Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02440:Cln3'

293408

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Cln3

Ensembl Gene

ENSMUSG00000030720

Gene Name

CLN3 lysosomal/endosomal transmembrane protein, battenin

Synonyms

battenin

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

IGL02440

Quality Score

Status

Chromosome

Chromosomal Location

126170571-126184991 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 126181954 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Arginine at position 36 (K36R)

Ref Sequence

ENSEMBL: ENSMUSP00000118054 (fasta)

Gene Model

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

AlphaFold

Q61124

Predicted Effect

probably benign
Transcript: ENSMUST00000032962
AA Change: K36R

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

SMART Domains

Protein: ENSMUSP00000032962
Gene: ENSMUSG00000030720
AA Change: K36R

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: K36R

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

SMART Domains

Protein: ENSMUSP00000081636
Gene: ENSMUSG00000030720
AA Change: K36R

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

Predicted Effect

probably benign
Transcript: ENSMUST00000098036
AA Change: K36R

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

SMART Domains

Protein: ENSMUSP00000095644
Gene: ENSMUSG00000030720
AA Change: K36R

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

Predicted Effect

probably benign
Transcript: ENSMUST00000116269
AA Change: K36R

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

SMART Domains

Protein: ENSMUSP00000111973
Gene: ENSMUSG00000030720
AA Change: K36R

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
AA Change: K36R

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

SMART Domains

Protein: ENSMUSP00000117561
Gene: ENSMUSG00000030720
AA Change: K36R

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

Predicted Effect

probably benign
Transcript: ENSMUST00000147086
AA Change: K36R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

Predicted Effect

probably benign
Transcript: ENSMUST00000150311
AA Change: K36R

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

SMART Domains

Protein: ENSMUSP00000116160
Gene: ENSMUSG00000030720
AA Change: K36R

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

Predicted Effect

probably benign
Transcript: ENSMUST00000150587
AA Change: K36R

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000118054
Gene: ENSMUSG00000030720
AA Change: K36R

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

Predicted Effect

probably benign
Transcript: ENSMUST00000150917
AA Change: K36R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000138688
Gene: ENSMUSG00000030720
AA Change: K36R

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

Predicted Effect

probably benign
Transcript: ENSMUST00000128970
AA Change: K36R

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

SMART Domains

Protein: ENSMUSP00000114901
Gene: ENSMUSG00000030720
AA Change: K36R

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134406

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134498

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128049

Predicted Effect

probably benign
Transcript: ENSMUST00000137646

Predicted Effect

probably benign
Transcript: ENSMUST00000138558

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134246

Predicted Effect

probably benign
Transcript: ENSMUST00000144173

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128225

Predicted Effect

probably benign
Transcript: ENSMUST00000131860

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184825

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153790

Coding Region Coverage

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
Atp8a1	A	G	5: 67,824,777 (GRCm39)		probably benign	Het
Bmt2	C	T	6: 13,628,609 (GRCm39)	R358Q	probably damaging	Het
C2cd6	A	G	1: 59,114,259 (GRCm39)	I182T	probably benign	Het
Calr3	T	C	8: 73,185,276 (GRCm39)	T100A	probably benign	Het
Ddx25	C	T	9: 35,468,974 (GRCm39)		probably benign	Het
Dmxl2	A	T	9: 54,313,899 (GRCm39)	V1677E	probably damaging	Het
Dnah10	A	G	5: 124,850,883 (GRCm39)	E1684G	probably damaging	Het
Dnah9	A	G	11: 65,846,072 (GRCm39)	S2989P	probably damaging	Het
F5	A	T	1: 164,034,635 (GRCm39)	T1845S	possibly damaging	Het
Folh1	G	T	7: 86,383,312 (GRCm39)	N478K	probably benign	Het
Gpr22	T	C	12: 31,759,139 (GRCm39)	I328V	probably damaging	Het
Itln1	C	T	1: 171,359,097 (GRCm39)	A128T	probably benign	Het
Itprid1	A	G	6: 55,861,713 (GRCm39)	T97A	possibly damaging	Het
Kank1	A	G	19: 25,410,272 (GRCm39)	K1322R	probably damaging	Het
Klhdc2	A	G	12: 69,350,414 (GRCm39)	Y153C	probably damaging	Het
Lonp2	T	A	8: 87,350,813 (GRCm39)	M1K	probably null	Het
Mtor	T	A	4: 148,630,886 (GRCm39)	M2281K	probably benign	Het
Mtor	T	A	4: 148,576,104 (GRCm39)	N1378K	probably benign	Het
Myo1e	G	A	9: 70,254,022 (GRCm39)	R557H	probably damaging	Het
Nedd4l	T	C	18: 65,296,244 (GRCm39)		probably null	Het
Or2r3	T	C	6: 42,449,100 (GRCm39)	D4G	probably benign	Het
Or2t46	A	T	11: 58,472,035 (GRCm39)	M122L	probably damaging	Het
Or2z9	T	A	8: 72,854,374 (GRCm39)	F257I	probably damaging	Het
Or9i16	A	T	19: 13,865,223 (GRCm39)	M117K	probably damaging	Het
Pcdh18	T	C	3: 49,699,052 (GRCm39)		probably benign	Het
Phldb1	T	C	9: 44,626,700 (GRCm39)	T582A	probably damaging	Het
Plxna2	A	T	1: 194,428,458 (GRCm39)	E509D	probably benign	Het
Poln	A	T	5: 34,286,474 (GRCm39)	D231E	probably damaging	Het
Prex2	G	A	1: 11,223,881 (GRCm39)	R735Q	possibly damaging	Het
Prpf40b	T	C	15: 99,204,747 (GRCm39)	S263P	probably damaging	Het
Sfmbt2	C	T	2: 10,573,194 (GRCm39)	A574V	probably damaging	Het
Slc12a3	T	C	8: 95,058,310 (GRCm39)	I152T	probably damaging	Het
Srrm1	G	A	4: 135,052,415 (GRCm39)	P658L	unknown	Het
Svep1	T	C	4: 58,145,293 (GRCm39)	I391V	probably benign	Het
Tbx4	A	G	11: 85,781,720 (GRCm39)	E80G	probably damaging	Het
Vmn2r22	A	G	6: 123,614,364 (GRCm39)	Y409H	probably benign	Het
Zfp691	T	G	4: 119,027,493 (GRCm39)	R246S	probably damaging	Het
Zfp846	T	C	9: 20,499,796 (GRCm39)		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
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
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

Posted On

2015-04-16