Mutagenetix > Incidental Mutation

Incidental Mutation 'R7556:Cln3'

584772

Institutional Source

Beutler Lab

Gene Symbol

Cln3

Ensembl Gene

ENSMUSG00000030720

Gene Name

CLN3 lysosomal/endosomal transmembrane protein, battenin

Synonyms

battenin

MMRRC Submission

045624-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7556 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

126170571-126184991 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 126174242 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Arginine at position 327 (Q327R)

Ref Sequence

ENSEMBL: ENSMUSP00000032962 (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: Q327R

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000032962
Gene: ENSMUSG00000030720
AA Change: Q327R

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000084589
AA Change: Q327R

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000081636
Gene: ENSMUSG00000030720
AA Change: Q327R

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000098036
AA Change: Q303R

PolyPhen 2 Score 0.952 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000095644
Gene: ENSMUSG00000030720
AA Change: Q303R

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000116269
AA Change: Q327R

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000111973
Gene: ENSMUSG00000030720
AA Change: Q327R

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

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

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931429L15Rik	C	T	9: 46,221,611 (GRCm39)	W11*	probably null	Het
A2ml1	A	G	6: 128,546,927 (GRCm39)	S401P	probably damaging	Het
Adamtsl1	T	A	4: 86,195,358 (GRCm39)	Y592N	probably benign	Het
Adh6b	C	T	3: 138,058,546 (GRCm39)	T76I	probably damaging	Het
Aebp2	C	A	6: 140,623,137 (GRCm39)	P503Q	probably benign	Het
Ankrd2	A	G	19: 42,028,839 (GRCm39)	D134G		Het
Atf7ip	T	C	6: 136,538,239 (GRCm39)	S491P	probably damaging	Het
Atp1a3	T	C	7: 24,680,991 (GRCm39)	D832G	probably benign	Het
Atrnl1	G	A	19: 57,643,278 (GRCm39)	V389I	probably benign	Het
Bahcc1	T	C	11: 120,178,589 (GRCm39)	S2383P	probably damaging	Het
Brd9	A	G	13: 74,092,886 (GRCm39)	D292G	possibly damaging	Het
Cacna1e	G	T	1: 154,348,419 (GRCm39)	Q781K	probably benign	Het
Ccdc9	T	C	7: 16,018,491 (GRCm39)		probably benign	Het
Cdc42ep4	C	G	11: 113,619,366 (GRCm39)	E342Q	probably damaging	Het
Celf3	C	T	3: 94,387,590 (GRCm39)	T54M	probably damaging	Het
Cenpn	T	C	8: 117,664,008 (GRCm39)	Y267H	probably damaging	Het
Chrnb4	T	C	9: 54,942,339 (GRCm39)	T312A	probably benign	Het
Clcn3	T	A	8: 61,382,521 (GRCm39)	T383S	probably damaging	Het
Cnep1r1	T	C	8: 88,851,761 (GRCm39)	L50P	probably damaging	Het
Cnot6	T	C	11: 49,566,144 (GRCm39)	N512S	probably benign	Het
Col7a1	T	A	9: 108,811,533 (GRCm39)		probably null	Het
Cryba4	C	T	5: 112,398,969 (GRCm39)	R25Q	probably damaging	Het
Dnah5	A	G	15: 28,290,389 (GRCm39)	I1260V	probably null	Het
Dock2	G	T	11: 34,611,778 (GRCm39)	T195K	probably benign	Het
Dpp9	A	T	17: 56,497,012 (GRCm39)	I740N	possibly damaging	Het
Fbxl21	A	T	13: 56,674,741 (GRCm39)	N31Y	probably benign	Het
Frat1	G	A	19: 41,818,959 (GRCm39)	R118Q	possibly damaging	Het
Gna11	A	G	10: 81,367,208 (GRCm39)	F228S		Het
Golgb1	A	T	16: 36,736,155 (GRCm39)	M1842L	probably benign	Het
Got1	A	T	19: 43,491,469 (GRCm39)	M327K	probably damaging	Het
H4c9	A	G	13: 22,225,414 (GRCm39)	I27T	probably damaging	Het
Hexa	T	A	9: 59,470,582 (GRCm39)	L468Q	probably damaging	Het
Ift57	G	A	16: 49,526,491 (GRCm39)	V178I	probably benign	Het
Kbtbd13	T	C	9: 65,298,757 (GRCm39)	T60A	probably benign	Het
Klk1b5	A	G	7: 43,496,649 (GRCm39)	T194A	probably damaging	Het
Krtap16-3	C	A	16: 88,759,666 (GRCm39)	G16C	unknown	Het
Lamb3	T	C	1: 193,014,757 (GRCm39)	S639P	probably benign	Het
Mapt	C	A	11: 104,189,528 (GRCm39)	P182Q	probably benign	Het
Mcf2l	A	G	8: 13,023,071 (GRCm39)	T86A	probably damaging	Het
Mecom	G	T	3: 30,041,220 (GRCm39)	H125N	probably benign	Het
Med18	T	C	4: 132,187,247 (GRCm39)	H84R	probably benign	Het
Muc2	A	G	7: 141,307,439 (GRCm39)	Y798C		Het
Mycbp	T	C	4: 123,799,060 (GRCm39)	Y17H	probably damaging	Het
Nacad	C	T	11: 6,551,272 (GRCm39)	V640M	possibly damaging	Het
Ncoa1	C	T	12: 4,320,794 (GRCm39)	V1092I	probably damaging	Het
Nomo1	A	G	7: 45,715,642 (GRCm39)	E696G	probably damaging	Het
Notch4	G	A	17: 34,794,444 (GRCm39)	C741Y	probably damaging	Het
Or10g7	A	G	9: 39,905,978 (GRCm39)	N291D	probably damaging	Het
Or6d12	C	T	6: 116,493,697 (GRCm39)	Q320*	probably null	Het
Osbpl10	C	A	9: 115,036,692 (GRCm39)	H229Q	probably damaging	Het
Pif1	A	T	9: 65,496,993 (GRCm39)		probably null	Het
Plk2	T	G	13: 110,533,122 (GRCm39)		probably null	Het
Ppp1r42	T	C	1: 10,065,408 (GRCm39)	H172R	probably benign	Het
Ring1	A	G	17: 34,240,688 (GRCm39)	I363T	possibly damaging	Het
Rnf168	T	G	16: 32,117,863 (GRCm39)	Y475D	probably damaging	Het
Sbf2	T	A	7: 109,913,260 (GRCm39)	K1671N	probably benign	Het
Sema6d	A	G	2: 124,496,109 (GRCm39)	N51S	probably damaging	Het
Setx	C	A	2: 29,036,505 (GRCm39)	Q997K	possibly damaging	Het
Skint5	T	G	4: 113,425,162 (GRCm39)	Q1088P	unknown	Het
Slc22a27	T	C	19: 7,843,119 (GRCm39)	D528G	probably damaging	Het
Slc6a7	T	A	18: 61,140,514 (GRCm39)	K173*	probably null	Het
Smc2	T	C	4: 52,457,379 (GRCm39)	F380L	probably benign	Het
Spata31d1a	T	C	13: 59,849,798 (GRCm39)	M777V	probably benign	Het
Stkld1	A	T	2: 26,837,307 (GRCm39)	N319I	possibly damaging	Het
Tanc2	T	C	11: 105,799,857 (GRCm39)	V93A		Het
Tbx20	T	C	9: 24,661,573 (GRCm39)		probably null	Het
Trbv20	G	A	6: 41,165,715 (GRCm39)	V47I	probably benign	Het
Trip4	A	T	9: 65,782,155 (GRCm39)	C192*	probably null	Het
Tsbp1	A	T	17: 34,656,691 (GRCm39)	I103F	unknown	Het
Tulp2	A	G	7: 45,168,005 (GRCm39)		probably null	Het
Ush2a	C	A	1: 188,689,690 (GRCm39)	P5084Q	probably benign	Het
Virma	T	C	4: 11,518,927 (GRCm39)	Y675H	probably damaging	Het
Vmn2r102	T	A	17: 19,898,093 (GRCm39)	N369K	probably benign	Het
Vmn2r59	A	T	7: 41,695,233 (GRCm39)	M393K	probably damaging	Het
Vmn2r69	GAAAA	GAAAAA	7: 85,060,768 (GRCm39)		probably null	Het
Xpot	A	G	10: 121,449,411 (GRCm39)	S30P	probably benign	Het
Zfp947	T	C	17: 22,364,597 (GRCm39)	Y359C	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
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
R7761:Cln3	UTSW	7	126,180,886 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCCTTTAGTGCTGTACTTAGGAAC -3'
(R):5'- AGAGATAGGGCTGAGGTTCC -3'

Sequencing Primer
(F):5'- CTGTACTTAGGAACGCTGGAGTACAC -3'
(R):5'- TTCGCTGCAGTTCGAGC -3'

Posted On

2019-10-17