Mutagenetix > Incidental Mutation

Incidental Mutation 'R6691:Cln3'

530416

Institutional Source

Beutler Lab

Gene Symbol

Cln3

Ensembl Gene

ENSMUSG00000030720

Gene Name

CLN3 lysosomal/endosomal transmembrane protein, battenin

Synonyms

battenin

MMRRC Submission

044809-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6691 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

126170571-126184991 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 126178606 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 143 (V143A)

Ref Sequence

ENSEMBL: ENSMUSP00000117561 (fasta)

Gene Model

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

AlphaFold

Q61124

Predicted Effect

possibly damaging
Transcript: ENSMUST00000032962
AA Change: V167A

PolyPhen 2 Score 0.694 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000032962
Gene: ENSMUSG00000030720
AA Change: V167A

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000084589
AA Change: V167A

PolyPhen 2 Score 0.694 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000081636
Gene: ENSMUSG00000030720
AA Change: V167A

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000098036
AA Change: V143A

PolyPhen 2 Score 0.694 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000095644
Gene: ENSMUSG00000030720
AA Change: V143A

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000116269
AA Change: V167A

PolyPhen 2 Score 0.694 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000111973
Gene: ENSMUSG00000030720
AA Change: V167A

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124177

Predicted Effect

possibly damaging
Transcript: ENSMUST00000125508
AA Change: V143A

PolyPhen 2 Score 0.821 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000117561
Gene: ENSMUSG00000030720
AA Change: V143A

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

possibly damaging
Transcript: ENSMUST00000128970
AA Change: V167A

PolyPhen 2 Score 0.694 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000114901
Gene: ENSMUSG00000030720
AA Change: V167A

Domain	Start	End	E-Value	Type
Pfam:CLN3	37	196	1.2e-87	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: ENSMUST00000150587

SMART Domains

Protein: ENSMUSP00000118054
Gene: ENSMUSG00000030720

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153790

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184825

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128225

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138285

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134246

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134406

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134498

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.7%
20x: 96.4%

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: 33 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2300009A05Rik	A	G	9: 63,306,236 (GRCm39)	Y90H	probably damaging	Het
Agk	A	G	6: 40,369,624 (GRCm39)	D337G	probably benign	Het
Amn	A	G	12: 111,241,831 (GRCm39)	H299R	possibly damaging	Het
Angptl4	A	G	17: 33,999,755 (GRCm39)		probably null	Het
AU040320	G	A	4: 126,730,463 (GRCm39)	M563I	possibly damaging	Het
Cachd1	T	C	4: 100,846,683 (GRCm39)	M1042T	probably benign	Het
Calcoco2	A	G	11: 95,990,934 (GRCm39)	S247P	unknown	Het
Cd209c	T	A	8: 3,995,680 (GRCm39)	I41L	probably benign	Het
Ceacam12	T	A	7: 17,803,149 (GRCm39)	V185D	possibly damaging	Het
Chpt1	A	T	10: 88,321,762 (GRCm39)		probably benign	Het
Clca3a1	G	C	3: 144,719,644 (GRCm39)	A442G	probably damaging	Het
Cldn8	T	C	16: 88,359,423 (GRCm39)	I167M	possibly damaging	Het
Dusp11	T	C	6: 85,938,507 (GRCm39)	H4R	possibly damaging	Het
Ephb3	T	A	16: 21,033,223 (GRCm39)	F69Y	probably damaging	Het
Gm11099	A	T	2: 58,749,485 (GRCm39)		probably benign	Het
Grik2	A	T	10: 49,149,021 (GRCm39)	Y521*	probably null	Het
Igf2r	A	G	17: 12,907,895 (GRCm39)	L2143P	probably damaging	Het
Kcnk1	T	C	8: 126,751,970 (GRCm39)	V192A	probably benign	Het
Or4a81	A	T	2: 89,619,332 (GRCm39)	Y121*	probably null	Het
Or8k53	A	C	2: 86,177,763 (GRCm39)	S116A	probably damaging	Het
Parp3	A	G	9: 106,350,891 (GRCm39)	S329P	probably benign	Het
Pld3	A	T	7: 27,231,741 (GRCm39)	N483K	probably benign	Het
Rbm33	A	T	5: 28,557,544 (GRCm39)	E252D	probably damaging	Het
Ryr2	T	C	13: 11,609,609 (GRCm39)	T4406A	probably benign	Het
Sgsm3	A	G	15: 80,893,063 (GRCm39)	D380G	possibly damaging	Het
Sorl1	G	T	9: 41,913,863 (GRCm39)	D1355E	probably damaging	Het
Sptbn1	A	G	11: 30,063,984 (GRCm39)	S1945P	probably damaging	Het
Ube2m	A	T	7: 12,770,396 (GRCm39)	F70I	probably damaging	Het
Ube3b	A	G	5: 114,546,185 (GRCm39)	I664V	probably benign	Het
Ugt1a7c	A	G	1: 88,023,378 (GRCm39)	E179G	possibly damaging	Het
Vps50	T	C	6: 3,504,939 (GRCm39)		probably null	Het
Xpo1	T	C	11: 23,236,875 (GRCm39)	L718P	probably damaging	Het
Zfp354c	A	G	11: 50,705,602 (GRCm39)	I491T	probably benign	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
R2202:Cln3	UTSW	7	126,178,390 (GRCm39)	missense	probably benign	0.11
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
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'- TAGAAAGTAGGGTGTGCTGC -3'
(R):5'- AGACCCTAGCCTGTCTGTTCAG -3'

Sequencing Primer
(F):5'- GTCCCAGGTAAGACAGCGATC -3'
(R):5'- AGTGACAGATCTGTTCTTAGCC -3'

Posted On

2018-08-01