Incidental Mutation 'R1669:Nlgn1'
ID |
187430 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Nlgn1
|
Ensembl Gene |
ENSMUSG00000063887 |
Gene Name |
neuroligin 1 |
Synonyms |
NL1, Nlg1, 6330415N05Rik |
MMRRC Submission |
039705-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R1669 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
25480379-26386609 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to A
at 25490298 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Leucine to Phenylalanine
at position 476
(L476F)
|
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: L476F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000074565 Gene: ENSMUSG00000063887 AA Change: L476F
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 |
possibly damaging
Transcript: ENSMUST00000108308
AA Change: L447F
PolyPhen 2
Score 0.849 (Sensitivity: 0.83; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000103944 Gene: ENSMUSG00000063887 AA Change: L447F
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 |
possibly damaging
Transcript: ENSMUST00000191835
AA Change: L447F
PolyPhen 2
Score 0.849 (Sensitivity: 0.83; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000142086 Gene: ENSMUSG00000063887 AA Change: L447F
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: L476F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000142200 Gene: ENSMUSG00000063887 AA Change: L476F
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 |
0.6467 |
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.5%
- 20x: 93.3%
|
Validation Efficiency |
99% (85/86) |
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: 81 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Ano10 |
A |
C |
9: 122,086,249 (GRCm39) |
L258R |
possibly damaging |
Het |
Ap3d1 |
A |
G |
10: 80,546,670 (GRCm39) |
|
probably benign |
Het |
Aplp2 |
G |
T |
9: 31,079,029 (GRCm39) |
|
probably benign |
Het |
Arhgap11a |
T |
C |
2: 113,672,257 (GRCm39) |
D237G |
possibly damaging |
Het |
Arhgef4 |
A |
T |
1: 34,771,239 (GRCm39) |
H1182L |
possibly damaging |
Het |
Ash1l |
G |
A |
3: 88,974,549 (GRCm39) |
|
probably null |
Het |
Bicdl1 |
C |
A |
5: 115,794,075 (GRCm39) |
V224L |
possibly damaging |
Het |
Cacna1h |
C |
A |
17: 25,602,445 (GRCm39) |
V1422L |
probably damaging |
Het |
Card10 |
T |
C |
15: 78,678,153 (GRCm39) |
E365G |
probably benign |
Het |
Cd180 |
C |
T |
13: 102,841,998 (GRCm39) |
T348I |
probably damaging |
Het |
Cds2 |
T |
A |
2: 132,137,439 (GRCm39) |
|
probably null |
Het |
Chaf1a |
C |
A |
17: 56,370,339 (GRCm39) |
D601E |
probably benign |
Het |
Coprs |
C |
T |
8: 13,935,704 (GRCm39) |
W12* |
probably null |
Het |
Cpsf3 |
T |
A |
12: 21,355,332 (GRCm39) |
M424K |
probably damaging |
Het |
Cxcl13 |
T |
A |
5: 96,106,600 (GRCm39) |
N57K |
probably damaging |
Het |
Dact1 |
C |
T |
12: 71,365,547 (GRCm39) |
T776M |
probably damaging |
Het |
Depdc1a |
A |
G |
3: 159,228,561 (GRCm39) |
K438E |
probably benign |
Het |
Dop1b |
T |
A |
16: 93,566,548 (GRCm39) |
S992T |
probably damaging |
Het |
Dusp11 |
A |
T |
6: 85,927,008 (GRCm39) |
H202Q |
probably benign |
Het |
Ezr |
T |
C |
17: 7,006,712 (GRCm39) |
E584G |
probably damaging |
Het |
F830104G03Rik |
A |
G |
3: 56,797,998 (GRCm39) |
V6A |
unknown |
Het |
Fam227a |
G |
A |
15: 79,504,878 (GRCm39) |
|
probably null |
Het |
Gapvd1 |
T |
G |
2: 34,620,694 (GRCm39) |
|
probably null |
Het |
Gm10267 |
T |
C |
18: 44,290,367 (GRCm39) |
R47G |
probably damaging |
Het |
Hectd3 |
T |
A |
4: 116,856,840 (GRCm39) |
D462E |
probably damaging |
Het |
Hfe |
A |
T |
13: 23,890,110 (GRCm39) |
L133* |
probably null |
Het |
Hpcal4 |
T |
C |
4: 123,082,869 (GRCm39) |
F72L |
probably damaging |
Het |
Itgb4 |
G |
A |
11: 115,882,156 (GRCm39) |
R825H |
probably benign |
Het |
Kcnh8 |
T |
A |
17: 53,200,996 (GRCm39) |
Y477N |
probably damaging |
Het |
Kctd1 |
T |
C |
18: 15,195,517 (GRCm39) |
N369D |
possibly damaging |
Het |
Kdm1b |
C |
T |
13: 47,222,024 (GRCm39) |
R488C |
probably damaging |
Het |
Kif1c |
C |
T |
11: 70,619,223 (GRCm39) |
L953F |
probably damaging |
Het |
Klra8 |
A |
T |
6: 130,092,592 (GRCm39) |
C236* |
probably null |
Het |
Lca5l |
T |
C |
16: 95,961,008 (GRCm39) |
R485G |
possibly damaging |
Het |
Lrrc2 |
A |
G |
9: 110,810,718 (GRCm39) |
T363A |
probably damaging |
Het |
Lsmem1 |
GTACATACATACATACATACATACATACA |
GTACATACATACATACATACATACATACATACA |
12: 40,235,260 (GRCm39) |
|
probably null |
Het |
Lyst |
G |
A |
13: 13,818,672 (GRCm39) |
G1314D |
possibly damaging |
Het |
Mmp10 |
A |
T |
9: 7,505,526 (GRCm39) |
|
probably null |
Het |
Mmp13 |
A |
G |
9: 7,277,926 (GRCm39) |
D273G |
probably benign |
Het |
Morc2a |
G |
A |
11: 3,625,885 (GRCm39) |
V162M |
probably benign |
Het |
Msh4 |
C |
T |
3: 153,582,357 (GRCm39) |
R417Q |
possibly damaging |
Het |
Nedd9 |
A |
T |
13: 41,465,270 (GRCm39) |
V790E |
probably damaging |
Het |
Nox4 |
C |
A |
7: 86,945,097 (GRCm39) |
Q118K |
probably benign |
Het |
Nxf1 |
A |
G |
19: 8,749,495 (GRCm39) |
T131A |
possibly damaging |
Het |
Oog3 |
C |
A |
4: 143,885,008 (GRCm39) |
R309S |
probably benign |
Het |
Oosp3 |
C |
T |
19: 11,678,378 (GRCm39) |
|
probably benign |
Het |
Or10a3 |
T |
A |
7: 108,479,920 (GRCm39) |
T298S |
probably benign |
Het |
Or2a7 |
T |
A |
6: 43,151,755 (GRCm39) |
S278R |
probably damaging |
Het |
Or2w6 |
A |
T |
13: 21,843,456 (GRCm39) |
S12R |
possibly damaging |
Het |
Or4c126 |
T |
A |
2: 89,824,144 (GRCm39) |
|
probably null |
Het |
Or51a42 |
A |
T |
7: 103,708,516 (GRCm39) |
S98T |
probably benign |
Het |
Or5b97 |
A |
T |
19: 12,878,652 (GRCm39) |
I164K |
possibly damaging |
Het |
P2ry6 |
A |
G |
7: 100,587,630 (GRCm39) |
V243A |
probably damaging |
Het |
Pgc |
C |
A |
17: 48,044,715 (GRCm39) |
P321T |
probably damaging |
Het |
Pramel22 |
T |
G |
4: 143,380,916 (GRCm39) |
E369A |
possibly damaging |
Het |
Prkd1 |
G |
A |
12: 50,441,709 (GRCm39) |
H277Y |
probably damaging |
Het |
Prkdc |
T |
A |
16: 15,551,922 (GRCm39) |
S2043T |
probably damaging |
Het |
Rasal3 |
T |
C |
17: 32,622,072 (GRCm39) |
N96D |
possibly damaging |
Het |
Rnf4 |
T |
C |
5: 34,508,624 (GRCm39) |
F162S |
probably damaging |
Het |
Ros1 |
A |
T |
10: 52,037,907 (GRCm39) |
N421K |
probably damaging |
Het |
Rtn4rl1 |
A |
G |
11: 75,156,753 (GRCm39) |
D395G |
probably benign |
Het |
Scn8a |
T |
G |
15: 100,909,001 (GRCm39) |
V823G |
probably damaging |
Het |
Sema3d |
T |
A |
5: 12,558,051 (GRCm39) |
|
probably benign |
Het |
Slc12a2 |
T |
C |
18: 58,037,307 (GRCm39) |
I501T |
probably damaging |
Het |
Slc12a7 |
C |
T |
13: 73,943,232 (GRCm39) |
T382I |
probably benign |
Het |
Slc16a12 |
T |
A |
19: 34,657,781 (GRCm39) |
I41L |
probably benign |
Het |
Slc1a1 |
C |
A |
19: 28,889,194 (GRCm39) |
T489K |
probably benign |
Het |
Slc24a3 |
C |
T |
2: 145,455,512 (GRCm39) |
P467L |
probably damaging |
Het |
Slco1a8 |
T |
A |
6: 141,933,415 (GRCm39) |
I457F |
probably benign |
Het |
Snai2 |
A |
T |
16: 14,524,908 (GRCm39) |
Y138F |
possibly damaging |
Het |
Sorcs1 |
A |
C |
19: 50,463,860 (GRCm39) |
Y197D |
probably damaging |
Het |
Sppl2a |
T |
A |
2: 126,759,714 (GRCm39) |
|
probably benign |
Het |
Srgap3 |
G |
A |
6: 112,699,865 (GRCm39) |
P1038S |
probably benign |
Het |
Ttn |
T |
C |
2: 76,554,807 (GRCm39) |
E30699G |
probably damaging |
Het |
Vmn2r124 |
T |
A |
17: 18,283,206 (GRCm39) |
M300K |
possibly damaging |
Het |
Vwf |
T |
C |
6: 125,624,869 (GRCm39) |
S1873P |
possibly damaging |
Het |
Wrap73 |
A |
G |
4: 154,240,588 (GRCm39) |
D360G |
probably damaging |
Het |
Zfp366 |
T |
C |
13: 99,366,069 (GRCm39) |
M410T |
probably damaging |
Het |
Zfp608 |
C |
T |
18: 55,120,811 (GRCm39) |
V259I |
probably benign |
Het |
Zfp69 |
C |
T |
4: 120,804,695 (GRCm39) |
|
probably benign |
Het |
Zfp995 |
T |
C |
17: 22,098,945 (GRCm39) |
T430A |
probably benign |
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 |
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 |
|
R6218:Nlgn1
|
UTSW |
3 |
25,490,257 (GRCm39) |
missense |
probably damaging |
1.00 |
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'- ATAGGGAACCTCATCCCCATGAGC -3'
(R):5'- CCCGATACCACATAGCCTTTGGAC -3'
Sequencing Primer
(F):5'- TGAGCTGCATCAGCCCAAG -3'
(R):5'- GGTGATGTAATACCAGATGACCCTC -3'
|
Posted On |
2014-05-09 |