Incidental Mutation 'IGL01414:Nlgn3'
ID80176
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Nlgn3
Ensembl Gene ENSMUSG00000031302
Gene Nameneuroligin 3
SynonymsNL3, A230085M13Rik, HNL3
Accession Numbers
Is this an essential gene? Non essential (E-score: 0.000) question?
Stock #IGL01414
Quality Score
Status
ChromosomeX
Chromosomal Location101299168-101325963 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to G at 101302260 bp
ZygosityHeterozygous
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] [ENSMUST00000130555] [ENSMUST00000151528]
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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: ENSMUST00000130555
AA Change: I93V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000122213
Gene: ENSMUSG00000031302
AA Change: I93V

DomainStartEndE-ValueType
Pfam:COesterase 16 510 4.6e-179 PFAM
Pfam:Abhydrolase_3 160 323 1.5e-7 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137664
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147443
Predicted Effect noncoding transcript
Transcript: ENSMUST00000148846
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

DomainStartEndE-ValueType
Pfam:COesterase 16 621 3.4e-207 PFAM
Pfam:Abhydrolase_3 200 363 1.2e-6 PFAM
transmembrane domain 705 727 N/A INTRINSIC
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
Agrn C T 4: 156,195,239 probably null Het
Arhgap45 T A 10: 80,027,104 S705T probably damaging Het
B4galt4 A G 16: 38,757,791 E200G probably damaging Het
Cdh12 A T 15: 21,492,689 N265Y probably damaging Het
Cerk T A 15: 86,159,142 T153S probably benign Het
Ddx58 C A 4: 40,222,176 V368F probably damaging Het
Ect2 A T 3: 27,127,729 probably benign Het
Ep300 T A 15: 81,627,266 probably benign Het
Gm26920 T G 7: 30,068,078 probably benign Het
Ighv1-66 T C 12: 115,593,309 Y51C probably benign Het
Ints1 T C 5: 139,758,498 D1503G probably benign Het
Lhpp A G 7: 132,642,520 K189E probably damaging Het
Myh13 A G 11: 67,342,472 T606A probably benign Het
Naip1 T C 13: 100,409,173 probably null Het
Nckap5 G T 1: 126,528,713 Q38K probably damaging Het
Nxpe2 A G 9: 48,320,623 F345L probably benign Het
Pcdhb22 A G 18: 37,519,496 N339S probably damaging Het
Rbbp7 T A X: 162,774,581 I322N probably damaging Het
Rprd2 A T 3: 95,765,525 F855L probably damaging Het
Scin A T 12: 40,124,699 H128Q probably damaging Het
Sema4g A G 19: 44,997,996 Y337C probably damaging Het
Stx6 C T 1: 155,201,945 R233C possibly damaging Het
Supt16 C T 14: 52,177,032 E438K probably benign Het
Trem3 G T 17: 48,249,815 V105L probably benign Het
Vmn2r108 T A 17: 20,471,680 M194L probably benign Het
Zfyve16 A T 13: 92,522,196 D402E probably benign Het
Other mutations in Nlgn3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01128:Nlgn3 APN X 101320092 missense probably benign 0.28
IGL01327:Nlgn3 APN X 101318622 missense probably benign 0.08
R1296:Nlgn3 UTSW X 101308916 splice site probably benign
R1794:Nlgn3 UTSW X 101320033 missense probably benign 0.30
R5144:Nlgn3 UTSW X 101318285 missense probably benign 0.21
R5145:Nlgn3 UTSW X 101318285 missense probably benign 0.21
R5146:Nlgn3 UTSW X 101318285 missense probably benign 0.21
R8677:Nlgn3 UTSW X 101308784 missense probably damaging 1.00
R8678:Nlgn3 UTSW X 101308784 missense probably damaging 1.00
R8684:Nlgn3 UTSW X 101319819 nonsense probably null
R8696:Nlgn3 UTSW X 101308784 missense probably damaging 1.00
Z1176:Nlgn3 UTSW X 101317982 missense probably benign 0.30
Z1176:Nlgn3 UTSW X 101319877 missense probably damaging 1.00
Posted On2013-11-05