Incidental Mutation 'R8304:Nlgn1'
| ID |
639373 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nlgn1
|
| Ensembl Gene |
ENSMUSG00000063887 |
| Gene Name |
neuroligin 1 |
| Synonyms |
NL1, Nlg1, 6330415N05Rik |
| MMRRC Submission |
067791-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R8304 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
25480379-26386609 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 26187534 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Tyrosine
at position 117
(C117Y)
|
| 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: C117Y
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: C117Y
| 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: C117Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: C117Y
| 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: C117Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: C117Y
| 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: C117Y
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: C117Y
| 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: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.9%
|
| Validation Efficiency |
98% (58/59) |
| 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: 58 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca9 |
A |
G |
11: 109,997,954 (GRCm39) |
|
probably null |
Het |
| Akap11 |
T |
C |
14: 78,750,672 (GRCm39) |
T572A |
|
Het |
| Amigo2 |
A |
T |
15: 97,144,038 (GRCm39) |
L128Q |
probably damaging |
Het |
| Ankrd12 |
A |
G |
17: 66,291,542 (GRCm39) |
I1297T |
possibly damaging |
Het |
| Arhgap32 |
T |
A |
9: 32,167,233 (GRCm39) |
C623* |
probably null |
Het |
| Armc2 |
T |
C |
10: 41,823,935 (GRCm39) |
Y511C |
probably damaging |
Het |
| Asb15 |
C |
T |
6: 24,559,296 (GRCm39) |
P147L |
possibly damaging |
Het |
| Caprin1 |
G |
T |
2: 103,599,862 (GRCm39) |
N604K |
probably damaging |
Het |
| Ccnl2 |
T |
C |
4: 155,897,679 (GRCm39) |
F113L |
probably benign |
Het |
| Cltc |
C |
T |
11: 86,616,087 (GRCm39) |
R393H |
probably benign |
Het |
| Cul4a |
G |
A |
8: 13,177,727 (GRCm39) |
C289Y |
possibly damaging |
Het |
| Cyp4a29 |
T |
A |
4: 115,111,653 (GRCm39) |
F477I |
probably damaging |
Het |
| Dapk2 |
C |
T |
9: 66,139,027 (GRCm39) |
A116V |
possibly damaging |
Het |
| Ddx60 |
T |
C |
8: 62,451,803 (GRCm39) |
I1231T |
possibly damaging |
Het |
| Eif5b |
A |
G |
1: 38,084,774 (GRCm39) |
I874V |
probably benign |
Het |
| Eral1 |
A |
T |
11: 77,966,828 (GRCm39) |
S196T |
probably damaging |
Het |
| Erc2 |
T |
G |
14: 27,375,122 (GRCm39) |
D113E |
probably damaging |
Het |
| Frmpd2 |
A |
G |
14: 33,274,066 (GRCm39) |
I1103V |
possibly damaging |
Het |
| Galm |
A |
G |
17: 80,490,766 (GRCm39) |
T308A |
probably damaging |
Het |
| Helz2 |
A |
T |
2: 180,871,950 (GRCm39) |
N2650K |
probably benign |
Het |
| Herc2 |
A |
G |
7: 55,809,186 (GRCm39) |
D2562G |
probably damaging |
Het |
| Hmmr |
G |
A |
11: 40,612,499 (GRCm39) |
S206F |
probably damaging |
Het |
| Hspbap1 |
T |
A |
16: 35,607,695 (GRCm39) |
L67* |
probably null |
Het |
| Irx3 |
T |
A |
8: 92,526,834 (GRCm39) |
D290V |
probably damaging |
Het |
| Kcns1 |
A |
T |
2: 164,010,022 (GRCm39) |
Y246N |
probably damaging |
Het |
| Kidins220 |
A |
G |
12: 25,107,127 (GRCm39) |
T1557A |
probably benign |
Het |
| Lrriq1 |
T |
C |
10: 103,069,929 (GRCm39) |
N29S |
possibly damaging |
Het |
| Mmp24 |
T |
C |
2: 155,641,759 (GRCm39) |
F196L |
possibly damaging |
Het |
| Mroh2b |
T |
C |
15: 4,955,119 (GRCm39) |
V704A |
probably damaging |
Het |
| Mst1 |
A |
G |
9: 107,958,803 (GRCm39) |
M112V |
probably benign |
Het |
| Myh8 |
C |
A |
11: 67,195,162 (GRCm39) |
H1659N |
possibly damaging |
Het |
| Opa1 |
C |
T |
16: 29,416,489 (GRCm39) |
T237M |
possibly damaging |
Het |
| Or2r2 |
C |
T |
6: 42,463,672 (GRCm39) |
V152I |
probably benign |
Het |
| Or51f5 |
A |
G |
7: 102,423,917 (GRCm39) |
Y62C |
possibly damaging |
Het |
| Or5v1 |
A |
T |
17: 37,810,261 (GRCm39) |
T240S |
probably damaging |
Het |
| Or8b57 |
A |
T |
9: 40,003,650 (GRCm39) |
I204N |
probably damaging |
Het |
| P3h1 |
C |
T |
4: 119,104,402 (GRCm39) |
T641M |
probably damaging |
Het |
| Pak5 |
T |
C |
2: 135,940,203 (GRCm39) |
H537R |
probably benign |
Het |
| Ppp1r12b |
A |
T |
1: 134,824,101 (GRCm39) |
L174Q |
possibly damaging |
Het |
| Prkg1 |
A |
G |
19: 30,701,584 (GRCm39) |
V326A |
possibly damaging |
Het |
| Psmb3 |
T |
A |
11: 97,601,995 (GRCm39) |
C122S |
probably benign |
Het |
| Sh3bgrl3 |
C |
A |
4: 133,855,312 (GRCm39) |
A45S |
probably benign |
Het |
| Slc25a47 |
T |
C |
12: 108,821,868 (GRCm39) |
V219A |
possibly damaging |
Het |
| Slfn9 |
A |
C |
11: 82,873,605 (GRCm39) |
S433A |
probably benign |
Het |
| Spata13 |
A |
T |
14: 60,993,957 (GRCm39) |
R1136S |
possibly damaging |
Het |
| Stab1 |
C |
A |
14: 30,870,911 (GRCm39) |
A1313S |
probably benign |
Het |
| Stim1 |
G |
A |
7: 102,084,688 (GRCm39) |
A547T |
possibly damaging |
Het |
| Taf5l |
A |
T |
8: 124,730,251 (GRCm39) |
I146N |
probably benign |
Het |
| Tbc1d12 |
A |
T |
19: 38,825,824 (GRCm39) |
E225V |
possibly damaging |
Het |
| Tesc |
T |
C |
5: 118,194,495 (GRCm39) |
Y135H |
probably benign |
Het |
| Tfg |
T |
C |
16: 56,521,581 (GRCm39) |
E145G |
possibly damaging |
Het |
| Tg |
T |
A |
15: 66,565,109 (GRCm39) |
C1150* |
probably null |
Het |
| Tmtc1 |
T |
C |
6: 148,172,883 (GRCm39) |
N616S |
probably damaging |
Het |
| Trpm7 |
A |
T |
2: 126,639,797 (GRCm39) |
W1600R |
probably damaging |
Het |
| Ttc17 |
A |
T |
2: 94,199,526 (GRCm39) |
|
probably benign |
Het |
| Zfand1 |
A |
T |
3: 10,413,615 (GRCm39) |
L24* |
probably null |
Het |
| Zfp282 |
AGCGGCGGCGGCGGCGGC |
AGCGGCGGCGGCGGC |
6: 47,881,722 (GRCm39) |
|
probably benign |
Het |
| Zfp770 |
A |
C |
2: 114,027,891 (GRCm39) |
F59L |
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 |
|
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'- CCCTGTGTTCCTGCAATGAAC -3'
(R):5'- TGTTTGCTACAGACTTTTCACGTAC -3'
Sequencing Primer
(F):5'- CAATGAACTCACCATCTTCAGTTGGG -3'
(R):5'- CACGTACTCTCTCAAAAGTTGG -3'
|
| Posted On |
2020-07-28 |
Incidental Mutation