Incidental Mutation 'R6218:Nlgn1'
| ID |
503828 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nlgn1
|
| Ensembl Gene |
ENSMUSG00000063887 |
| Gene Name |
neuroligin 1 |
| Synonyms |
NL1, Nlg1, 6330415N05Rik |
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R6218 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
25480379-26386609 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 25490257 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Glutamic Acid
at position 490
(V490E)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000142200
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000075054]
[ENSMUST00000108308]
[ENSMUST00000191835]
[ENSMUST00000193603]
|
| AlphaFold |
Q99K10 |
| PDB Structure |
Crystal structure of a synaptic adhesion complex [X-RAY DIFFRACTION]
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000075054
AA Change: V490E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: V490E
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:COesterase
|
29 |
626 |
4.8e-199 |
PFAM |
|
Pfam:Abhydrolase_3
|
196 |
302 |
2.2e-8 |
PFAM |
|
transmembrane domain
|
697 |
719 |
N/A |
INTRINSIC |
|
low complexity region
|
720 |
731 |
N/A |
INTRINSIC |
|
low complexity region
|
796 |
809 |
N/A |
INTRINSIC |
|
low complexity region
|
816 |
827 |
N/A |
INTRINSIC |
|
low complexity region
|
829 |
839 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000108308
AA Change: V461E
PolyPhen 2
Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: V461E
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:COesterase
|
29 |
597 |
2.5e-190 |
PFAM |
|
Pfam:Abhydrolase_3
|
176 |
306 |
4.3e-8 |
PFAM |
|
transmembrane domain
|
668 |
690 |
N/A |
INTRINSIC |
|
low complexity region
|
691 |
702 |
N/A |
INTRINSIC |
|
low complexity region
|
767 |
780 |
N/A |
INTRINSIC |
|
low complexity region
|
787 |
798 |
N/A |
INTRINSIC |
|
low complexity region
|
800 |
810 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000191835
AA Change: V461E
PolyPhen 2
Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: V461E
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:COesterase
|
29 |
597 |
2.5e-190 |
PFAM |
|
Pfam:Abhydrolase_3
|
176 |
306 |
4.3e-8 |
PFAM |
|
transmembrane domain
|
668 |
690 |
N/A |
INTRINSIC |
|
low complexity region
|
691 |
702 |
N/A |
INTRINSIC |
|
low complexity region
|
767 |
780 |
N/A |
INTRINSIC |
|
low complexity region
|
787 |
798 |
N/A |
INTRINSIC |
|
low complexity region
|
800 |
810 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000193603
AA Change: V490E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: V490E
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:COesterase
|
29 |
626 |
1.2e-186 |
PFAM |
|
Pfam:Abhydrolase_3
|
196 |
309 |
3.7e-8 |
PFAM |
|
transmembrane domain
|
697 |
719 |
N/A |
INTRINSIC |
|
low complexity region
|
720 |
731 |
N/A |
INTRINSIC |
|
low complexity region
|
796 |
809 |
N/A |
INTRINSIC |
|
low complexity region
|
816 |
827 |
N/A |
INTRINSIC |
|
low complexity region
|
829 |
839 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.6002 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.5%
- 20x: 98.5%
|
| Validation Efficiency |
100% (65/65) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele are viable and fertile but display impaired NMDA receptor-mediated synaptic transmission onto CA1 pyramidal cells. [provided by MGI curators]
|
| Allele List at MGI |
All alleles(4) : Targeted(3) Gene trapped(1)
|
| Other mutations in this stock |
Total: 66 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2300003K06Rik |
G |
T |
11: 99,728,730 (GRCm39) |
Q38K |
probably benign |
Het |
| 9930111J21Rik2 |
A |
T |
11: 48,910,134 (GRCm39) |
N766K |
probably benign |
Het |
| Adam15 |
A |
C |
3: 89,251,190 (GRCm39) |
I505S |
probably benign |
Het |
| Apc2 |
T |
C |
10: 80,142,254 (GRCm39) |
M391T |
probably damaging |
Het |
| Arsi |
G |
A |
18: 61,049,723 (GRCm39) |
G202E |
probably benign |
Het |
| Bclaf1 |
A |
G |
10: 20,210,374 (GRCm39) |
S840G |
probably benign |
Het |
| Cacna2d4 |
A |
G |
6: 119,216,021 (GRCm39) |
Y96C |
probably damaging |
Het |
| Cald1 |
CAAAA |
CAAA |
6: 34,724,863 (GRCm39) |
|
probably null |
Het |
| Ddhd1 |
A |
G |
14: 45,851,633 (GRCm39) |
L141P |
probably damaging |
Het |
| Dnaaf3 |
A |
T |
7: 4,526,671 (GRCm39) |
S469T |
probably benign |
Het |
| Dzip3 |
A |
T |
16: 48,778,828 (GRCm39) |
M323K |
possibly damaging |
Het |
| Eci2 |
T |
A |
13: 35,177,048 (GRCm39) |
|
probably null |
Het |
| Fam227b |
A |
T |
2: 125,968,882 (GRCm39) |
V64E |
probably damaging |
Het |
| Galnt2 |
A |
G |
8: 125,070,054 (GRCm39) |
I524V |
probably benign |
Het |
| Gm10549 |
C |
A |
18: 33,597,358 (GRCm39) |
|
probably benign |
Het |
| Gm3443 |
T |
A |
19: 21,533,110 (GRCm39) |
S25T |
probably damaging |
Het |
| Gpr22 |
T |
A |
12: 31,761,616 (GRCm39) |
K14* |
probably null |
Het |
| Grip1 |
T |
C |
10: 119,822,251 (GRCm39) |
S405P |
possibly damaging |
Het |
| Helz2 |
T |
C |
2: 180,877,738 (GRCm39) |
H1020R |
probably damaging |
Het |
| Helz2 |
C |
A |
2: 180,874,087 (GRCm39) |
V2136L |
probably benign |
Het |
| Il36rn |
G |
A |
2: 24,167,502 (GRCm39) |
|
probably benign |
Het |
| Iqsec1 |
T |
A |
6: 90,666,617 (GRCm39) |
S607C |
probably damaging |
Het |
| Irag1 |
G |
A |
7: 110,476,112 (GRCm39) |
T819M |
probably benign |
Het |
| Klhl2 |
A |
T |
8: 65,205,801 (GRCm39) |
Y373* |
probably null |
Het |
| L3mbtl3 |
T |
C |
10: 26,168,645 (GRCm39) |
I595V |
unknown |
Het |
| Large2 |
T |
C |
2: 92,200,981 (GRCm39) |
D65G |
probably damaging |
Het |
| Lrrfip1 |
T |
C |
1: 91,009,881 (GRCm39) |
Y122H |
probably damaging |
Het |
| Map1b |
A |
T |
13: 99,569,714 (GRCm39) |
D1002E |
unknown |
Het |
| Mink1 |
C |
T |
11: 70,489,720 (GRCm39) |
T59I |
possibly damaging |
Het |
| Myo7b |
T |
C |
18: 32,092,507 (GRCm39) |
N2097D |
probably benign |
Het |
| Nbea |
C |
A |
3: 55,535,905 (GRCm39) |
C2893F |
probably damaging |
Het |
| Or2w1b |
G |
A |
13: 21,300,401 (GRCm39) |
E180K |
probably damaging |
Het |
| Or2y3 |
A |
G |
17: 38,393,620 (GRCm39) |
M83T |
probably damaging |
Het |
| Or4c123 |
G |
T |
2: 89,127,306 (GRCm39) |
H103N |
probably damaging |
Het |
| Or4f62 |
T |
C |
2: 111,986,701 (GRCm39) |
I135T |
probably damaging |
Het |
| Or4k2 |
C |
A |
14: 50,424,135 (GRCm39) |
D180Y |
probably damaging |
Het |
| Pctp |
A |
G |
11: 89,878,144 (GRCm39) |
I130T |
probably benign |
Het |
| Pdcl3 |
T |
C |
1: 39,027,152 (GRCm39) |
|
probably null |
Het |
| Pheta2 |
T |
A |
15: 82,227,917 (GRCm39) |
H145Q |
probably benign |
Het |
| Pira12 |
A |
T |
7: 3,897,031 (GRCm39) |
S602T |
possibly damaging |
Het |
| Pkp1 |
T |
C |
1: 135,807,646 (GRCm39) |
K541E |
probably damaging |
Het |
| Plekhh2 |
G |
A |
17: 84,898,992 (GRCm39) |
V990I |
probably benign |
Het |
| Ppp1r3a |
A |
T |
6: 14,718,430 (GRCm39) |
V828D |
probably damaging |
Het |
| Prrc2b |
T |
C |
2: 32,098,823 (GRCm39) |
Y712H |
probably damaging |
Het |
| Prune2 |
T |
C |
19: 17,098,926 (GRCm39) |
S1477P |
probably benign |
Het |
| Psma5 |
A |
G |
3: 108,187,118 (GRCm39) |
K239R |
probably benign |
Het |
| Rhobtb1 |
G |
C |
10: 69,106,286 (GRCm39) |
A284P |
probably benign |
Het |
| Samsn1 |
G |
A |
16: 75,742,162 (GRCm39) |
|
noncoding transcript |
Het |
| Scel |
A |
G |
14: 103,809,478 (GRCm39) |
T273A |
probably benign |
Het |
| Slc22a5 |
T |
A |
11: 53,782,444 (GRCm39) |
|
probably benign |
Het |
| Slc25a37 |
A |
T |
14: 69,486,953 (GRCm39) |
M110K |
possibly damaging |
Het |
| Slc6a2 |
A |
T |
8: 93,708,609 (GRCm39) |
M242L |
probably benign |
Het |
| Slc8a3 |
C |
A |
12: 81,246,341 (GRCm39) |
W904L |
probably benign |
Het |
| Ss18l1 |
G |
A |
2: 179,696,905 (GRCm39) |
V109I |
probably benign |
Het |
| Tbx5 |
C |
T |
5: 119,991,663 (GRCm39) |
H245Y |
probably damaging |
Het |
| Thumpd2 |
C |
A |
17: 81,360,342 (GRCm39) |
L244F |
probably damaging |
Het |
| Tmem107 |
T |
A |
11: 68,962,241 (GRCm39) |
V66E |
probably damaging |
Het |
| Tnr |
T |
C |
1: 159,715,884 (GRCm39) |
V882A |
possibly damaging |
Het |
| Top2b |
T |
G |
14: 16,409,189 (GRCm38) |
I777M |
probably damaging |
Het |
| Ttbk1 |
A |
G |
17: 46,781,733 (GRCm39) |
V340A |
possibly damaging |
Het |
| Veph1 |
T |
C |
3: 66,162,481 (GRCm39) |
E59G |
probably damaging |
Het |
| Vmn1r234 |
T |
A |
17: 21,449,983 (GRCm39) |
M299K |
possibly damaging |
Het |
| Vps13b |
T |
C |
15: 35,770,610 (GRCm39) |
Y2018H |
probably benign |
Het |
| Zbtb11 |
A |
G |
16: 55,818,436 (GRCm39) |
E620G |
probably benign |
Het |
| Zfp418 |
A |
G |
7: 7,185,627 (GRCm39) |
H530R |
possibly damaging |
Het |
| Zfp764l1 |
C |
T |
7: 126,992,581 (GRCm39) |
A10T |
possibly damaging |
Het |
|
| Other mutations in Nlgn1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00510:Nlgn1
|
APN |
3 |
25,490,654 (GRCm39) |
missense |
probably benign |
0.02 |
|
IGL00543:Nlgn1
|
APN |
3 |
25,487,945 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00960:Nlgn1
|
APN |
3 |
25,966,861 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01533:Nlgn1
|
APN |
3 |
25,490,527 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
IGL02146:Nlgn1
|
APN |
3 |
25,966,846 (GRCm39) |
missense |
probably damaging |
0.96 |
|
IGL02616:Nlgn1
|
APN |
3 |
25,488,409 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL03342:Nlgn1
|
APN |
3 |
26,187,411 (GRCm39) |
missense |
probably damaging |
1.00 |
|
ligation
|
UTSW |
3 |
25,490,199 (GRCm39) |
nonsense |
probably null |
|
|
G1citation:Nlgn1
|
UTSW |
3 |
26,187,796 (GRCm39) |
missense |
probably benign |
0.00 |
|
P0018:Nlgn1
|
UTSW |
3 |
25,490,741 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0010:Nlgn1
|
UTSW |
3 |
25,490,006 (GRCm39) |
splice site |
probably benign |
|
|
R0010:Nlgn1
|
UTSW |
3 |
25,490,006 (GRCm39) |
splice site |
probably benign |
|
|
R0123:Nlgn1
|
UTSW |
3 |
25,490,089 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0134:Nlgn1
|
UTSW |
3 |
25,490,089 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0294:Nlgn1
|
UTSW |
3 |
26,187,625 (GRCm39) |
missense |
probably benign |
0.23 |
|
R0798:Nlgn1
|
UTSW |
3 |
25,488,410 (GRCm39) |
missense |
probably benign |
0.05 |
|
R1051:Nlgn1
|
UTSW |
3 |
25,966,869 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1116:Nlgn1
|
UTSW |
3 |
25,488,038 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1289:Nlgn1
|
UTSW |
3 |
25,488,400 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R1522:Nlgn1
|
UTSW |
3 |
25,490,073 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1550:Nlgn1
|
UTSW |
3 |
25,966,808 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1669:Nlgn1
|
UTSW |
3 |
25,490,298 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1853:Nlgn1
|
UTSW |
3 |
26,187,671 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
R1856:Nlgn1
|
UTSW |
3 |
25,494,201 (GRCm39) |
nonsense |
probably null |
|
|
R1935:Nlgn1
|
UTSW |
3 |
26,385,939 (GRCm39) |
utr 5 prime |
probably benign |
|
|
R1936:Nlgn1
|
UTSW |
3 |
26,385,939 (GRCm39) |
utr 5 prime |
probably benign |
|
|
R1952:Nlgn1
|
UTSW |
3 |
25,490,464 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1953:Nlgn1
|
UTSW |
3 |
25,490,464 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2004:Nlgn1
|
UTSW |
3 |
25,488,034 (GRCm39) |
missense |
probably benign |
0.29 |
|
R2114:Nlgn1
|
UTSW |
3 |
26,187,414 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2116:Nlgn1
|
UTSW |
3 |
26,187,414 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2198:Nlgn1
|
UTSW |
3 |
25,487,925 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2994:Nlgn1
|
UTSW |
3 |
25,490,162 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3056:Nlgn1
|
UTSW |
3 |
25,487,860 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
R4190:Nlgn1
|
UTSW |
3 |
25,488,062 (GRCm39) |
missense |
probably benign |
|
|
R4196:Nlgn1
|
UTSW |
3 |
25,488,556 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4613:Nlgn1
|
UTSW |
3 |
25,490,186 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4654:Nlgn1
|
UTSW |
3 |
26,187,850 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R4757:Nlgn1
|
UTSW |
3 |
25,490,507 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R4757:Nlgn1
|
UTSW |
3 |
25,490,332 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4815:Nlgn1
|
UTSW |
3 |
25,490,194 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4884:Nlgn1
|
UTSW |
3 |
25,966,838 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4966:Nlgn1
|
UTSW |
3 |
25,974,401 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R5119:Nlgn1
|
UTSW |
3 |
25,487,958 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5842:Nlgn1
|
UTSW |
3 |
26,187,892 (GRCm39) |
splice site |
probably null |
|
|
R6397:Nlgn1
|
UTSW |
3 |
25,487,827 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
R6500:Nlgn1
|
UTSW |
3 |
25,488,094 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R6822:Nlgn1
|
UTSW |
3 |
26,187,796 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6846:Nlgn1
|
UTSW |
3 |
25,490,506 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7047:Nlgn1
|
UTSW |
3 |
25,490,199 (GRCm39) |
nonsense |
probably null |
|
|
R7147:Nlgn1
|
UTSW |
3 |
26,187,509 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7754:Nlgn1
|
UTSW |
3 |
25,488,467 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7886:Nlgn1
|
UTSW |
3 |
25,490,071 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8184:Nlgn1
|
UTSW |
3 |
25,490,363 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8261:Nlgn1
|
UTSW |
3 |
25,487,816 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
R8304:Nlgn1
|
UTSW |
3 |
26,187,534 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8364:Nlgn1
|
UTSW |
3 |
25,490,140 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8503:Nlgn1
|
UTSW |
3 |
26,187,522 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9035:Nlgn1
|
UTSW |
3 |
25,488,595 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9053:Nlgn1
|
UTSW |
3 |
25,488,607 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9209:Nlgn1
|
UTSW |
3 |
25,966,804 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9268:Nlgn1
|
UTSW |
3 |
25,490,548 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R9368:Nlgn1
|
UTSW |
3 |
25,488,622 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9492:Nlgn1
|
UTSW |
3 |
25,488,480 (GRCm39) |
nonsense |
probably null |
|
|
R9596:Nlgn1
|
UTSW |
3 |
25,488,587 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9647:Nlgn1
|
UTSW |
3 |
25,488,182 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9697:Nlgn1
|
UTSW |
3 |
25,494,035 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
Z1176:Nlgn1
|
UTSW |
3 |
25,490,768 (GRCm39) |
missense |
probably benign |
0.12 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGTCATTACTACTGCACTCAACATC -3'
(R):5'- GCCAGTGATTTCGACTTTGCTG -3'
Sequencing Primer
(F):5'- CTCAACATCACATCATTCTTGGAG -3'
(R):5'- TTCGACTTTGCTGTTTCTAATTTTG -3'
|
| Posted On |
2018-02-27 |
Incidental Mutation