Incidental Mutation 'IGL01414:Nlgn3'
| ID |
80176 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Nlgn3
|
| Ensembl Gene |
ENSMUSG00000031302 |
| Gene Name |
neuroligin 3 |
| Synonyms |
A230085M13Rik, NL3, NLG3, HNL3 |
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
IGL01414
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
X |
| Chromosomal Location |
100342785-100364956 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 100345866 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 93
(I93V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000066304
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000065858]
[ENSMUST00000087948]
[ENSMUST00000087956]
[ENSMUST00000117203]
[ENSMUST00000117706]
[ENSMUST00000118111]
[ENSMUST00000151528]
[ENSMUST00000130555]
|
| AlphaFold |
Q8BYM5 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000065858
AA Change: I93V
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000066304
Gene: ENSMUSG00000031302
AA Change: I93V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:COesterase
|
16 |
601 |
2.3e-194 |
PFAM |
|
Pfam:Abhydrolase_3
|
180 |
342 |
1.7e-7 |
PFAM |
|
transmembrane domain
|
685 |
707 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000087948
|
| SMART Domains |
Protein: ENSMUSP00000085260
Gene: ENSMUSG00000079487
| Domain | Start | End | E-Value | Type |
|---|
|
Med12
|
101 |
161 |
2.98e-24 |
SMART |
|
low complexity region
|
273 |
282 |
N/A |
INTRINSIC |
|
Pfam:Med12-LCEWAV
|
287 |
758 |
1.5e-184 |
PFAM |
|
low complexity region
|
1220 |
1231 |
N/A |
INTRINSIC |
|
low complexity region
|
1245 |
1267 |
N/A |
INTRINSIC |
|
low complexity region
|
1394 |
1412 |
N/A |
INTRINSIC |
|
low complexity region
|
1469 |
1480 |
N/A |
INTRINSIC |
|
low complexity region
|
1732 |
1774 |
N/A |
INTRINSIC |
|
low complexity region
|
1780 |
1794 |
N/A |
INTRINSIC |
|
Pfam:Med12-PQL
|
1821 |
2024 |
1.2e-79 |
PFAM |
|
SCOP:d1bg1a1
|
2056 |
2129 |
3e-4 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000087956
|
| SMART Domains |
Protein: ENSMUSP00000085269
Gene: ENSMUSG00000079487
| Domain | Start | End | E-Value | Type |
|---|
|
Med12
|
101 |
161 |
2.98e-24 |
SMART |
|
low complexity region
|
273 |
282 |
N/A |
INTRINSIC |
|
Pfam:Med12-LCEWAV
|
286 |
758 |
1.8e-213 |
PFAM |
|
low complexity region
|
1220 |
1231 |
N/A |
INTRINSIC |
|
low complexity region
|
1245 |
1267 |
N/A |
INTRINSIC |
|
low complexity region
|
1394 |
1412 |
N/A |
INTRINSIC |
|
low complexity region
|
1469 |
1480 |
N/A |
INTRINSIC |
|
low complexity region
|
1732 |
1774 |
N/A |
INTRINSIC |
|
low complexity region
|
1780 |
1794 |
N/A |
INTRINSIC |
|
Pfam:Med12-PQL
|
1819 |
1970 |
1.5e-57 |
PFAM |
|
Pfam:Med12-PQL
|
1968 |
2004 |
5.7e-18 |
PFAM |
|
SCOP:d1bg1a1
|
2035 |
2108 |
4e-4 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000113671
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000117203
|
| SMART Domains |
Protein: ENSMUSP00000112729
Gene: ENSMUSG00000079487
| Domain | Start | End | E-Value | Type |
|---|
|
Med12
|
101 |
161 |
2.98e-24 |
SMART |
|
low complexity region
|
273 |
282 |
N/A |
INTRINSIC |
|
Pfam:Med12-LCEWAV
|
286 |
758 |
3.8e-214 |
PFAM |
|
low complexity region
|
1220 |
1231 |
N/A |
INTRINSIC |
|
low complexity region
|
1245 |
1267 |
N/A |
INTRINSIC |
|
low complexity region
|
1394 |
1412 |
N/A |
INTRINSIC |
|
low complexity region
|
1469 |
1480 |
N/A |
INTRINSIC |
|
low complexity region
|
1732 |
1774 |
N/A |
INTRINSIC |
|
low complexity region
|
1780 |
1794 |
N/A |
INTRINSIC |
|
Pfam:Med12-PQL
|
1819 |
2025 |
1.5e-100 |
PFAM |
|
SCOP:d1lsha3
|
2048 |
2107 |
4e-4 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000117706
|
| SMART Domains |
Protein: ENSMUSP00000112852
Gene: ENSMUSG00000079487
| Domain | Start | End | E-Value | Type |
|---|
|
Med12
|
101 |
161 |
2.98e-24 |
SMART |
|
low complexity region
|
273 |
282 |
N/A |
INTRINSIC |
|
Pfam:Med12-LCEWAV
|
286 |
758 |
3.7e-214 |
PFAM |
|
low complexity region
|
1220 |
1231 |
N/A |
INTRINSIC |
|
low complexity region
|
1245 |
1267 |
N/A |
INTRINSIC |
|
low complexity region
|
1394 |
1412 |
N/A |
INTRINSIC |
|
low complexity region
|
1469 |
1480 |
N/A |
INTRINSIC |
|
low complexity region
|
1732 |
1774 |
N/A |
INTRINSIC |
|
low complexity region
|
1780 |
1794 |
N/A |
INTRINSIC |
|
Pfam:Med12-PQL
|
1819 |
1966 |
7.5e-63 |
PFAM |
|
Pfam:Med12-PQL
|
1964 |
2000 |
1.1e-18 |
PFAM |
|
SCOP:d1lsha3
|
2023 |
2082 |
4e-4 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000118111
|
| SMART Domains |
Protein: ENSMUSP00000113863
Gene: ENSMUSG00000031302
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:COesterase
|
3 |
487 |
3.6e-161 |
PFAM |
|
Pfam:Abhydrolase_3
|
66 |
232 |
2.4e-7 |
PFAM |
|
transmembrane domain
|
571 |
593 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000151528
AA Change: I93V
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000123283
Gene: ENSMUSG00000031302
AA Change: I93V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:COesterase
|
16 |
621 |
3.4e-207 |
PFAM |
|
Pfam:Abhydrolase_3
|
200 |
363 |
1.2e-6 |
PFAM |
|
transmembrane domain
|
705 |
727 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000130555
AA Change: I93V
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000122213
Gene: ENSMUSG00000031302
AA Change: I93V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:COesterase
|
16 |
510 |
4.6e-179 |
PFAM |
|
Pfam:Abhydrolase_3
|
160 |
323 |
1.5e-7 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148846
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147443
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137664
|
| Coding Region Coverage |
|
| 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. Mutations in this gene may be associated with autism and Asperger syndrome. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Oct 2009]
PHENOTYPE: Homozygous null mice show impaired context and cued conditioning, hyperactivity, altered social behavior, less vocalization, smaller brains, and impaired olfaction. Males carrying a knock-in allele show impaired social interaction, and enhanced spatial learning and inhibitory synaptic transmission. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 26 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Agrn |
C |
T |
4: 156,279,696 (GRCm39) |
|
probably null |
Het |
| Arhgap45 |
T |
A |
10: 79,862,938 (GRCm39) |
S705T |
probably damaging |
Het |
| B4galt4 |
A |
G |
16: 38,578,153 (GRCm39) |
E200G |
probably damaging |
Het |
| Cdh12 |
A |
T |
15: 21,492,775 (GRCm39) |
N265Y |
probably damaging |
Het |
| Cerk |
T |
A |
15: 86,043,343 (GRCm39) |
T153S |
probably benign |
Het |
| Ect2 |
A |
T |
3: 27,181,878 (GRCm39) |
|
probably benign |
Het |
| Ep300 |
T |
A |
15: 81,511,467 (GRCm39) |
|
probably benign |
Het |
| Gm26920 |
T |
G |
7: 29,767,503 (GRCm39) |
|
probably benign |
Het |
| Ighv1-66 |
T |
C |
12: 115,556,929 (GRCm39) |
Y51C |
probably benign |
Het |
| Ints1 |
T |
C |
5: 139,744,253 (GRCm39) |
D1503G |
probably benign |
Het |
| Lhpp |
A |
G |
7: 132,244,249 (GRCm39) |
K189E |
probably damaging |
Het |
| Myh13 |
A |
G |
11: 67,233,298 (GRCm39) |
T606A |
probably benign |
Het |
| Naip1 |
T |
C |
13: 100,545,681 (GRCm39) |
|
probably null |
Het |
| Nckap5 |
G |
T |
1: 126,456,450 (GRCm39) |
Q38K |
probably damaging |
Het |
| Nxpe2 |
A |
G |
9: 48,231,923 (GRCm39) |
F345L |
probably benign |
Het |
| Pcdhb22 |
A |
G |
18: 37,652,549 (GRCm39) |
N339S |
probably damaging |
Het |
| Rbbp7 |
T |
A |
X: 161,557,577 (GRCm39) |
I322N |
probably damaging |
Het |
| Rigi |
C |
A |
4: 40,222,176 (GRCm39) |
V368F |
probably damaging |
Het |
| Rprd2 |
A |
T |
3: 95,672,837 (GRCm39) |
F855L |
probably damaging |
Het |
| Scin |
A |
T |
12: 40,174,698 (GRCm39) |
H128Q |
probably damaging |
Het |
| Sema4g |
A |
G |
19: 44,986,435 (GRCm39) |
Y337C |
probably damaging |
Het |
| Stx6 |
C |
T |
1: 155,077,691 (GRCm39) |
R233C |
possibly damaging |
Het |
| Supt16 |
C |
T |
14: 52,414,489 (GRCm39) |
E438K |
probably benign |
Het |
| Trem3 |
G |
T |
17: 48,556,843 (GRCm39) |
V105L |
probably benign |
Het |
| Vmn2r108 |
T |
A |
17: 20,691,942 (GRCm39) |
M194L |
probably benign |
Het |
| Zfyve16 |
A |
T |
13: 92,658,704 (GRCm39) |
D402E |
probably benign |
Het |
|
| Other mutations in Nlgn3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01128:Nlgn3
|
APN |
X |
100,363,698 (GRCm39) |
missense |
probably benign |
0.28 |
|
IGL01327:Nlgn3
|
APN |
X |
100,362,228 (GRCm39) |
missense |
probably benign |
0.08 |
|
R1296:Nlgn3
|
UTSW |
X |
100,352,522 (GRCm39) |
splice site |
probably benign |
|
|
R1794:Nlgn3
|
UTSW |
X |
100,363,639 (GRCm39) |
missense |
probably benign |
0.30 |
|
R5144:Nlgn3
|
UTSW |
X |
100,361,891 (GRCm39) |
missense |
probably benign |
0.21 |
|
R5145:Nlgn3
|
UTSW |
X |
100,361,891 (GRCm39) |
missense |
probably benign |
0.21 |
|
R5146:Nlgn3
|
UTSW |
X |
100,361,891 (GRCm39) |
missense |
probably benign |
0.21 |
|
R8677:Nlgn3
|
UTSW |
X |
100,352,390 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8678:Nlgn3
|
UTSW |
X |
100,352,390 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8684:Nlgn3
|
UTSW |
X |
100,363,425 (GRCm39) |
nonsense |
probably null |
|
|
R8696:Nlgn3
|
UTSW |
X |
100,352,390 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8905:Nlgn3
|
UTSW |
X |
100,352,390 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8906:Nlgn3
|
UTSW |
X |
100,352,390 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9231:Nlgn3
|
UTSW |
X |
100,352,390 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9232:Nlgn3
|
UTSW |
X |
100,352,390 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9234:Nlgn3
|
UTSW |
X |
100,352,390 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9235:Nlgn3
|
UTSW |
X |
100,352,390 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9236:Nlgn3
|
UTSW |
X |
100,352,390 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9253:Nlgn3
|
UTSW |
X |
100,352,390 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Nlgn3
|
UTSW |
X |
100,363,483 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Nlgn3
|
UTSW |
X |
100,361,588 (GRCm39) |
missense |
probably benign |
0.30 |
|
| Posted On |
2013-11-05 |
Incidental Mutation