Incidental Mutation 'G1citation:Nlgn1'
ID |
660720 |
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 # |
G1citation (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
25480379-26386609 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 26187796 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Alanine
at position 30
(T30A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000142086
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000075054]
[ENSMUST00000108308]
[ENSMUST00000191835]
[ENSMUST00000193603]
|
AlphaFold |
Q99K10 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000075054
AA Change: T30A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
SMART Domains |
Protein: ENSMUSP00000074565 Gene: ENSMUSG00000063887 AA Change: T30A
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
AA Change: T30A
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
SMART Domains |
Protein: ENSMUSP00000103944 Gene: ENSMUSG00000063887 AA Change: T30A
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
AA Change: T30A
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
SMART Domains |
Protein: ENSMUSP00000142086 Gene: ENSMUSG00000063887 AA Change: T30A
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: ENSMUST00000193603
AA Change: T30A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
SMART Domains |
Protein: ENSMUSP00000142200 Gene: ENSMUSG00000063887 AA Change: T30A
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 |
0.0755 |
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.7%
|
Validation Efficiency |
94% (46/49) |
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: 47 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adam11 |
G |
A |
11: 102,667,501 (GRCm39) |
R687Q |
possibly damaging |
Het |
AI987944 |
A |
G |
7: 41,024,232 (GRCm39) |
L249P |
probably damaging |
Het |
Ankrd28 |
T |
A |
14: 31,458,797 (GRCm39) |
|
probably null |
Het |
Bahcc1 |
T |
C |
11: 120,178,547 (GRCm39) |
S2369P |
probably damaging |
Het |
Birc6 |
T |
C |
17: 74,887,377 (GRCm39) |
S902P |
possibly damaging |
Het |
Birc6 |
A |
T |
17: 74,905,039 (GRCm39) |
K1277N |
probably damaging |
Het |
Brwd1 |
T |
C |
16: 95,842,474 (GRCm39) |
E821G |
probably benign |
Het |
Cct8l1 |
T |
C |
5: 25,722,937 (GRCm39) |
S551P |
possibly damaging |
Het |
Cmtm1 |
TCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGG |
TCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGG |
8: 105,036,334 (GRCm39) |
|
probably null |
Het |
Cyp2c39 |
A |
T |
19: 39,525,261 (GRCm39) |
D188V |
probably damaging |
Het |
Dclk3 |
G |
T |
9: 111,268,405 (GRCm39) |
A25S |
probably benign |
Het |
Dpep2 |
A |
T |
8: 106,711,873 (GRCm39) |
M518K |
probably benign |
Het |
Dst |
T |
C |
1: 34,314,755 (GRCm39) |
V6462A |
probably damaging |
Het |
Entpd3 |
T |
C |
9: 120,391,104 (GRCm39) |
|
probably null |
Het |
Epm2aip1 |
T |
C |
9: 111,101,624 (GRCm39) |
V199A |
probably damaging |
Het |
Fam193b |
A |
G |
13: 55,689,504 (GRCm39) |
|
probably benign |
Het |
Fam50b |
G |
A |
13: 34,931,084 (GRCm39) |
E187K |
possibly damaging |
Het |
Fat1 |
A |
G |
8: 45,479,441 (GRCm39) |
D2829G |
probably damaging |
Het |
Fcgbp |
T |
A |
7: 27,806,781 (GRCm39) |
Y2250N |
probably damaging |
Het |
Grik5 |
C |
T |
7: 24,745,780 (GRCm39) |
R431Q |
possibly damaging |
Het |
H2-Aa |
C |
T |
17: 34,506,651 (GRCm39) |
|
probably null |
Het |
Igsf9 |
T |
A |
1: 172,324,730 (GRCm39) |
S883T |
possibly damaging |
Het |
Kcnh7 |
T |
G |
2: 62,618,248 (GRCm39) |
I414L |
probably damaging |
Het |
Kcnma1 |
T |
C |
14: 24,053,812 (GRCm39) |
|
probably null |
Het |
Kcnmb1 |
T |
C |
11: 33,914,686 (GRCm39) |
|
probably benign |
Het |
Kmt2d |
A |
G |
15: 98,747,340 (GRCm39) |
|
probably benign |
Het |
Krt9 |
TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC |
TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC |
11: 100,079,903 (GRCm39) |
|
probably benign |
Het |
Nucb1 |
A |
G |
7: 45,148,289 (GRCm39) |
F175L |
probably damaging |
Het |
Pax6 |
T |
A |
2: 105,516,268 (GRCm39) |
V182E |
probably benign |
Het |
Ptger1 |
A |
G |
8: 84,395,279 (GRCm39) |
D252G |
probably benign |
Het |
Rexo4 |
T |
C |
2: 26,850,283 (GRCm39) |
D275G |
probably damaging |
Het |
Ripk4 |
T |
C |
16: 97,547,236 (GRCm39) |
D342G |
probably damaging |
Het |
Rpl10l |
A |
T |
12: 66,330,987 (GRCm39) |
C49S |
possibly damaging |
Het |
Sema7a |
T |
C |
9: 57,867,619 (GRCm39) |
F457S |
probably damaging |
Het |
Shank3 |
G |
A |
15: 89,415,830 (GRCm39) |
D155N |
probably damaging |
Het |
Smpd3 |
G |
A |
8: 106,992,596 (GRCm39) |
|
probably benign |
Het |
Smpd4 |
T |
C |
16: 17,458,097 (GRCm39) |
V465A |
probably damaging |
Het |
Sohlh2 |
T |
C |
3: 55,115,107 (GRCm39) |
V364A |
probably damaging |
Het |
Sos2 |
C |
T |
12: 69,697,423 (GRCm39) |
R99Q |
probably damaging |
Het |
Spry2 |
G |
A |
14: 106,130,791 (GRCm39) |
Q132* |
probably null |
Het |
Tbx19 |
G |
T |
1: 164,967,709 (GRCm39) |
P346Q |
probably damaging |
Het |
Tdrd6 |
A |
G |
17: 43,938,106 (GRCm39) |
Y981H |
probably damaging |
Het |
Tinag |
T |
C |
9: 76,938,984 (GRCm39) |
K165E |
probably benign |
Het |
Tubb4a |
A |
T |
17: 57,387,904 (GRCm39) |
I374N |
probably damaging |
Het |
Umodl1 |
C |
T |
17: 31,205,528 (GRCm39) |
Q708* |
probably null |
Het |
Vmn2r3 |
A |
T |
3: 64,194,876 (GRCm39) |
V14E |
probably benign |
Het |
Zfp82 |
G |
A |
7: 29,755,712 (GRCm39) |
L457F |
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 |
|
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 |
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'- TGGTTCTGGAGGCTGGAAAC -3'
(R):5'- AGAAACTGGAGCTGCATTCTACC -3'
Sequencing Primer
(F):5'- AGGCTGGAAACGATGTTCTCC -3'
(R):5'- GGAGCTGCATTCTACCACCATTC -3'
|
Posted On |
2021-02-01 |