Incidental Mutation 'R2198:Nlgn1'
ID |
238478 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Nlgn1
|
Ensembl Gene |
ENSMUSG00000063887 |
Gene Name |
neuroligin 1 |
Synonyms |
NL1, Nlg1, 6330415N05Rik |
MMRRC Submission |
040200-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R2198 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
25480379-26386609 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 25487925 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Methionine to Isoleucine
at position 803
(M803I)
|
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: M803I
PolyPhen 2
Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000074565 Gene: ENSMUSG00000063887 AA Change: M803I
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: M774I
PolyPhen 2
Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000103944 Gene: ENSMUSG00000063887 AA Change: M774I
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: M774I
PolyPhen 2
Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000142086 Gene: ENSMUSG00000063887 AA Change: M774I
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: M803I
PolyPhen 2
Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000142200 Gene: ENSMUSG00000063887 AA Change: M803I
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 |
0.1443 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.8%
|
Validation Efficiency |
98% (60/61) |
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: 57 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adra1a |
T |
C |
14: 66,875,385 (GRCm39) |
I120T |
probably damaging |
Het |
Akr1c21 |
C |
T |
13: 4,627,464 (GRCm39) |
P186L |
probably damaging |
Het |
Alpk2 |
T |
C |
18: 65,483,255 (GRCm39) |
K251R |
probably benign |
Het |
Ank2 |
T |
C |
3: 126,728,226 (GRCm39) |
E789G |
possibly damaging |
Het |
Bag3 |
AAAGG |
AAAGGAAGG |
7: 128,147,493 (GRCm39) |
|
probably null |
Het |
Cacna2d4 |
T |
C |
6: 119,324,220 (GRCm39) |
|
probably benign |
Het |
Carf |
G |
A |
1: 60,180,643 (GRCm39) |
R355H |
probably damaging |
Het |
Cdh20 |
A |
T |
1: 104,875,047 (GRCm39) |
|
probably null |
Het |
Celf6 |
G |
T |
9: 59,510,622 (GRCm39) |
L169F |
possibly damaging |
Het |
Cep295nl |
A |
T |
11: 118,223,419 (GRCm39) |
I475N |
probably benign |
Het |
Chdh |
T |
A |
14: 29,753,489 (GRCm39) |
S133T |
possibly damaging |
Het |
Cnot6l |
C |
T |
5: 96,227,800 (GRCm39) |
D478N |
possibly damaging |
Het |
Ctnna3 |
C |
A |
10: 64,838,524 (GRCm39) |
T867K |
probably benign |
Het |
Ctse |
T |
G |
1: 131,600,185 (GRCm39) |
Y311* |
probably null |
Het |
Ddx60 |
T |
A |
8: 62,411,097 (GRCm39) |
M453K |
possibly damaging |
Het |
Dnah9 |
A |
G |
11: 65,750,325 (GRCm39) |
F3927L |
possibly damaging |
Het |
Dsg4 |
T |
C |
18: 20,594,499 (GRCm39) |
S543P |
probably benign |
Het |
Dspp |
A |
T |
5: 104,323,567 (GRCm39) |
T237S |
probably benign |
Het |
Eml6 |
T |
G |
11: 29,800,935 (GRCm39) |
H357P |
probably benign |
Het |
Epha3 |
T |
C |
16: 63,664,507 (GRCm39) |
I38V |
possibly damaging |
Het |
Erap1 |
C |
T |
13: 74,794,806 (GRCm39) |
T155I |
probably damaging |
Het |
Erh |
T |
C |
12: 80,689,559 (GRCm39) |
|
probably benign |
Het |
F5 |
A |
T |
1: 164,034,603 (GRCm39) |
K1834M |
probably damaging |
Het |
Fyn |
A |
G |
10: 39,405,541 (GRCm39) |
E269G |
probably benign |
Het |
Gm4884 |
A |
G |
7: 40,690,229 (GRCm39) |
T42A |
probably benign |
Het |
Grm1 |
T |
G |
10: 10,658,520 (GRCm39) |
R323S |
probably damaging |
Het |
Gstt4 |
T |
C |
10: 75,658,235 (GRCm39) |
D8G |
probably damaging |
Het |
Gvin-ps3 |
T |
A |
7: 105,682,758 (GRCm39) |
M166L |
probably benign |
Het |
Ldlr |
A |
G |
9: 21,643,698 (GRCm39) |
D94G |
probably damaging |
Het |
Mrpl54 |
G |
A |
10: 81,101,575 (GRCm39) |
|
probably null |
Het |
Naip2 |
A |
T |
13: 100,289,100 (GRCm39) |
F1210Y |
probably damaging |
Het |
Nifk |
A |
G |
1: 118,257,130 (GRCm39) |
R88G |
probably benign |
Het |
Or2r11 |
A |
G |
6: 42,437,950 (GRCm39) |
M1T |
probably null |
Het |
Or2y16 |
C |
T |
11: 49,334,786 (GRCm39) |
S36F |
probably benign |
Het |
Or6c88 |
T |
A |
10: 129,406,915 (GRCm39) |
Y130* |
probably null |
Het |
Or8g18 |
G |
A |
9: 39,149,048 (GRCm39) |
T224I |
possibly damaging |
Het |
Pip4k2a |
A |
T |
2: 18,852,466 (GRCm39) |
M272K |
probably damaging |
Het |
Ppp1cb |
G |
T |
5: 32,640,704 (GRCm39) |
C139F |
probably damaging |
Het |
Rad23b |
G |
A |
4: 55,385,497 (GRCm39) |
G345R |
possibly damaging |
Het |
Shc4 |
A |
T |
2: 125,481,266 (GRCm39) |
V548E |
possibly damaging |
Het |
Slc26a9 |
A |
G |
1: 131,691,001 (GRCm39) |
|
probably benign |
Het |
Slc8a1 |
T |
A |
17: 81,715,685 (GRCm39) |
K783* |
probably null |
Het |
Sobp |
A |
C |
10: 42,898,520 (GRCm39) |
I355S |
possibly damaging |
Het |
Thbs4 |
A |
G |
13: 92,899,779 (GRCm39) |
Y491H |
possibly damaging |
Het |
Tle2 |
T |
C |
10: 81,426,147 (GRCm39) |
V727A |
probably damaging |
Het |
Tmprss9 |
C |
T |
10: 80,723,293 (GRCm39) |
P251L |
probably damaging |
Het |
Tnks |
A |
T |
8: 35,315,803 (GRCm39) |
D994E |
probably benign |
Het |
Tnks |
C |
T |
8: 35,340,221 (GRCm39) |
D466N |
probably benign |
Het |
Tonsl |
A |
G |
15: 76,520,872 (GRCm39) |
F394L |
probably benign |
Het |
Trpa1 |
T |
A |
1: 14,980,970 (GRCm39) |
Y144F |
probably benign |
Het |
Usp22 |
A |
G |
11: 61,050,163 (GRCm39) |
F324S |
probably damaging |
Het |
Vmn1r78 |
G |
T |
7: 11,886,487 (GRCm39) |
V33F |
probably benign |
Het |
Wdr81 |
C |
T |
11: 75,336,907 (GRCm39) |
R1494Q |
probably benign |
Het |
Wdr87-ps |
G |
T |
7: 29,226,697 (GRCm39) |
|
noncoding transcript |
Het |
Zc3h14 |
G |
A |
12: 98,719,068 (GRCm39) |
M144I |
probably damaging |
Het |
Zc3h14 |
G |
A |
12: 98,719,069 (GRCm39) |
V145M |
possibly damaging |
Het |
Zfp82 |
T |
C |
7: 29,756,936 (GRCm39) |
T49A |
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 |
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 |
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'- TGAGAGTCTTCCGAGTTGAAAGC -3'
(R):5'- AACCCATGCTCCAGAAGAGG -3'
Sequencing Primer
(F):5'- TCTTCCGAGTTGAAAGCCAAGG -3'
(R):5'- GCTCCAGAAGAGGAAATTATGTCTC -3'
|
Posted On |
2014-10-02 |