Mutagenetix > Incidental Mutation

Incidental Mutation 'R2202:Cln3'

238749

Institutional Source

Beutler Lab

Gene Symbol

Cln3

Ensembl Gene

ENSMUSG00000030720

Gene Name

CLN3 lysosomal/endosomal transmembrane protein, battenin

Synonyms

battenin

MMRRC Submission

040204-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2202 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

126170571-126184991 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 126178390 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Leucine at position 211 (H211L)

Ref Sequence

ENSEMBL: ENSMUSP00000111973 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032962] [ENSMUST00000084589] [ENSMUST00000098036] [ENSMUST00000116269] [ENSMUST00000125508] [ENSMUST00000150587] [ENSMUST00000150917] [ENSMUST00000128970] [ENSMUST00000150311] [ENSMUST00000147086]

AlphaFold

Q61124

Predicted Effect

probably benign
Transcript: ENSMUST00000032962
AA Change: H211L

PolyPhen 2 Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000032962
Gene: ENSMUSG00000030720
AA Change: H211L

Domain	Start	End	E-Value	Type
Pfam:CLN3	37	438	3.5e-215	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000084589
AA Change: H211L

PolyPhen 2 Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000081636
Gene: ENSMUSG00000030720
AA Change: H211L

Domain	Start	End	E-Value	Type
Pfam:CLN3	37	438	3.5e-215	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000098036
AA Change: H187L

PolyPhen 2 Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000095644
Gene: ENSMUSG00000030720
AA Change: H187L

Domain	Start	End	E-Value	Type
Pfam:CLN3	37	414	4.3e-191	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000116269
AA Change: H211L

PolyPhen 2 Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000111973
Gene: ENSMUSG00000030720
AA Change: H211L

Domain	Start	End	E-Value	Type
Pfam:CLN3	39	437	1.6e-140	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124177

Predicted Effect

probably benign
Transcript: ENSMUST00000125508

SMART Domains

Protein: ENSMUSP00000117561
Gene: ENSMUSG00000030720

Domain	Start	End	E-Value	Type
Pfam:CLN3	37	76	1.2e-17	PFAM
Pfam:CLN3	73	151	2.8e-38	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128049

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128225

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134406

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134498

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138285

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153790

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184825

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134246

Predicted Effect

probably benign
Transcript: ENSMUST00000150587

SMART Domains

Protein: ENSMUSP00000118054
Gene: ENSMUSG00000030720

Domain	Start	End	E-Value	Type
Pfam:CLN3	37	70	4.1e-15	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000150917

SMART Domains

Protein: ENSMUSP00000138688
Gene: ENSMUSG00000030720

Domain	Start	End	E-Value	Type
Pfam:CLN3	37	77	1.6e-18	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000128970

SMART Domains

Protein: ENSMUSP00000114901
Gene: ENSMUSG00000030720

Domain	Start	End	E-Value	Type
Pfam:CLN3	37	196	1.2e-87	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000150311

SMART Domains

Protein: ENSMUSP00000116160
Gene: ENSMUSG00000030720

Domain	Start	End	E-Value	Type
Pfam:CLN3	37	69	1.5e-14	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000147086

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.5%
20x: 95.6%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a transmembrane protein called battenin that is involved in lysosomal function. Mutations in this, as well as other neuronal ceroid-lipofuscinosis genes, cause a number of neurodegenerative diseases collectively known as neuronal ceroid lipofuscinoses, the most common of which is juvenile neuronal ceroid-lipofuscinosis (Batten disease). Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2016]
PHENOTYPE: Nullizygous mutations can result in neuronal ceroid lipofuscinosis, degeneration of the retina, cerebral cortex and cerebellum, hypertrophy of hippocampal interneuron populations, gliosis, neurological deficits, and premature death. Homozygotes for a null allele show impaired water and K+ balance. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610040J01Rik	T	C	5: 64,056,011 (GRCm39)	V249A	possibly damaging	Het
9930111J21Rik2	C	G	11: 48,910,149 (GRCm39)	L761F	probably damaging	Het
Abca1	G	A	4: 53,090,291 (GRCm39)	T386I	probably damaging	Het
Abca14	T	C	7: 119,888,764 (GRCm39)	Y1237H	probably benign	Het
Abi3bp	C	T	16: 56,471,088 (GRCm39)	R578*	probably null	Het
Abi3bp	T	G	16: 56,433,566 (GRCm39)	L550R	probably benign	Het
Adamts7	A	T	9: 90,062,729 (GRCm39)	K394N	probably damaging	Het
Ahdc1	A	G	4: 132,793,220 (GRCm39)	E1487G	possibly damaging	Het
AI987944	T	C	7: 41,023,950 (GRCm39)	E343G	probably damaging	Het
Ankrd26	T	A	6: 118,500,843 (GRCm39)	H876L	possibly damaging	Het
Atg16l1	A	C	1: 87,694,737 (GRCm39)	Q138P	probably benign	Het
Atp1b1	G	T	1: 164,281,084 (GRCm39)	T11K	probably benign	Het
Calr3	A	G	8: 73,188,683 (GRCm39)	L40S	probably damaging	Het
Ccar1	A	C	10: 62,581,066 (GRCm39)	D1119E	unknown	Het
Cdan1	C	A	2: 120,551,241 (GRCm39)	C1093F	probably damaging	Het
Cdk12	T	G	11: 98,101,464 (GRCm39)	S441A	unknown	Het
Ces4a	T	A	8: 105,872,746 (GRCm39)	V333E	probably damaging	Het
Cfap61	T	C	2: 146,056,600 (GRCm39)	L1193P	probably damaging	Het
Chd2	A	T	7: 73,128,416 (GRCm39)	D856E	probably benign	Het
Chil3	T	C	3: 106,071,562 (GRCm39)	D34G	probably benign	Het
Cpa1	A	G	6: 30,641,818 (GRCm39)	D214G	probably damaging	Het
Cttnbp2	T	G	6: 18,408,693 (GRCm39)	D976A	probably benign	Het
Dcstamp	T	A	15: 39,617,708 (GRCm39)	V39E	probably damaging	Het
Dicer1	C	T	12: 104,697,297 (GRCm39)	V87M	possibly damaging	Het
Duox1	A	G	2: 122,175,194 (GRCm39)	T1331A	probably benign	Het
Elapor1	C	T	3: 108,382,359 (GRCm39)	G270E	probably damaging	Het
Fam184a	T	A	10: 53,528,530 (GRCm39)	Q29L	probably damaging	Het
Fcer2a	T	C	8: 3,738,557 (GRCm39)	E60G	possibly damaging	Het
Flnc	C	T	6: 29,459,507 (GRCm39)	P2536S	probably damaging	Het
Fnbp1l	A	T	3: 122,340,611 (GRCm39)	M463K	probably benign	Het
Garem2	A	G	5: 30,319,762 (GRCm39)	D408G	probably benign	Het
Gm6370	T	A	5: 146,430,539 (GRCm39)	D241E	probably benign	Het
Gpc3	T	A	X: 51,486,083 (GRCm39)	I344F	probably damaging	Het
Gtf2e1	T	A	16: 37,331,904 (GRCm39)	E390D	possibly damaging	Het
Hmgcs2	T	A	3: 98,198,499 (GRCm39)	I134N	probably damaging	Het
Il15ra	T	A	2: 11,723,155 (GRCm39)		probably null	Het
Ints8	A	T	4: 11,225,712 (GRCm39)	M615K	possibly damaging	Het
Irak1	G	A	X: 73,060,744 (GRCm39)	T193I	probably damaging	Het
Jmjd1c	A	G	10: 67,075,242 (GRCm39)		probably null	Het
Knstrn	T	A	2: 118,661,456 (GRCm39)		probably null	Het
Letm1	C	A	5: 33,926,830 (GRCm39)	V156L	possibly damaging	Het
Lrrc24	G	A	15: 76,607,111 (GRCm39)	P95L	probably damaging	Het
Map2k2	T	C	10: 80,955,213 (GRCm39)	S14P	probably damaging	Het
Me3	T	C	7: 89,499,589 (GRCm39)	Y535H	probably damaging	Het
Nfatc2ip	T	C	7: 125,990,467 (GRCm39)	E178G	probably benign	Het
Nop56	T	A	2: 130,119,488 (GRCm39)	I51N	probably damaging	Het
Ntn4	C	T	10: 93,543,215 (GRCm39)	R314W	probably damaging	Het
Nudt5	A	T	2: 5,860,794 (GRCm39)	I22F	possibly damaging	Het
Or10a2	T	A	7: 106,673,523 (GRCm39)	W163R	probably damaging	Het
Or2m12	C	T	16: 19,105,047 (GRCm39)	A149T	probably benign	Het
Or4p23	C	G	2: 88,576,953 (GRCm39)	G93A	probably benign	Het
Pbrm1	A	G	14: 30,754,406 (GRCm39)	D142G	possibly damaging	Het
Pdcl	A	T	2: 37,242,056 (GRCm39)	N231K	probably benign	Het
Pdlim2	C	T	14: 70,402,228 (GRCm39)	R296H	probably damaging	Het
Pid1	T	A	1: 84,016,159 (GRCm39)	I69F	probably damaging	Het
Pkhd1	A	G	1: 20,607,584 (GRCm39)	S1091P	probably benign	Het
Plcb4	T	C	2: 135,844,514 (GRCm39)	I144T	probably benign	Het
Plxnd1	T	C	6: 115,939,725 (GRCm39)	N1418S	probably benign	Het
Pmm1	T	C	15: 81,840,601 (GRCm39)	T82A	probably benign	Het
Prrc2b	C	A	2: 32,113,476 (GRCm39)	Q1970K	probably damaging	Het
Ptprz1	C	T	6: 23,000,649 (GRCm39)	T913M	possibly damaging	Het
Ralgapa1	T	C	12: 55,659,585 (GRCm39)		probably null	Het
Rbm8a2	T	C	1: 175,806,420 (GRCm39)	E19G	possibly damaging	Het
Rgs3	T	C	4: 62,608,741 (GRCm39)	S336P	probably damaging	Het
Saxo5	A	T	8: 3,529,028 (GRCm39)	D201V	probably benign	Het
Serpina11	G	T	12: 103,952,233 (GRCm39)	T179K	probably damaging	Het
Serpina1f	T	C	12: 103,659,655 (GRCm39)	N209S	possibly damaging	Het
Serpinf2	G	A	11: 75,327,588 (GRCm39)	T159I	probably benign	Het
Slc19a1	T	C	10: 76,877,758 (GRCm39)	C98R	possibly damaging	Het
Slc22a20	A	T	19: 6,021,553 (GRCm39)	I483N	possibly damaging	Het
Spata31d1d	A	G	13: 59,879,435 (GRCm39)	C34R	possibly damaging	Het
Stoml2	G	T	4: 43,030,243 (GRCm39)	Y119*	probably null	Het
Susd1	A	G	4: 59,349,843 (GRCm39)	L531P	possibly damaging	Het
Timd5	A	G	11: 46,419,394 (GRCm39)	N70S	probably benign	Het
Tln1	C	T	4: 43,553,083 (GRCm39)		probably null	Het
Tmem39b	A	C	4: 129,587,716 (GRCm39)	S32A	probably benign	Het
Tmx3	T	C	18: 90,546,037 (GRCm39)	F206S	probably damaging	Het
Tnfsf14	T	C	17: 57,497,638 (GRCm39)	D198G	possibly damaging	Het
Trappc10	A	G	10: 78,034,876 (GRCm39)		probably null	Het
Tssk2	A	G	16: 17,716,603 (GRCm39)	D2G	possibly damaging	Het
Ttn	T	C	2: 76,601,985 (GRCm39)	N18559S	possibly damaging	Het
Ube3b	G	A	5: 114,527,135 (GRCm39)	V118M	probably damaging	Het
Vmn1r23	T	C	6: 57,903,604 (GRCm39)	D58G	probably benign	Het
Vmn2r53	T	A	7: 12,335,366 (GRCm39)	Y98F	probably damaging	Het
Vmn2r58	T	A	7: 41,513,594 (GRCm39)	N350Y	probably benign	Het
Vmn2r82	A	T	10: 79,192,519 (GRCm39)	H32L	probably benign	Het
Wsb1	T	C	11: 79,131,212 (GRCm39)	I395V	probably benign	Het
Zbtb47	A	G	9: 121,591,703 (GRCm39)	T8A	possibly damaging	Het
Zfat	T	C	15: 68,051,709 (GRCm39)	D695G	probably benign	Het
Zfp358	G	T	8: 3,546,995 (GRCm39)	V526F	possibly damaging	Het
Zmat1	A	G	X: 133,873,861 (GRCm39)	L476P	possibly damaging	Het

Other mutations in Cln3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01084:Cln3	APN	7	126,174,426 (GRCm39)	missense	probably damaging	1.00
IGL01603:Cln3	APN	7	126,174,526 (GRCm39)	missense	probably benign	0.30
IGL02216:Cln3	APN	7	126,174,514 (GRCm39)	critical splice donor site	probably null
IGL02440:Cln3	APN	7	126,181,954 (GRCm39)	missense	probably benign	0.01
IGL03118:Cln3	APN	7	126,174,569 (GRCm39)	missense	probably null	0.00
R0326:Cln3	UTSW	7	126,182,217 (GRCm39)	start codon destroyed	probably damaging	0.96
R0610:Cln3	UTSW	7	126,179,361 (GRCm39)	missense	probably damaging	1.00
R1256:Cln3	UTSW	7	126,182,208 (GRCm39)	missense	probably damaging	0.98
R2136:Cln3	UTSW	7	126,181,971 (GRCm39)	missense	probably benign	0.00
R3977:Cln3	UTSW	7	126,179,308 (GRCm39)	splice site	probably benign
R4563:Cln3	UTSW	7	126,171,730 (GRCm39)	missense	probably damaging	0.98
R4690:Cln3	UTSW	7	126,174,565 (GRCm39)	missense	possibly damaging	0.61
R4936:Cln3	UTSW	7	126,174,393 (GRCm39)	missense	probably damaging	1.00
R5668:Cln3	UTSW	7	126,171,558 (GRCm39)	missense	probably benign	0.01
R5726:Cln3	UTSW	7	126,174,673 (GRCm39)	missense	probably null	0.00
R6385:Cln3	UTSW	7	126,174,207 (GRCm39)	missense	probably null	1.00
R6591:Cln3	UTSW	7	126,178,606 (GRCm39)	missense	possibly damaging	0.82
R6691:Cln3	UTSW	7	126,178,606 (GRCm39)	missense	possibly damaging	0.82
R6891:Cln3	UTSW	7	126,181,975 (GRCm39)	missense	possibly damaging	0.88
R7173:Cln3	UTSW	7	126,178,589 (GRCm39)	missense	probably damaging	1.00
R7214:Cln3	UTSW	7	126,181,942 (GRCm39)	missense	probably damaging	1.00
R7426:Cln3	UTSW	7	126,180,912 (GRCm39)	missense	probably benign	0.31
R7520:Cln3	UTSW	7	126,180,852 (GRCm39)	missense	probably damaging	1.00
R7556:Cln3	UTSW	7	126,174,242 (GRCm39)	missense	probably damaging	0.97
R7761:Cln3	UTSW	7	126,180,886 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GAGTCGCACAGCTAACACAG -3'
(R):5'- TGCCTTCTACCCCAGGTAAG -3'

Sequencing Primer
(F):5'- ACTCTGAGATTCCACCTGAGG -3'
(R):5'- TACCCCAGGTAAGCGGCC -3'

Posted On

2014-10-02