Incidental Mutation 'R9697:Nlgn1'
| ID |
729347 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nlgn1
|
| Ensembl Gene |
ENSMUSG00000063887 |
| Gene Name |
neuroligin 1 |
| Synonyms |
NL1, Nlg1, 6330415N05Rik |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R9697 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
25480379-26386609 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 25494035 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 305
(T305A)
|
| 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 |
possibly damaging
Transcript: ENSMUST00000075054
AA Change: T305A
PolyPhen 2
Score 0.525 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: T305A
| 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 benign
Transcript: ENSMUST00000108308
|
| SMART Domains |
Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
| 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 benign
Transcript: ENSMUST00000191835
|
| SMART Domains |
Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
| 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: ENSMUST00000193603
AA Change: T305A
PolyPhen 2
Score 0.525 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: T305A
| 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 |
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.6%
- 20x: 96.0%
|
| Validation Efficiency |
|
| 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: 62 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1600012H06Rik |
C |
T |
17: 15,163,769 (GRCm39) |
|
probably benign |
Het |
| 9330182O14Rik |
C |
T |
15: 40,005,500 (GRCm39) |
|
probably benign |
Het |
| Adamts19 |
C |
A |
18: 59,101,834 (GRCm39) |
P635T |
probably damaging |
Het |
| Adgrf1 |
T |
C |
17: 43,625,362 (GRCm39) |
W857R |
possibly damaging |
Het |
| Ak9 |
T |
G |
10: 41,298,968 (GRCm39) |
Y1556* |
probably null |
Het |
| Ang2 |
T |
C |
14: 51,433,326 (GRCm39) |
I19V |
probably benign |
Het |
| Ano3 |
T |
A |
2: 110,496,253 (GRCm39) |
T834S |
probably damaging |
Het |
| As3mt |
A |
T |
19: 46,708,420 (GRCm39) |
I236F |
probably benign |
Het |
| Asns |
A |
T |
6: 7,689,268 (GRCm39) |
I78N |
probably damaging |
Het |
| Bet1 |
G |
A |
6: 4,082,471 (GRCm39) |
T44M |
probably damaging |
Het |
| Cabyr |
T |
C |
18: 12,884,407 (GRCm39) |
V298A |
possibly damaging |
Het |
| Cacna1c |
A |
G |
6: 118,589,598 (GRCm39) |
V1601A |
|
Het |
| Ccni |
A |
T |
5: 93,350,201 (GRCm39) |
M26K |
probably damaging |
Het |
| Cdhr2 |
T |
C |
13: 54,867,679 (GRCm39) |
I503T |
probably damaging |
Het |
| Cfap54 |
T |
C |
10: 92,792,851 (GRCm39) |
K1754R |
unknown |
Het |
| Cfap69 |
A |
G |
5: 5,676,041 (GRCm39) |
V218A |
possibly damaging |
Het |
| Clcn3 |
A |
G |
8: 61,372,518 (GRCm39) |
L741P |
probably damaging |
Het |
| Cntnap1 |
T |
C |
11: 101,068,828 (GRCm39) |
F124L |
possibly damaging |
Het |
| Col20a1 |
G |
A |
2: 180,641,577 (GRCm39) |
G673D |
probably benign |
Het |
| Col4a2 |
A |
G |
8: 11,487,628 (GRCm39) |
I977V |
probably benign |
Het |
| Cyp3a59 |
A |
T |
5: 146,031,190 (GRCm39) |
I118F |
probably damaging |
Het |
| Dgcr8 |
A |
T |
16: 18,098,283 (GRCm39) |
D369E |
probably benign |
Het |
| Dhtkd1 |
T |
C |
2: 5,919,651 (GRCm39) |
T577A |
probably benign |
Het |
| Dock2 |
A |
T |
11: 34,204,417 (GRCm39) |
M1375K |
probably benign |
Het |
| Fa2h |
G |
A |
8: 112,074,659 (GRCm39) |
H315Y |
probably damaging |
Het |
| Foxd2 |
G |
A |
4: 114,765,684 (GRCm39) |
P112L |
unknown |
Het |
| Gin1 |
A |
G |
1: 97,712,897 (GRCm39) |
I317V |
probably benign |
Het |
| Gpr180 |
G |
A |
14: 118,391,302 (GRCm39) |
G235R |
probably damaging |
Het |
| H2-T3 |
T |
A |
17: 36,500,744 (GRCm39) |
Y33F |
probably damaging |
Het |
| Idh2 |
TCCCAGG |
T |
7: 79,748,079 (GRCm39) |
|
probably benign |
Het |
| Il12rb1 |
G |
A |
8: 71,263,874 (GRCm39) |
W145* |
probably null |
Het |
| Il6ra |
A |
G |
3: 89,785,219 (GRCm39) |
V330A |
probably benign |
Het |
| Impdh2 |
T |
C |
9: 108,438,847 (GRCm39) |
S67P |
possibly damaging |
Het |
| Ltbp3 |
T |
A |
19: 5,792,521 (GRCm39) |
S85T |
probably benign |
Het |
| Magi3 |
A |
G |
3: 103,956,458 (GRCm39) |
|
probably null |
Het |
| Mettl4 |
T |
A |
17: 95,034,806 (GRCm39) |
I430F |
probably damaging |
Het |
| Mmd |
T |
A |
11: 90,167,579 (GRCm39) |
F203I |
probably damaging |
Het |
| Ntn1 |
A |
G |
11: 68,168,356 (GRCm39) |
V367A |
probably damaging |
Het |
| Or2w1b |
A |
T |
13: 21,299,892 (GRCm39) |
H10L |
probably benign |
Het |
| Or5b107 |
G |
A |
19: 13,142,888 (GRCm39) |
C170Y |
possibly damaging |
Het |
| Pcdh12 |
T |
C |
18: 38,415,022 (GRCm39) |
H701R |
possibly damaging |
Het |
| Pcgf3 |
G |
A |
5: 108,621,773 (GRCm39) |
|
probably null |
Het |
| Pik3c2g |
G |
A |
6: 139,913,517 (GRCm39) |
V972M |
unknown |
Het |
| Pink1 |
A |
G |
4: 138,041,323 (GRCm39) |
C563R |
possibly damaging |
Het |
| Prol1 |
A |
T |
5: 88,466,426 (GRCm39) |
N3I |
probably benign |
Het |
| Ptpro |
T |
G |
6: 137,363,288 (GRCm39) |
I474S |
probably damaging |
Het |
| Rabgef1 |
A |
G |
5: 130,241,781 (GRCm39) |
E395G |
probably benign |
Het |
| Rpgrip1l |
G |
T |
8: 91,987,391 (GRCm39) |
H889N |
possibly damaging |
Het |
| Sapcd2 |
T |
A |
2: 25,262,925 (GRCm39) |
C161* |
probably null |
Het |
| Sbsn |
GAAAAGGAAGCAGAAAAAGTGGCCCATGGGGTACAGAATGGAGTCAACCAGGCTCAAAAGGAAGCAGAAAAAGTGGCCCATGGGGTACAGAATGGAGTCAACCAGGCTCAAAAGGAAGCAGAAAAAGTGGCCCATGGGGTACAGAATGGAGTCAACCAGGCTCAAAAGGAAGCAGAAAAAGTGGCCCA |
GAAAAGGAAGCAGAAAAAGTGGCCCATGGGGTACAGAATGGAGTCAACCAGGCTCAAAAGGAAGCAGAAAAAGTGGCCCATGGGGTACAGAATGGAGTCAACCAGGCTCAAAAGGAAGCAGAAAAAGTGGCCCA |
7: 30,452,391 (GRCm39) |
|
probably benign |
Het |
| Spen |
A |
G |
4: 141,196,275 (GRCm39) |
L3625P |
probably damaging |
Het |
| Stil |
T |
C |
4: 114,878,701 (GRCm39) |
I379T |
probably benign |
Het |
| Stim1 |
A |
G |
7: 102,078,014 (GRCm39) |
D172G |
|
Het |
| Timm50 |
A |
G |
7: 28,010,350 (GRCm39) |
L68P |
probably damaging |
Het |
| Tlr9 |
C |
T |
9: 106,100,723 (GRCm39) |
R5* |
probably null |
Het |
| Top1mt |
A |
T |
15: 75,547,874 (GRCm39) |
Y71N |
probably damaging |
Het |
| Trpv4 |
A |
G |
5: 114,771,285 (GRCm39) |
Y415H |
possibly damaging |
Het |
| Try10 |
C |
T |
6: 41,331,041 (GRCm39) |
|
probably benign |
Het |
| Uhrf2 |
A |
G |
19: 30,063,780 (GRCm39) |
E581G |
probably damaging |
Het |
| Usp17lb |
G |
A |
7: 104,490,495 (GRCm39) |
T144I |
possibly damaging |
Het |
| Vmn1r64 |
T |
C |
7: 5,886,859 (GRCm39) |
N228S |
probably benign |
Het |
| Vwa1 |
G |
A |
4: 155,857,336 (GRCm39) |
P154L |
probably 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 |
|
|
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 |
|
Z1176:Nlgn1
|
UTSW |
3 |
25,490,768 (GRCm39) |
missense |
probably benign |
0.12 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTGAAAATGCATCTTACCCAGCTC -3'
(R):5'- AAGGAAACTACGGGCTCCTTG -3'
Sequencing Primer
(F):5'- TCTTACCCAGCTCCATGGAAG -3'
(R):5'- GAAACTACGGGCTCCTTGACCTC -3'
|
| Posted On |
2022-10-06 |
Incidental Mutation