A	T	7: 29,550,381 (GRCm39)		probably benign	Het
Zfp980	G	A	4: 145,428,653 (GRCm39)	G461S	probably benign	Het

Other mutations in Cln6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01586:Cln6	APN	9	62,751,900 (GRCm39)	missense	probably damaging	0.98
IGL01601:Cln6	APN	9	62,754,252 (GRCm39)	missense	probably damaging	0.99
IGL02351:Cln6	APN	9	62,754,407 (GRCm39)	missense	probably benign	0.01
IGL02358:Cln6	APN	9	62,754,407 (GRCm39)	missense	probably benign	0.01
boost	UTSW	9	62,754,375 (GRCm39)	missense	probably damaging	1.00
R1113:Cln6	UTSW	9	62,758,143 (GRCm39)	missense	probably damaging	1.00
R1308:Cln6	UTSW	9	62,758,143 (GRCm39)	missense	probably damaging	1.00
R3690:Cln6	UTSW	9	62,754,252 (GRCm39)	missense	possibly damaging	0.87
R3746:Cln6	UTSW	9	62,754,284 (GRCm39)	missense	probably benign
R3898:Cln6	UTSW	9	62,757,934 (GRCm39)	missense	probably damaging	1.00
R4576:Cln6	UTSW	9	62,746,231 (GRCm39)	missense	probably benign	0.35
R4996:Cln6	UTSW	9	62,757,937 (GRCm39)	missense	probably damaging	0.98
R6048:Cln6	UTSW	9	62,751,908 (GRCm39)	missense	probably damaging	1.00
R7348:Cln6	UTSW	9	62,756,458 (GRCm39)	missense	probably benign	0.14
R7450:Cln6	UTSW	9	62,757,912 (GRCm39)	missense	probably damaging	1.00
R7565:Cln6	UTSW	9	62,758,039 (GRCm39)	missense	possibly damaging	0.86
R7837:Cln6	UTSW	9	62,756,330 (GRCm39)	missense
R7982:Cln6	UTSW	9	62,756,450 (GRCm39)	missense	possibly damaging	0.69
R9206:Cln6	UTSW	9	62,756,465 (GRCm39)	missense	probably benign	0.24
R9208:Cln6	UTSW	9	62,756,465 (GRCm39)	missense	probably benign	0.24
R9210:Cln6	UTSW	9	62,757,973 (GRCm39)	missense	probably damaging	1.00
R9212:Cln6	UTSW	9	62,757,973 (GRCm39)	missense	probably damaging	1.00
R9311:Cln6	UTSW	9	62,757,900 (GRCm39)	missense	probably damaging	1.00
R9369:Cln6	UTSW	9	62,754,431 (GRCm39)	missense	probably damaging	0.98
R9618:Cln6	UTSW	9	62,758,111 (GRCm39)	missense	probably damaging	0.99
R9627:Cln6	UTSW	9	62,754,303 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CACATCGTAATTGAGGCAGGGG -3'
(R):5'- TGACAGTAGACAACAGTGCC -3'

Sequencing Primer
(F):5'- TTGAGGCAGGGGCATGC -3'
(R):5'- GTAGACAACAGTGCCTTCCCTC -3'

Posted On

2016-06-06