Incidental Mutation 'IGL01327:Nlgn3'
ID 74327
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) question?
Stock # IGL01327
Quality Score
Status
Chromosome X
Chromosomal Location 100342785-100364956 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 100362228 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 399 (V399A)
Ref Sequence ENSEMBL: ENSMUSP00000113863 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000065858] [ENSMUST00000118111] [ENSMUST00000130555] [ENSMUST00000151528]
AlphaFold Q8BYM5
Predicted Effect probably benign
Transcript: ENSMUST00000065858
AA Change: V513A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000066304
Gene: ENSMUSG00000031302
AA Change: V513A

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 noncoding transcript
Transcript: ENSMUST00000113671
Predicted Effect probably benign
Transcript: ENSMUST00000118111
AA Change: V399A

PolyPhen 2 Score 0.077 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000113863
Gene: ENSMUSG00000031302
AA Change: V399A

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: V493A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000122213
Gene: ENSMUSG00000031302
AA Change: V493A

DomainStartEndE-ValueType
Pfam:COesterase 16 510 4.6e-179 PFAM
Pfam:Abhydrolase_3 160 323 1.5e-7 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144860
Predicted Effect probably benign
Transcript: ENSMUST00000151528
AA Change: V533A

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000123283
Gene: ENSMUSG00000031302
AA Change: V533A

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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2510039O18Rik T A 4: 148,029,521 (GRCm39) V497E probably damaging Het
Adcy7 T G 8: 89,045,418 (GRCm39) probably benign Het
Aldh1a2 T A 9: 71,193,248 (GRCm39) F486I possibly damaging Het
Alox12 T A 11: 70,145,375 (GRCm39) H66L probably benign Het
Apoh T G 11: 108,288,187 (GRCm39) Y102D probably damaging Het
Arl9 T C 5: 77,154,401 (GRCm39) V43A possibly damaging Het
Atf6 A G 1: 170,616,175 (GRCm39) probably null Het
Atp4a T A 7: 30,412,675 (GRCm39) I127N possibly damaging Het
AY358078 T A 14: 52,043,166 (GRCm39) probably benign Het
Baat T G 4: 49,490,338 (GRCm39) K249Q probably damaging Het
Brat1 C T 5: 140,703,963 (GRCm39) Q739* probably null Het
C8g A G 2: 25,389,089 (GRCm39) F165L probably damaging Het
Cel T G 2: 28,447,967 (GRCm39) D353A possibly damaging Het
Col6a1 G T 10: 76,546,813 (GRCm39) T803K unknown Het
Cpxm1 A G 2: 130,238,277 (GRCm39) L95P probably benign Het
Ctsr A G 13: 61,310,489 (GRCm39) probably benign Het
Cyth1 A G 11: 118,084,439 (GRCm39) probably null Het
Dync1h1 A T 12: 110,583,126 (GRCm39) probably benign Het
Ezh1 C T 11: 101,094,262 (GRCm39) C407Y probably damaging Het
Fam243 T C 16: 92,117,661 (GRCm39) Y209C probably benign Het
Gm3696 A T 14: 18,435,903 (GRCm39) W38R probably benign Het
Gm9611 T C 14: 42,116,622 (GRCm39) T39A possibly damaging Het
Gnpat T A 8: 125,605,372 (GRCm39) L287H probably damaging Het
Golm1 G T 13: 59,792,958 (GRCm39) N182K possibly damaging Het
Hdac6 T C X: 7,798,013 (GRCm39) M899V probably benign Het
Hsf3 T A X: 95,358,578 (GRCm39) M272L probably benign Het
Kif19a C T 11: 114,672,625 (GRCm39) probably benign Het
Lcn2 T G 2: 32,276,030 (GRCm39) Y100S possibly damaging Het
Lrrc8d T A 5: 105,960,131 (GRCm39) S180R probably damaging Het
Ly6h A G 15: 75,436,948 (GRCm39) probably benign Het
Macf1 T C 4: 123,403,705 (GRCm39) N705D probably benign Het
Mst1r C T 9: 107,785,043 (GRCm39) P234S probably benign Het
Msto1 T A 3: 88,817,939 (GRCm39) probably null Het
Myo5a T A 9: 75,094,820 (GRCm39) probably benign Het
Nipa1 T C 7: 55,629,409 (GRCm39) I235V probably benign Het
Or1d2 T A 11: 74,255,738 (GRCm39) M81K possibly damaging Het
Or2b28 A G 13: 21,531,377 (GRCm39) N93S probably benign Het
Pih1d1 T C 7: 44,809,399 (GRCm39) S289P probably benign Het
Ppl T C 16: 4,905,508 (GRCm39) N1596D probably benign Het
Psmb6 T A 11: 70,417,412 (GRCm39) S114R possibly damaging Het
Pum1 C A 4: 130,457,854 (GRCm39) Q289K probably damaging Het
Shkbp1 T C 7: 27,054,676 (GRCm39) I75V probably benign Het
Slc24a3 T A 2: 145,444,478 (GRCm39) I284N probably benign Het
Slc44a3 C T 3: 121,320,842 (GRCm39) G53D probably damaging Het
Slc9a4 A C 1: 40,668,565 (GRCm39) D736A probably benign Het
Stra6 A G 9: 58,059,854 (GRCm39) D605G probably benign Het
Tas2r126 T A 6: 42,411,684 (GRCm39) H72Q probably benign Het
Tbrg1 C T 9: 37,564,408 (GRCm39) R166Q probably benign Het
Thumpd1 C T 7: 119,319,925 (GRCm39) G14R probably benign Het
Ticrr C T 7: 79,344,209 (GRCm39) T1358I probably benign Het
Tmtc2 A T 10: 105,184,340 (GRCm39) N518K probably benign Het
Trpm4 C A 7: 44,964,497 (GRCm39) W533C probably damaging Het
Tsen54 T C 11: 115,712,538 (GRCm39) Y119H possibly damaging Het
Tulp3 G A 6: 128,304,597 (GRCm39) T219M probably damaging Het
Usp19 T C 9: 108,376,160 (GRCm39) L1000S possibly damaging Het
Vps16 A T 2: 130,279,616 (GRCm39) Y43F probably benign Het
Vsig1 T A X: 139,838,429 (GRCm39) V283E possibly damaging Het
Other mutations in Nlgn3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01128:Nlgn3 APN X 100,363,698 (GRCm39) missense probably benign 0.28
IGL01414:Nlgn3 APN X 100,345,866 (GRCm39) missense probably benign 0.00
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 2013-10-07