Mutagenetix > Incidental Mutation

Incidental Mutation 'R1256:Cln3'

151454

Institutional Source

Beutler Lab

Gene Symbol

Cln3

Ensembl Gene

ENSMUSG00000030720

Gene Name

CLN3 lysosomal/endosomal transmembrane protein, battenin

Synonyms

battenin

MMRRC Submission

039323-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1256 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

126170571-126184991 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 126182208 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 4 (S4P)

Ref Sequence

ENSEMBL: ENSMUSP00000138688 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032962] [ENSMUST00000039522] [ENSMUST00000084589] [ENSMUST00000098036] [ENSMUST00000116269] [ENSMUST00000125508] [ENSMUST00000147086] [ENSMUST00000150587] [ENSMUST00000150311] [ENSMUST00000150917] [ENSMUST00000128970] [ENSMUST00000131860] [ENSMUST00000137646] [ENSMUST00000138558] [ENSMUST00000144173]

AlphaFold

Q61124

Predicted Effect

probably benign
Transcript: ENSMUST00000032962
AA Change: S4P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000032962
Gene: ENSMUSG00000030720
AA Change: S4P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000039522

SMART Domains

Protein: ENSMUSP00000042028
Gene: ENSMUSG00000042759

Domain	Start	End	E-Value	Type
low complexity region	45	59	N/A	INTRINSIC
low complexity region	171	181	N/A	INTRINSIC
low complexity region	351	363	N/A	INTRINSIC
low complexity region	381	396	N/A	INTRINSIC
low complexity region	465	476	N/A	INTRINSIC
low complexity region	588	608	N/A	INTRINSIC
low complexity region	837	862	N/A	INTRINSIC
low complexity region	869	881	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000084589
AA Change: S4P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000081636
Gene: ENSMUSG00000030720
AA Change: S4P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000098036
AA Change: S4P

PolyPhen 2 Score 0.293 (Sensitivity: 0.91; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000095644
Gene: ENSMUSG00000030720
AA Change: S4P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000116269
AA Change: S4P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000111973
Gene: ENSMUSG00000030720
AA Change: S4P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000125508
AA Change: S4P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000117561
Gene: ENSMUSG00000030720
AA Change: S4P

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: ENSMUST00000147086
AA Change: S4P

PolyPhen 2 Score 0.608 (Sensitivity: 0.87; Specificity: 0.91)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000150587
AA Change: S4P

PolyPhen 2 Score 0.953 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000118054
Gene: ENSMUSG00000030720
AA Change: S4P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000150311
AA Change: S4P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000116160
Gene: ENSMUSG00000030720
AA Change: S4P

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000150917
AA Change: S4P

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000138688
Gene: ENSMUSG00000030720
AA Change: S4P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000128970
AA Change: S4P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000114901
Gene: ENSMUSG00000030720
AA Change: S4P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000131860

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128225

Predicted Effect

probably benign
Transcript: ENSMUST00000137646

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153790

Predicted Effect

probably benign
Transcript: ENSMUST00000138558

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134246

Predicted Effect

probably benign
Transcript: ENSMUST00000144173

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134406

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134498

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184825

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.4%

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: 38 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb10	C	T	8: 124,688,791 (GRCm39)	G495D	probably damaging	Het
Apaf1	A	G	10: 90,894,268 (GRCm39)	Y456H	probably benign	Het
Arhgef11	A	G	3: 87,634,442 (GRCm39)	N791S	possibly damaging	Het
Brat1	A	G	5: 140,695,962 (GRCm39)	Q66R	possibly damaging	Het
Capn10	C	T	1: 92,874,668 (GRCm39)	T633M	probably damaging	Het
Ccdc186	G	T	19: 56,786,053 (GRCm39)	L661I	probably benign	Het
Cnot10	G	T	9: 114,439,749 (GRCm39)	S520Y	probably damaging	Het
Csmd1	A	T	8: 16,129,978 (GRCm39)	F1715I	probably damaging	Het
Ezh2	A	T	6: 47,518,789 (GRCm39)	C545*	probably null	Het
Hivep1	C	T	13: 42,335,307 (GRCm39)	S2282F	probably damaging	Het
Jag2	T	C	12: 112,878,039 (GRCm39)	E564G	possibly damaging	Het
Kcnj16	A	G	11: 110,916,262 (GRCm39)	H308R	probably damaging	Het
Magi3	C	T	3: 103,935,126 (GRCm39)	V936I	probably benign	Het
Mcu	G	T	10: 59,290,790 (GRCm39)	A279E	probably damaging	Het
Msln	A	G	17: 25,973,157 (GRCm39)	C13R	probably damaging	Het
Nes	A	G	3: 87,883,883 (GRCm39)	D714G	probably benign	Het
Nif3l1	T	A	1: 58,494,808 (GRCm39)	V259D	probably damaging	Het
Or4c127	A	T	2: 89,832,911 (GRCm39)	M54L	possibly damaging	Het
Or5k14	A	C	16: 58,693,206 (GRCm39)	Y102*	probably null	Het
Or8g18	G	C	9: 39,149,547 (GRCm39)	P58A	probably benign	Het
Pcdhb9	A	G	18: 37,536,169 (GRCm39)	D721G	possibly damaging	Het
Pepd	A	C	7: 34,620,917 (GRCm39)	T61P	possibly damaging	Het
Pkd1l2	C	T	8: 117,746,282 (GRCm39)		probably null	Het
Poglut3	A	C	9: 53,299,762 (GRCm39)	R90S	possibly damaging	Het
Psip1	A	G	4: 83,392,604 (GRCm39)	S102P	probably benign	Het
Ralgapa1	T	C	12: 55,809,446 (GRCm39)	E443G	possibly damaging	Het
Rnf20	A	G	4: 49,638,230 (GRCm39)	D114G	probably benign	Het
Schip1	A	T	3: 68,402,375 (GRCm39)	I151F	probably benign	Het
Smarca2	A	G	19: 26,659,373 (GRCm39)	I888V	probably benign	Het
Smg1	T	C	7: 117,802,310 (GRCm39)	T263A	probably damaging	Het
Spn	T	C	7: 126,735,445 (GRCm39)	K354R	possibly damaging	Het
Sspo	G	A	6: 48,434,573 (GRCm39)	A1022T	probably damaging	Het
Strn	A	C	17: 78,972,046 (GRCm39)		probably null	Het
Tstd3	T	C	4: 21,759,627 (GRCm39)	I79M	probably damaging	Het
Txnl4a	A	G	18: 80,250,487 (GRCm39)	I28V	probably benign	Het
Uty	T	C	Y: 1,134,884 (GRCm39)	D928G	probably damaging	Het
Vps26c	A	G	16: 94,313,225 (GRCm39)	L22P	probably damaging	Het
Vsx2	T	A	12: 84,623,085 (GRCm39)	L163Q	probably 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
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
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'- GCATTCTTCCAAAGGACACTCCGAC -3'
(R):5'- GTGTATAGCAGACAGCGGAACCTG -3'

Sequencing Primer
(F):5'- TCCGACTATCCAACCGAGGG -3'
(R):5'- AGCGGAACCTGGGACTG -3'

Posted On

2014-01-29