Mutagenetix > Incidental Mutation

Incidental Mutation 'R4936:Cln3'

380380

Institutional Source

Beutler Lab

Gene Symbol

Cln3

Ensembl Gene

ENSMUSG00000030720

Gene Name

CLN3 lysosomal/endosomal transmembrane protein, battenin

Synonyms

battenin

MMRRC Submission

042536-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4936 (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 126174393 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Leucine at position 315 (H315L)

Ref Sequence

ENSEMBL: ENSMUSP00000111973 (fasta)

Gene Model

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

AlphaFold

Q61124

Predicted Effect

probably damaging
Transcript: ENSMUST00000032962
AA Change: H315L

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

SMART Domains

Protein: ENSMUSP00000032962
Gene: ENSMUSG00000030720
AA Change: H315L

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000084589
AA Change: H315L

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

SMART Domains

Protein: ENSMUSP00000081636
Gene: ENSMUSG00000030720
AA Change: H315L

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000098036
AA Change: H291L

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

SMART Domains

Protein: ENSMUSP00000095644
Gene: ENSMUSG00000030720
AA Change: H291L

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000116269
AA Change: H315L

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

SMART Domains

Protein: ENSMUSP00000111973
Gene: ENSMUSG00000030720
AA Change: H315L

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: ENSMUST00000128225

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184825

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139766

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138285

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153790

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: ENSMUST00000150917

SMART Domains

Protein: ENSMUSP00000138688
Gene: ENSMUSG00000030720

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

Coding Region Coverage

1x: 98.9%
3x: 98.0%
10x: 95.0%
20x: 87.5%

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2300002M23Rik	T	A	17: 35,879,212 (GRCm39)	F183L	possibly damaging	Het
4930590J08Rik	T	A	6: 91,921,245 (GRCm39)	M775K	probably damaging	Het
Actn1	T	G	12: 80,219,772 (GRCm39)	I700L	probably benign	Het
Adam5	T	C	8: 25,276,287 (GRCm39)	Y460C	probably damaging	Het
Akna	C	T	4: 63,313,502 (GRCm39)	G207E	probably damaging	Het
Ank2	T	A	3: 126,748,688 (GRCm39)	H527L	possibly damaging	Het
Anks1	C	A	17: 28,207,779 (GRCm39)	N383K	probably damaging	Het
Apba3	C	T	10: 81,105,204 (GRCm39)		probably null	Het
Atp9b	C	A	18: 80,779,308 (GRCm39)	V1121F	possibly damaging	Het
Bsn	T	C	9: 107,988,960 (GRCm39)	Y2264C	probably damaging	Het
Bst1	A	G	5: 43,997,799 (GRCm39)	D266G	probably damaging	Het
Cep55	A	G	19: 38,060,202 (GRCm39)		probably null	Het
Ces4a	G	A	8: 105,864,729 (GRCm39)	G69S	probably damaging	Het
Ckb	T	C	12: 111,637,664 (GRCm39)	K156E	probably benign	Het
Cnot6l	A	G	5: 96,227,796 (GRCm39)	F479S	probably damaging	Het
Col1a1	A	G	11: 94,837,958 (GRCm39)	D826G	unknown	Het
Cyp27a1	T	C	1: 74,774,564 (GRCm39)	V194A	probably benign	Het
Dis3l2	C	T	1: 86,971,890 (GRCm39)	P643S	probably benign	Het
Dpf3	T	C	12: 83,378,740 (GRCm39)	D108G	probably damaging	Het
Eif2b4	C	T	5: 31,350,241 (GRCm39)	G27D	probably benign	Het
Eif4a1	T	G	11: 69,563,251 (GRCm39)		probably benign	Het
Espl1	A	T	15: 102,213,372 (GRCm39)	D566V	probably damaging	Het
Ext2	T	A	2: 93,644,024 (GRCm39)	R86*	probably null	Het
Fasn	A	T	11: 120,706,911 (GRCm39)	F914I	probably damaging	Het
Fbf1	A	G	11: 116,043,378 (GRCm39)	L477P	probably benign	Het
Fsd1	A	T	17: 56,303,452 (GRCm39)	K441N	possibly damaging	Het
Fsip2	T	A	2: 82,815,384 (GRCm39)	S3706T	probably benign	Het
Gabra5	A	T	7: 57,058,547 (GRCm39)	N400K	probably benign	Het
Gimap8	G	T	6: 48,633,068 (GRCm39)	G296W	probably damaging	Het
Gli2	A	G	1: 118,763,870 (GRCm39)	V1427A	probably benign	Het
Gm7334	A	T	17: 51,005,855 (GRCm39)	Y47F	probably damaging	Het
Gm8674	T	G	13: 50,054,791 (GRCm39)		noncoding transcript	Het
Gmeb2	G	T	2: 180,896,039 (GRCm39)	T377K	probably benign	Het
Gp9	T	A	6: 87,756,229 (GRCm39)	D81E	probably benign	Het
Il5ra	T	A	6: 106,715,123 (GRCm39)	I212F	possibly damaging	Het
Klhl18	G	T	9: 110,258,029 (GRCm39)	N470K	possibly damaging	Het
Lfng	G	T	5: 140,598,150 (GRCm39)		probably null	Het
Lpo	A	G	11: 87,701,166 (GRCm39)	I430T	probably benign	Het
Lrrc31	C	T	3: 30,743,417 (GRCm39)	D183N	probably damaging	Het
Meis2	T	C	2: 115,694,893 (GRCm39)	T410A	probably benign	Het
Myo6	A	G	9: 80,214,963 (GRCm39)	D1232G	probably damaging	Het
Ncapd2	C	T	6: 125,146,803 (GRCm39)	R1261H	probably benign	Het
Nfkb1	C	T	3: 135,319,743 (GRCm39)	V251M	probably damaging	Het
Nmbr	C	A	10: 14,642,730 (GRCm39)	H96Q	probably damaging	Het
Nop14	C	T	5: 34,809,737 (GRCm39)	R256H	probably damaging	Het
Nqo2	T	A	13: 34,165,501 (GRCm39)	Y133N	probably damaging	Het
Or1f12	T	C	13: 21,721,357 (GRCm39)	I273V	probably benign	Het
Or5w20	A	G	2: 87,727,157 (GRCm39)	I213V	probably benign	Het
Pbld2	C	A	10: 62,888,017 (GRCm39)	S168R	probably damaging	Het
Pcdhb7	G	T	18: 37,475,202 (GRCm39)	G113*	probably null	Het
Pcdhb7	G	T	18: 37,475,203 (GRCm39)	G113V	probably damaging	Het
Pdgfra	A	T	5: 75,355,687 (GRCm39)	T1066S	probably damaging	Het
Prdm8	A	T	5: 98,332,881 (GRCm39)		probably null	Het
Prdm8	G	T	5: 98,332,882 (GRCm39)		probably null	Het
Prkg1	T	C	19: 30,563,775 (GRCm39)	Y479C	probably benign	Het
Pudp	T	C	18: 50,701,539 (GRCm39)	T65A	probably benign	Het
Rbbp6	C	T	7: 122,598,926 (GRCm39)		probably benign	Het
Rcc1	C	G	4: 132,063,046 (GRCm39)	V187L	probably damaging	Het
Rims2	T	A	15: 39,301,124 (GRCm39)	M285K	probably damaging	Het
Rtkn2	T	C	10: 67,877,745 (GRCm39)	*602Q	probably null	Het
Rxfp3	T	G	15: 11,036,866 (GRCm39)	S169R	probably damaging	Het
Sardh	T	C	2: 27,118,253 (GRCm39)		probably null	Het
Slc24a2	A	T	4: 87,145,584 (GRCm39)	F157I	probably damaging	Het
Slc25a20	T	C	9: 108,559,191 (GRCm39)	Y186H	probably damaging	Het
Slc25a24	A	G	3: 109,070,864 (GRCm39)	R408G	probably damaging	Het
Slc44a5	T	G	3: 153,959,353 (GRCm39)	I348S	probably damaging	Het
Slc8a2	A	T	7: 15,868,100 (GRCm39)	K111*	probably null	Het
Smc5	A	G	19: 23,211,367 (GRCm39)	V589A	probably damaging	Het
Thbd	A	T	2: 148,249,655 (GRCm39)	I71N	probably damaging	Het
Thsd7b	T	C	1: 129,605,882 (GRCm39)	M541T	probably benign	Het
Tie1	T	A	4: 118,341,968 (GRCm39)		silent	Het
Tln1	A	G	4: 43,547,522 (GRCm39)	F813S	possibly damaging	Het
Tnrc18	A	T	5: 142,751,732 (GRCm39)	L1191*	probably null	Het
Tubb2a	A	C	13: 34,259,240 (GRCm39)	Y183*	probably null	Het
Ubr4	T	A	4: 139,123,877 (GRCm39)	V343E	probably damaging	Het
Vmn2r93	A	T	17: 18,524,327 (GRCm39)	D107V	possibly damaging	Het
Vwa5a	T	G	9: 38,647,494 (GRCm39)	S624R	probably benign	Het
Wwox	G	A	8: 115,433,098 (GRCm39)	V255I	probably benign	Het
Wwp1	T	C	4: 19,638,804 (GRCm39)	K546E	probably damaging	Het
Xirp2	T	A	2: 67,340,163 (GRCm39)	F801L	possibly damaging	Het
Zfp407	T	C	18: 84,577,589 (GRCm39)	I1175V	probably benign	Het
Zfp646	T	A	7: 127,480,933 (GRCm39)	C1037S	possibly damaging	Het
Zfp786	A	T	6: 47,798,202 (GRCm39)	C245*	probably null	Het
Zfp827	T	C	8: 79,787,812 (GRCm39)	V326A	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
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'- CGTATTCGGCAACATTGGAG -3'
(R):5'- GACTCTTCCAGGGTCTCTTGTG -3'

Sequencing Primer
(F):5'- CGTATTCGGCAACATTGGAGAGAAG -3'
(R):5'- CAGGGTCTCTTGTGGTACATCATC -3'

Posted On

2016-04-15