Incidental Mutation 'R1794:Nlgn3'
ID 202091
Institutional Source Beutler Lab
Gene Symbol Nlgn3
Ensembl Gene ENSMUSG00000031302
Gene Name neuroligin 3
Synonyms A230085M13Rik, NL3, NLG3, HNL3
MMRRC Submission 039824-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1794 (G1)
Quality Score 222
Status Not validated
Chromosome X
Chromosomal Location 100342785-100364956 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 100363639 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Arginine at position 636 (H636R)
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: H750R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000066304
Gene: ENSMUSG00000031302
AA Change: H750R

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: H636R

PolyPhen 2 Score 0.298 (Sensitivity: 0.91; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000113863
Gene: ENSMUSG00000031302
AA Change: H636R

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
SMART Domains Protein: ENSMUSP00000122213
Gene: ENSMUSG00000031302

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: H770R

PolyPhen 2 Score 0.203 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000123283
Gene: ENSMUSG00000031302
AA Change: H770R

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
  • 1x: 97.4%
  • 3x: 96.7%
  • 10x: 94.8%
  • 20x: 91.1%
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Anxa7 A G 14: 20,521,535 (GRCm39) Y54H unknown Het
Arhgef3 A G 14: 27,119,562 (GRCm39) T331A probably benign Het
Arhgef40 G T 14: 52,227,387 (GRCm39) C477F possibly damaging Het
Arsi G A 18: 61,049,723 (GRCm39) G202E probably benign Het
Atp13a5 C A 16: 29,140,527 (GRCm39) R343L probably damaging Het
Brdt ACAGCAGCAGCAGCAGC ACAGCAGCAGCAGC 5: 107,507,719 (GRCm39) probably benign Het
Btbd2 G T 10: 80,479,747 (GRCm39) D426E probably damaging Het
Cabin1 A C 10: 75,561,579 (GRCm39) I974R possibly damaging Het
Cacna1i G A 15: 80,273,323 (GRCm39) V1670M probably damaging Het
Cc2d2a C A 5: 43,845,594 (GRCm39) Q288K probably damaging Het
Ccl20 T A 1: 83,095,550 (GRCm39) I37K possibly damaging Het
Cdcp1 A G 9: 123,019,159 (GRCm39) V40A probably benign Het
Cdcp1 T C 9: 123,044,896 (GRCm39) T27A probably benign Het
Cdh4 C T 2: 179,528,635 (GRCm39) T581I probably damaging Het
Cgn A G 3: 94,669,864 (GRCm39) probably null Het
Col7a1 G A 9: 108,794,996 (GRCm39) G1493D unknown Het
Creb3 A G 4: 43,563,302 (GRCm39) E133G probably benign Het
Dchs1 T C 7: 105,420,927 (GRCm39) T498A probably benign Het
Dis3l A C 9: 64,225,058 (GRCm39) V413G possibly damaging Het
Dnah6 T C 6: 73,001,941 (GRCm39) E3865G probably damaging Het
Fam219b A G 9: 57,446,564 (GRCm39) Y139C probably damaging Het
Fat3 A T 9: 15,908,432 (GRCm39) Y2523* probably null Het
Fat3 A T 9: 15,908,434 (GRCm39) Y2523N probably benign Het
Fmnl1 T C 11: 103,087,973 (GRCm39) S40P probably benign Het
Gm4792 T C 10: 94,134,352 (GRCm39) D6G unknown Het
Hhat G T 1: 192,376,214 (GRCm39) Y306* probably null Het
Hmcn1 A G 1: 150,474,036 (GRCm39) I4802T probably benign Het
Hmcn1 G A 1: 150,502,903 (GRCm39) T3908I probably damaging Het
Hsph1 A T 5: 149,554,238 (GRCm39) N79K probably damaging Het
Ikbke T A 1: 131,186,955 (GRCm39) Y579F probably damaging Het
Jak2 A G 19: 29,276,957 (GRCm39) D838G probably benign Het
Klhdc7b T C 15: 89,271,223 (GRCm39) S702P probably benign Het
Lingo3 C A 10: 80,671,432 (GRCm39) R166L probably benign Het
Lins1 T C 7: 66,361,657 (GRCm39) F436S probably damaging Het
Lman1 T C 18: 66,124,755 (GRCm39) D328G probably benign Het
Lox A G 18: 52,661,379 (GRCm39) C232R probably damaging Het
Lrrc59 T C 11: 94,529,421 (GRCm39) V165A probably benign Het
Map9 A G 3: 82,287,528 (GRCm39) D50G probably damaging Het
Marchf1 T A 8: 66,839,594 (GRCm39) Y126N possibly damaging Het
Mcf2l T C 8: 12,965,982 (GRCm39) F3L probably benign Het
Mslnl G A 17: 25,961,908 (GRCm39) V128M probably damaging Het
Nin G A 12: 70,090,569 (GRCm39) Q949* probably null Het
Notch2 A G 3: 98,006,863 (GRCm39) D411G possibly damaging Het
Or4c52 A G 2: 89,845,364 (GRCm39) Y30C probably damaging Het
Or5b24 G C 19: 12,912,332 (GRCm39) A77P probably damaging Het
Pate7 T A 9: 35,688,418 (GRCm39) I56F probably benign Het
Plekha7 A G 7: 115,739,916 (GRCm39) V579A probably damaging Het
Prrc2c T C 1: 162,533,528 (GRCm39) probably benign Het
Rab7b T C 1: 131,624,806 (GRCm39) probably null Het
Reg3b G T 6: 78,349,197 (GRCm39) probably null Het
Rgs20 A G 1: 4,980,795 (GRCm39) Y177H probably damaging Het
Ripk3 G T 14: 56,022,786 (GRCm39) N379K probably benign Het
Rnf220 G T 4: 117,164,765 (GRCm39) Q7K probably benign Het
Ros1 T A 10: 52,000,199 (GRCm39) K1109* probably null Het
Slc22a7 T G 17: 46,744,079 (GRCm39) R460S probably damaging Het
Slc4a2 A G 5: 24,644,326 (GRCm39) M975V probably damaging Het
Slc4a3 A T 1: 75,533,952 (GRCm39) I1100F probably damaging Het
Smco1 A G 16: 32,092,950 (GRCm39) E207G probably benign Het
Snrnp200 A G 2: 127,058,656 (GRCm39) E369G probably benign Het
Spata31d1e T C 13: 59,890,434 (GRCm39) E44G probably benign Het
Tcf4 T A 18: 69,790,924 (GRCm39) M178K probably benign Het
Tex2 T C 11: 106,458,728 (GRCm39) probably benign Het
Tjp1 A T 7: 64,972,877 (GRCm39) I521N probably damaging Het
Tmem203 A G 2: 25,146,006 (GRCm39) T109A probably benign Het
Tmem50b T C 16: 91,374,917 (GRCm39) I126V probably benign Het
Ugcg C T 4: 59,207,798 (GRCm39) P46S probably benign Het
Ush2a T C 1: 188,595,006 (GRCm39) F3813L probably benign Het
Vmn1r203 C T 13: 22,708,521 (GRCm39) R101W probably damaging Het
Vmn2r79 G A 7: 86,650,621 (GRCm39) V136I probably benign Het
Wdr38 A G 2: 38,890,741 (GRCm39) Y205C probably damaging Het
Zfp248 A G 6: 118,406,264 (GRCm39) F442L probably damaging Het
Znrf4 A G 17: 56,818,599 (GRCm39) I236T probably damaging Het
Other mutations in Nlgn3
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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
Predicted Primers PCR Primer
(F):5'- CTGAATTAAGTGTCACTATCGCTG -3'
(R):5'- AGCCCAGTACTGTTGAACCC -3'

Sequencing Primer
(F):5'- TCACTATCGCTGTGGGGGC -3'
(R):5'- CCCTGCGGCAAAGGTGTTATAG -3'
Posted On 2014-06-23