Incidental Mutation 'IGL03052:Chl1'
| ID |
392177 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Chl1
|
| Ensembl Gene |
ENSMUSG00000030077 |
| Gene Name |
cell adhesion molecule L1-like |
| Synonyms |
A530023M13Rik, close homolog of L1, LICAM2, CALL |
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.458)
|
| Stock # |
IGL03052 (G1)
|
| Quality Score |
127 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
103487372-103709999 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 103668628 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Serine
at position 470
(T470S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000145026
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000066905]
[ENSMUST00000203830]
[ENSMUST00000203912]
|
| AlphaFold |
P70232 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000066905
AA Change: T454S
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000063933
Gene: ENSMUSG00000030077
AA Change: T454S
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
|
IG_like
|
48 |
116 |
3.14e-2 |
SMART |
|
IG
|
138 |
225 |
1.36e-5 |
SMART |
|
IGc2
|
253 |
317 |
3.76e-17 |
SMART |
|
IGc2
|
343 |
408 |
1.61e-7 |
SMART |
|
IGc2
|
436 |
501 |
1.56e-5 |
SMART |
|
IG
|
521 |
609 |
6.02e-7 |
SMART |
|
IG_like
|
539 |
598 |
1.27e-1 |
SMART |
|
FN3
|
612 |
695 |
2.24e-13 |
SMART |
|
FN3
|
712 |
794 |
1.92e-3 |
SMART |
|
FN3
|
810 |
901 |
2.3e-1 |
SMART |
|
FN3
|
916 |
1002 |
4.09e-7 |
SMART |
|
transmembrane domain
|
1082 |
1104 |
N/A |
INTRINSIC |
|
Pfam:Bravo_FIGEY
|
1105 |
1190 |
3.9e-33 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000203830
AA Change: T454S
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000144758
Gene: ENSMUSG00000030077
AA Change: T454S
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
|
IG_like
|
48 |
116 |
3.14e-2 |
SMART |
|
IG
|
138 |
225 |
1.36e-5 |
SMART |
|
IGc2
|
253 |
317 |
3.76e-17 |
SMART |
|
IGc2
|
343 |
408 |
1.61e-7 |
SMART |
|
IGc2
|
436 |
501 |
1.56e-5 |
SMART |
|
IG
|
521 |
609 |
6.02e-7 |
SMART |
|
IG_like
|
539 |
598 |
1.27e-1 |
SMART |
|
FN3
|
612 |
695 |
2.24e-13 |
SMART |
|
FN3
|
712 |
794 |
1.92e-3 |
SMART |
|
FN3
|
810 |
901 |
2.3e-1 |
SMART |
|
FN3
|
916 |
1002 |
4.09e-7 |
SMART |
|
transmembrane domain
|
1082 |
1104 |
N/A |
INTRINSIC |
|
Pfam:Bravo_FIGEY
|
1105 |
1190 |
3.9e-33 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000203912
AA Change: T470S
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000145026
Gene: ENSMUSG00000030077
AA Change: T470S
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
|
IG_like
|
48 |
116 |
3.14e-2 |
SMART |
|
IG
|
138 |
225 |
1.36e-5 |
SMART |
|
IGc2
|
269 |
333 |
3.76e-17 |
SMART |
|
IGc2
|
359 |
424 |
1.61e-7 |
SMART |
|
IGc2
|
452 |
517 |
1.56e-5 |
SMART |
|
IG
|
537 |
625 |
6.02e-7 |
SMART |
|
IG_like
|
555 |
614 |
1.27e-1 |
SMART |
|
FN3
|
628 |
711 |
2.24e-13 |
SMART |
|
FN3
|
728 |
810 |
1.92e-3 |
SMART |
|
FN3
|
826 |
917 |
2.3e-1 |
SMART |
|
FN3
|
932 |
1018 |
4.09e-7 |
SMART |
|
transmembrane domain
|
1044 |
1066 |
N/A |
INTRINSIC |
|
Pfam:Bravo_FIGEY
|
1067 |
1131 |
2.5e-12 |
PFAM |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 0.0%
- 3x: 0.0%
- 10x: 0.0%
- 20x: 0.0%
|
| Validation Efficiency |
100% (53/53) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the L1 gene family of neural cell adhesion molecules. It is a neural recognition molecule that may be involved in signal transduction pathways. The deletion of one copy of this gene may be responsible for mental defects in patients with 3p- syndrome. This protein may also play a role in the growth of certain cancers. Alternate splicing results in both coding and non-coding variants. [provided by RefSeq, Nov 2011]
PHENOTYPE: Homozygous mutation of this gene results in enlargement of the lateral ventricles and altered hippocampal mossy fiber organization. Mutant animals exhibit altered exploratory behavior. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 56 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acap3 |
T |
C |
4: 155,987,815 (GRCm39) |
F517S |
probably damaging |
Het |
| Afap1l1 |
A |
G |
18: 61,881,894 (GRCm39) |
V267A |
probably benign |
Het |
| Asap1 |
A |
G |
15: 64,025,683 (GRCm39) |
|
probably benign |
Het |
| Bcl6 |
T |
C |
16: 23,793,788 (GRCm39) |
|
probably benign |
Het |
| Ccdc73 |
C |
A |
2: 104,782,281 (GRCm39) |
H212Q |
possibly damaging |
Het |
| Cct5 |
A |
T |
15: 31,597,633 (GRCm39) |
H85Q |
probably damaging |
Het |
| Cfap69 |
A |
C |
5: 5,639,206 (GRCm39) |
L238R |
probably damaging |
Het |
| Cnga4 |
T |
C |
7: 105,053,932 (GRCm39) |
S12P |
probably benign |
Het |
| Cyp2c29 |
C |
T |
19: 39,275,662 (GRCm39) |
T34M |
possibly damaging |
Het |
| Cyp2c67 |
T |
C |
19: 39,637,329 (GRCm39) |
D49G |
possibly damaging |
Het |
| Dab2ip |
A |
G |
2: 35,533,909 (GRCm39) |
Q45R |
probably benign |
Het |
| Ddhd1 |
A |
G |
14: 45,858,240 (GRCm39) |
V164A |
probably damaging |
Het |
| Dnaaf8 |
A |
T |
16: 4,795,358 (GRCm39) |
|
noncoding transcript |
Het |
| Dnah7c |
A |
G |
1: 46,671,309 (GRCm39) |
Y1566C |
probably damaging |
Het |
| Dnase1l2 |
T |
C |
17: 24,659,968 (GRCm39) |
|
probably benign |
Het |
| Dock2 |
G |
T |
11: 34,182,853 (GRCm39) |
N1593K |
probably benign |
Het |
| Dpp6 |
G |
T |
5: 27,914,506 (GRCm39) |
M530I |
probably benign |
Het |
| Epm2a |
T |
C |
10: 11,332,974 (GRCm39) |
V269A |
possibly damaging |
Het |
| Fcna |
G |
C |
2: 25,520,693 (GRCm39) |
|
probably benign |
Het |
| Fgf2 |
A |
G |
3: 37,403,161 (GRCm39) |
S55G |
probably benign |
Het |
| Frem3 |
C |
T |
8: 81,341,159 (GRCm39) |
P1151S |
probably damaging |
Het |
| Gm15737 |
T |
C |
6: 92,846,481 (GRCm39) |
|
probably benign |
Het |
| Gpi-ps |
T |
A |
8: 5,689,816 (GRCm39) |
|
noncoding transcript |
Het |
| Gvin-ps6 |
T |
C |
7: 106,022,902 (GRCm39) |
|
noncoding transcript |
Het |
| Hoxa3 |
G |
A |
6: 52,147,267 (GRCm39) |
|
probably benign |
Het |
| Larp7-ps |
A |
G |
4: 92,079,287 (GRCm39) |
L178P |
probably benign |
Het |
| Macf1 |
T |
C |
4: 123,281,188 (GRCm39) |
I3770V |
probably damaging |
Het |
| Mapk15 |
G |
T |
15: 75,865,731 (GRCm39) |
R8L |
probably benign |
Het |
| Mecom |
C |
T |
3: 30,015,112 (GRCm39) |
|
probably benign |
Het |
| Mknk2 |
C |
T |
10: 80,505,496 (GRCm39) |
R154H |
probably benign |
Het |
| Mrgprb3 |
A |
T |
7: 48,293,341 (GRCm39) |
V70E |
possibly damaging |
Het |
| Mtdh |
A |
G |
15: 34,140,876 (GRCm39) |
K570E |
possibly damaging |
Het |
| Myo5c |
G |
T |
9: 75,159,798 (GRCm39) |
|
probably benign |
Het |
| Myom2 |
T |
C |
8: 15,173,442 (GRCm39) |
|
probably benign |
Het |
| Or52m2 |
C |
T |
7: 102,263,656 (GRCm39) |
R180Q |
probably benign |
Het |
| Or5b124 |
T |
C |
19: 13,611,090 (GRCm39) |
I205T |
probably benign |
Het |
| Or7g25 |
A |
T |
9: 19,159,938 (GRCm39) |
Y252* |
probably null |
Het |
| Pcca |
A |
T |
14: 123,124,513 (GRCm39) |
M695L |
probably benign |
Het |
| Pcdha2 |
A |
T |
18: 37,074,670 (GRCm39) |
D767V |
probably damaging |
Het |
| Plekhs1 |
G |
A |
19: 56,459,189 (GRCm39) |
D16N |
probably benign |
Het |
| Prr11 |
T |
C |
11: 86,994,478 (GRCm39) |
N56S |
possibly damaging |
Het |
| Rxfp2 |
A |
T |
5: 149,966,645 (GRCm39) |
|
probably benign |
Het |
| Sacs |
G |
T |
14: 61,445,307 (GRCm39) |
G2451V |
probably damaging |
Het |
| Scarb1 |
G |
A |
5: 125,371,163 (GRCm39) |
A4V |
probably damaging |
Het |
| Scart2 |
G |
A |
7: 139,828,827 (GRCm39) |
C162Y |
probably damaging |
Het |
| Sik3 |
C |
A |
9: 46,109,447 (GRCm39) |
T475K |
probably damaging |
Het |
| Slco1b2 |
A |
T |
6: 141,594,311 (GRCm39) |
I59L |
probably benign |
Het |
| Sspo |
G |
A |
6: 48,437,387 (GRCm39) |
G1382R |
probably damaging |
Het |
| Stx16 |
C |
A |
2: 173,934,231 (GRCm39) |
P145T |
probably benign |
Het |
| Tnrc18 |
G |
A |
5: 142,760,974 (GRCm39) |
A674V |
unknown |
Het |
| Uqcrq |
A |
G |
11: 53,321,476 (GRCm39) |
V14A |
possibly damaging |
Het |
| Vmn2r79 |
A |
T |
7: 86,652,799 (GRCm39) |
E497V |
probably benign |
Het |
| Vps8 |
T |
A |
16: 21,267,115 (GRCm39) |
I166K |
probably damaging |
Het |
| Vwa8 |
A |
G |
14: 79,302,361 (GRCm39) |
D1010G |
probably benign |
Het |
| Wnk1 |
T |
A |
6: 119,921,760 (GRCm39) |
|
probably benign |
Het |
| Zfand3 |
T |
A |
17: 30,279,798 (GRCm39) |
M29K |
probably benign |
Het |
|
| Other mutations in Chl1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00590:Chl1
|
APN |
6 |
103,670,022 (GRCm39) |
missense |
probably benign |
0.08 |
|
IGL00786:Chl1
|
APN |
6 |
103,652,106 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00959:Chl1
|
APN |
6 |
103,686,211 (GRCm39) |
splice site |
probably null |
|
|
IGL01109:Chl1
|
APN |
6 |
103,692,354 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01354:Chl1
|
APN |
6 |
103,642,814 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL01367:Chl1
|
APN |
6 |
103,706,186 (GRCm39) |
missense |
probably benign |
0.42 |
|
IGL01371:Chl1
|
APN |
6 |
103,692,325 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01599:Chl1
|
APN |
6 |
103,685,445 (GRCm39) |
missense |
probably benign |
0.34 |
|
IGL01724:Chl1
|
APN |
6 |
103,626,534 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02001:Chl1
|
APN |
6 |
103,619,017 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
IGL02066:Chl1
|
APN |
6 |
103,675,185 (GRCm39) |
missense |
probably benign |
0.39 |
|
IGL02122:Chl1
|
APN |
6 |
103,652,098 (GRCm39) |
missense |
probably benign |
0.39 |
|
IGL02340:Chl1
|
APN |
6 |
103,675,086 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02420:Chl1
|
APN |
6 |
103,692,330 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02421:Chl1
|
APN |
6 |
103,694,541 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02429:Chl1
|
APN |
6 |
103,641,770 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02825:Chl1
|
APN |
6 |
103,645,764 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
IGL02858:Chl1
|
APN |
6 |
103,618,949 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03169:Chl1
|
APN |
6 |
103,642,928 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03185:Chl1
|
APN |
6 |
103,642,824 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03189:Chl1
|
APN |
6 |
103,660,168 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
IGL03288:Chl1
|
APN |
6 |
103,652,058 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03404:Chl1
|
APN |
6 |
103,670,052 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0060:Chl1
|
UTSW |
6 |
103,688,019 (GRCm39) |
splice site |
probably benign |
|
|
R0060:Chl1
|
UTSW |
6 |
103,688,019 (GRCm39) |
splice site |
probably benign |
|
|
R0062:Chl1
|
UTSW |
6 |
103,726,613 (GRCm39) |
missense |
unknown |
|
|
R0314:Chl1
|
UTSW |
6 |
103,624,262 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0322:Chl1
|
UTSW |
6 |
103,678,844 (GRCm39) |
splice site |
probably benign |
|
|
R0685:Chl1
|
UTSW |
6 |
103,685,503 (GRCm39) |
splice site |
probably null |
|
|
R0702:Chl1
|
UTSW |
6 |
103,683,583 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1056:Chl1
|
UTSW |
6 |
103,652,038 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
R1138:Chl1
|
UTSW |
6 |
103,670,140 (GRCm39) |
missense |
probably benign |
0.05 |
|
R1483:Chl1
|
UTSW |
6 |
103,624,248 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1571:Chl1
|
UTSW |
6 |
103,685,445 (GRCm39) |
missense |
probably benign |
0.34 |
|
R1620:Chl1
|
UTSW |
6 |
103,667,203 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1645:Chl1
|
UTSW |
6 |
103,660,141 (GRCm39) |
missense |
probably benign |
0.06 |
|
R1773:Chl1
|
UTSW |
6 |
103,624,292 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1852:Chl1
|
UTSW |
6 |
103,676,120 (GRCm39) |
splice site |
probably null |
|
|
R1891:Chl1
|
UTSW |
6 |
103,691,544 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R2146:Chl1
|
UTSW |
6 |
103,692,362 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2147:Chl1
|
UTSW |
6 |
103,692,362 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2148:Chl1
|
UTSW |
6 |
103,692,362 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2163:Chl1
|
UTSW |
6 |
103,688,192 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2291:Chl1
|
UTSW |
6 |
103,692,354 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2920:Chl1
|
UTSW |
6 |
103,672,304 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3611:Chl1
|
UTSW |
6 |
103,675,116 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3979:Chl1
|
UTSW |
6 |
103,692,245 (GRCm39) |
nonsense |
probably null |
|
|
R4987:Chl1
|
UTSW |
6 |
103,651,938 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5266:Chl1
|
UTSW |
6 |
103,677,504 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5478:Chl1
|
UTSW |
6 |
103,660,182 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5523:Chl1
|
UTSW |
6 |
103,685,675 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5887:Chl1
|
UTSW |
6 |
103,694,565 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5986:Chl1
|
UTSW |
6 |
103,686,152 (GRCm39) |
missense |
probably benign |
0.45 |
|
R6101:Chl1
|
UTSW |
6 |
103,669,993 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6179:Chl1
|
UTSW |
6 |
103,660,204 (GRCm39) |
missense |
probably benign |
0.38 |
|
R6366:Chl1
|
UTSW |
6 |
103,706,197 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R6634:Chl1
|
UTSW |
6 |
103,667,220 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6824:Chl1
|
UTSW |
6 |
103,691,510 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6913:Chl1
|
UTSW |
6 |
103,642,909 (GRCm39) |
nonsense |
probably null |
|
|
R7097:Chl1
|
UTSW |
6 |
103,683,409 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7122:Chl1
|
UTSW |
6 |
103,683,409 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7198:Chl1
|
UTSW |
6 |
103,683,517 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7203:Chl1
|
UTSW |
6 |
103,668,635 (GRCm39) |
missense |
probably benign |
0.13 |
|
R7527:Chl1
|
UTSW |
6 |
103,688,162 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7625:Chl1
|
UTSW |
6 |
103,706,086 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7667:Chl1
|
UTSW |
6 |
103,672,456 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R7683:Chl1
|
UTSW |
6 |
103,668,613 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
R7712:Chl1
|
UTSW |
6 |
103,688,063 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R7838:Chl1
|
UTSW |
6 |
103,668,635 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7863:Chl1
|
UTSW |
6 |
103,683,475 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R7874:Chl1
|
UTSW |
6 |
103,667,224 (GRCm39) |
missense |
probably benign |
0.22 |
|
R7998:Chl1
|
UTSW |
6 |
103,706,250 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8044:Chl1
|
UTSW |
6 |
103,683,593 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R8059:Chl1
|
UTSW |
6 |
103,651,948 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R8462:Chl1
|
UTSW |
6 |
103,706,130 (GRCm39) |
missense |
probably benign |
0.11 |
|
R8558:Chl1
|
UTSW |
6 |
103,685,390 (GRCm39) |
missense |
probably benign |
0.14 |
|
R8827:Chl1
|
UTSW |
6 |
103,670,111 (GRCm39) |
missense |
probably benign |
|
|
R8865:Chl1
|
UTSW |
6 |
103,685,822 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8939:Chl1
|
UTSW |
6 |
103,642,868 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9092:Chl1
|
UTSW |
6 |
103,645,815 (GRCm39) |
unclassified |
probably benign |
|
|
Z1177:Chl1
|
UTSW |
6 |
103,674,910 (GRCm39) |
start gained |
probably benign |
|
|
Z1177:Chl1
|
UTSW |
6 |
103,670,057 (GRCm39) |
nonsense |
probably null |
|
|
Z1191:Chl1
|
UTSW |
6 |
103,660,172 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- ACTCTTTCAGAATGTGCTGACTTTG -3'
(R):5'- CTGGCCAGTGTTTTCAGGAG -3'
Sequencing Primer
(F):5'- TTCTTTAGAATGGGCCAAGGAC -3'
(R):5'- CCAGTGTTTTCAGGAGAGACAAG -3'
|
| Posted On |
2016-06-09 |
Incidental Mutation