Incidental Mutation 'R2136:Cln3'
| ID |
235819 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Cln3
|
| Ensembl Gene |
ENSMUSG00000030720 |
| Gene Name |
CLN3 lysosomal/endosomal transmembrane protein, battenin |
| Synonyms |
battenin |
| MMRRC Submission |
040139-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2136 (G1)
|
| Quality Score |
198 |
|
Status
|
Not validated
|
| Chromosome |
7 |
| Chromosomal Location |
126170571-126184991 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 126181971 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Arginine
at position 30
(S30R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000114555
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000032962]
[ENSMUST00000039522]
[ENSMUST00000084589]
[ENSMUST00000098036]
[ENSMUST00000116269]
[ENSMUST00000125508]
[ENSMUST00000150311]
[ENSMUST00000150917]
[ENSMUST00000147086]
[ENSMUST00000150587]
[ENSMUST00000128970]
[ENSMUST00000144173]
[ENSMUST00000137646]
[ENSMUST00000131860]
[ENSMUST00000138558]
|
| AlphaFold |
Q61124 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000032962
AA Change: S30R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000032962
Gene: ENSMUSG00000030720
AA Change: S30R
| 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: S30R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000081636
Gene: ENSMUSG00000030720
AA Change: S30R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:CLN3
|
37 |
438 |
3.5e-215 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000098036
AA Change: S30R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000095644
Gene: ENSMUSG00000030720
AA Change: S30R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:CLN3
|
37 |
414 |
4.3e-191 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000116269
AA Change: S30R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000111973
Gene: ENSMUSG00000030720
AA Change: S30R
| 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: S30R
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000117561
Gene: ENSMUSG00000030720
AA Change: S30R
| 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: ENSMUST00000150311
AA Change: S30R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000116160
Gene: ENSMUSG00000030720
AA Change: S30R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:CLN3
|
37 |
69 |
1.5e-14 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000150917
AA Change: S30R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000138688
Gene: ENSMUSG00000030720
AA Change: S30R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:CLN3
|
37 |
77 |
1.6e-18 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000147086
AA Change: S30R
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000150587
AA Change: S30R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000118054
Gene: ENSMUSG00000030720
AA Change: S30R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:CLN3
|
37 |
70 |
4.1e-15 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000128970
AA Change: S30R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000114901
Gene: ENSMUSG00000030720
AA Change: S30R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:CLN3
|
37 |
196 |
1.2e-87 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000144173
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000134406
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128049
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000137646
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000134498
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000131860
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128225
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000138558
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000134246
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153790
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000184825
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.6%
- 20x: 95.9%
|
| 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 |
|---|
| A930003A15Rik |
T |
G |
16: 19,702,530 (GRCm39) |
|
noncoding transcript |
Het |
| Abca5 |
T |
C |
11: 110,210,658 (GRCm39) |
T174A |
probably benign |
Het |
| Abcg3 |
G |
A |
5: 105,114,680 (GRCm39) |
S279L |
probably benign |
Het |
| Acap3 |
T |
C |
4: 155,981,369 (GRCm39) |
L85P |
probably damaging |
Het |
| Adgrl3 |
A |
G |
5: 81,660,101 (GRCm39) |
K290R |
probably damaging |
Het |
| Ankhd1 |
A |
G |
18: 36,780,674 (GRCm39) |
T1909A |
probably benign |
Het |
| Asap1 |
T |
C |
15: 63,982,808 (GRCm39) |
D832G |
probably damaging |
Het |
| Atp6v0a2 |
T |
A |
5: 124,795,552 (GRCm39) |
L702Q |
possibly damaging |
Het |
| Bsn |
A |
G |
9: 107,990,430 (GRCm39) |
V1774A |
probably damaging |
Het |
| Cd209e |
T |
C |
8: 3,903,248 (GRCm39) |
E48G |
probably benign |
Het |
| Cdadc1 |
T |
C |
14: 59,805,493 (GRCm39) |
|
probably null |
Het |
| Cfap65 |
C |
CA |
1: 74,956,432 (GRCm39) |
|
probably null |
Het |
| Cluap1 |
C |
T |
16: 3,751,636 (GRCm39) |
R332W |
probably damaging |
Het |
| Crb1 |
A |
T |
1: 139,265,163 (GRCm39) |
V85E |
probably benign |
Het |
| Crocc |
G |
A |
4: 140,760,265 (GRCm39) |
R789W |
probably damaging |
Het |
| Cwh43 |
A |
G |
5: 73,572,397 (GRCm39) |
I212V |
probably benign |
Het |
| Cyp2t4 |
C |
A |
7: 26,857,585 (GRCm39) |
F391L |
probably benign |
Het |
| Dhx35 |
G |
T |
2: 158,673,781 (GRCm39) |
R404L |
probably damaging |
Het |
| Disp1 |
A |
G |
1: 182,869,942 (GRCm39) |
L826S |
probably damaging |
Het |
| Dync2h1 |
T |
A |
9: 7,122,772 (GRCm39) |
E2061D |
probably damaging |
Het |
| Ep300 |
T |
A |
15: 81,524,648 (GRCm39) |
Y1393N |
unknown |
Het |
| Fap |
C |
T |
2: 62,354,551 (GRCm39) |
G446D |
possibly damaging |
Het |
| Fat3 |
A |
G |
9: 16,288,347 (GRCm39) |
I392T |
probably benign |
Het |
| Fpr-rs4 |
CAGGAA |
CA |
17: 18,242,596 (GRCm39) |
|
probably null |
Het |
| Glipr1l1 |
T |
C |
10: 111,896,381 (GRCm39) |
V56A |
probably damaging |
Het |
| Grsf1 |
A |
G |
5: 88,820,517 (GRCm39) |
V7A |
probably benign |
Het |
| Hmcn1 |
G |
A |
1: 150,509,410 (GRCm39) |
A3646V |
probably damaging |
Het |
| Ipo9 |
A |
T |
1: 135,322,023 (GRCm39) |
I569N |
probably damaging |
Het |
| Irs1 |
G |
T |
1: 82,267,763 (GRCm39) |
P151Q |
probably damaging |
Het |
| Kalrn |
T |
C |
16: 34,128,094 (GRCm39) |
D491G |
possibly damaging |
Het |
| Kctd7 |
T |
C |
5: 130,181,207 (GRCm39) |
L210P |
probably damaging |
Het |
| Lifr |
C |
A |
15: 7,211,338 (GRCm39) |
D625E |
possibly damaging |
Het |
| Lrguk |
T |
C |
6: 34,020,454 (GRCm39) |
V201A |
probably benign |
Het |
| Mark1 |
A |
G |
1: 184,651,770 (GRCm39) |
V135A |
probably damaging |
Het |
| Mical2 |
T |
A |
7: 111,870,722 (GRCm39) |
D70E |
possibly damaging |
Het |
| Mrc1 |
T |
C |
2: 14,275,000 (GRCm39) |
Y434H |
probably damaging |
Het |
| Myh10 |
C |
A |
11: 68,695,540 (GRCm39) |
Q1556K |
probably damaging |
Het |
| Nav1 |
G |
A |
1: 135,382,174 (GRCm39) |
T1400I |
probably null |
Het |
| Or1j11 |
A |
G |
2: 36,311,950 (GRCm39) |
D180G |
probably damaging |
Het |
| Or2a7 |
A |
G |
6: 43,151,435 (GRCm39) |
K172E |
probably benign |
Het |
| Or4b13 |
A |
C |
2: 90,082,597 (GRCm39) |
V245G |
probably damaging |
Het |
| Or4f4b |
T |
C |
2: 111,313,961 (GRCm39) |
V62A |
probably damaging |
Het |
| Or4p7 |
T |
A |
2: 88,221,663 (GRCm39) |
I24N |
probably benign |
Het |
| Or5d43 |
T |
C |
2: 88,104,584 (GRCm39) |
K270E |
probably damaging |
Het |
| Or5e1 |
G |
A |
7: 108,354,430 (GRCm39) |
M122I |
possibly damaging |
Het |
| Osmr |
T |
A |
15: 6,881,943 (GRCm39) |
Q67L |
probably damaging |
Het |
| Pan2 |
T |
G |
10: 128,149,506 (GRCm39) |
V522G |
possibly damaging |
Het |
| Pard3 |
T |
G |
8: 128,103,366 (GRCm39) |
|
probably null |
Het |
| Pcdhgc5 |
G |
T |
18: 37,953,166 (GRCm39) |
A147S |
possibly damaging |
Het |
| Pcsk9 |
T |
C |
4: 106,303,967 (GRCm39) |
I506V |
probably benign |
Het |
| Polr3d |
GCCCCC |
GCCCC |
14: 70,680,487 (GRCm39) |
|
probably null |
Het |
| Prdm4 |
G |
A |
10: 85,729,215 (GRCm39) |
R731* |
probably null |
Het |
| Prdx6b |
T |
A |
2: 80,123,507 (GRCm39) |
D105E |
probably damaging |
Het |
| Prss3b |
A |
G |
6: 41,012,396 (GRCm39) |
F6S |
probably benign |
Het |
| Rab42 |
A |
G |
4: 132,029,790 (GRCm39) |
L144P |
probably damaging |
Het |
| Ralbp1 |
T |
A |
17: 66,171,661 (GRCm39) |
K104M |
probably damaging |
Het |
| Resf1 |
T |
A |
6: 149,230,320 (GRCm39) |
I1122K |
probably benign |
Het |
| Rrp12 |
A |
G |
19: 41,881,038 (GRCm39) |
V131A |
probably damaging |
Het |
| Sbno1 |
C |
T |
5: 124,525,597 (GRCm39) |
|
probably null |
Het |
| Sbno2 |
A |
T |
10: 79,898,527 (GRCm39) |
I645N |
probably damaging |
Het |
| Scfd2 |
T |
C |
5: 74,367,028 (GRCm39) |
K624R |
probably benign |
Het |
| Sgk2 |
C |
A |
2: 162,841,099 (GRCm39) |
|
probably null |
Het |
| Sirt4 |
A |
G |
5: 115,617,760 (GRCm39) |
S299P |
probably benign |
Het |
| Skic3 |
T |
C |
13: 76,321,473 (GRCm39) |
S1322P |
possibly damaging |
Het |
| Slit2 |
C |
T |
5: 48,461,567 (GRCm39) |
A1521V |
probably benign |
Het |
| Socs7 |
T |
G |
11: 97,263,933 (GRCm39) |
V275G |
possibly damaging |
Het |
| Spink11 |
G |
A |
18: 44,323,554 (GRCm39) |
P102S |
probably benign |
Het |
| Tacc3 |
A |
G |
5: 33,828,748 (GRCm39) |
N534D |
probably damaging |
Het |
| Tas2r115 |
T |
C |
6: 132,714,309 (GRCm39) |
Y214C |
probably damaging |
Het |
| Tcaf1 |
A |
T |
6: 42,650,454 (GRCm39) |
M875K |
probably benign |
Het |
| Ttc22 |
T |
A |
4: 106,479,869 (GRCm39) |
L41Q |
possibly damaging |
Het |
| Vasn |
T |
A |
16: 4,467,659 (GRCm39) |
C535* |
probably null |
Het |
| Vcan |
T |
A |
13: 89,837,856 (GRCm39) |
I2563F |
probably damaging |
Het |
| Vmn2r63 |
T |
G |
7: 42,576,297 (GRCm39) |
Q505H |
probably damaging |
Het |
| Vmn2r65 |
T |
G |
7: 84,592,781 (GRCm39) |
Q475H |
probably damaging |
Het |
| Zbtb43 |
T |
C |
2: 33,344,532 (GRCm39) |
Y231C |
probably damaging |
Het |
| Zfp292 |
A |
G |
4: 34,810,266 (GRCm39) |
V931A |
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 |
|
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'- AACTGCTTTTCACAACTTGGC -3'
(R):5'- TTGGGAATGACCACCTCTGC -3'
Sequencing Primer
(F):5'- TGGCTGTCCTGGAACTCAC -3'
(R):5'- GACCACCTCTGCCCGCG -3'
|
| Posted On |
2014-10-01 |
Incidental Mutation