Incidental Mutation 'R1952:Nlgn1'
ID 217359
Institutional Source Beutler Lab
Gene Symbol Nlgn1
Ensembl Gene ENSMUSG00000063887
Gene Name neuroligin 1
Synonyms NL1, Nlg1, 6330415N05Rik
MMRRC Submission 039966-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1952 (G1)
Quality Score 225
Status Not validated
Chromosome 3
Chromosomal Location 25480379-26386609 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 25490464 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Valine at position 421 (D421V)
Ref Sequence ENSEMBL: ENSMUSP00000142200 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000075054] [ENSMUST00000108308] [ENSMUST00000191835] [ENSMUST00000193603]
AlphaFold Q99K10
PDB Structure Crystal structure of a synaptic adhesion complex [X-RAY DIFFRACTION]
Predicted Effect probably damaging
Transcript: ENSMUST00000075054
AA Change: D421V

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: D421V

DomainStartEndE-ValueType
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 possibly damaging
Transcript: ENSMUST00000108308
AA Change: D392V

PolyPhen 2 Score 0.453 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: D392V

DomainStartEndE-ValueType
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 possibly damaging
Transcript: ENSMUST00000191835
AA Change: D392V

PolyPhen 2 Score 0.453 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: D392V

DomainStartEndE-ValueType
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 damaging
Transcript: ENSMUST00000193603
AA Change: D421V

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: D421V

DomainStartEndE-ValueType
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
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.9%
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. [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: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700024G13Rik A G 14: 32,110,293 (GRCm39) V6A possibly damaging Het
Accsl G T 2: 93,689,778 (GRCm39) H376Q probably damaging Het
Adgrg1 T C 8: 95,735,119 (GRCm39) probably null Het
Alyref C G 11: 120,486,758 (GRCm39) V168L probably damaging Het
Ankrd12 T C 17: 66,338,566 (GRCm39) D128G probably damaging Het
Bcl2l14 A G 6: 134,409,329 (GRCm39) Y301C probably damaging Het
Camsap3 A G 8: 3,654,789 (GRCm39) T804A probably damaging Het
Capn11 A T 17: 45,953,885 (GRCm39) W154R probably damaging Het
Cd44 T A 2: 102,683,432 (GRCm39) T201S probably damaging Het
Cers4 G A 8: 4,573,461 (GRCm39) W319* probably null Het
Col27a1 T A 4: 63,202,130 (GRCm39) probably null Het
Crnkl1 G A 2: 145,770,120 (GRCm39) A241V probably damaging Het
Cyp2c68 T C 19: 39,700,972 (GRCm39) Y282C probably benign Het
Dmd T A X: 82,874,123 (GRCm39) I1342N probably damaging Het
Dusp7 T A 9: 106,248,028 (GRCm39) C219S probably benign Het
Epha7 A G 4: 28,950,474 (GRCm39) N759S probably damaging Het
Fat1 T C 8: 45,486,963 (GRCm39) V3413A probably benign Het
Gls2 A G 10: 128,045,231 (GRCm39) H576R probably benign Het
Gm4884 G A 7: 40,693,671 (GRCm39) V547M probably benign Het
Hap1 A G 11: 100,243,105 (GRCm39) V174A probably damaging Het
Il12rb2 A G 6: 67,269,300 (GRCm39) S838P probably damaging Het
Ints8 T C 4: 11,221,150 (GRCm39) I742V probably benign Het
Katnal2 G T 18: 77,067,707 (GRCm39) S411R probably benign Het
Lrp1 A C 10: 127,403,300 (GRCm39) V2091G probably damaging Het
Mettl21c A T 1: 44,056,368 (GRCm39) D20E probably damaging Het
Mib1 A T 18: 10,812,077 (GRCm39) E991D possibly damaging Het
Mip T C 10: 128,061,772 (GRCm39) S8P possibly damaging Het
Mllt6 T C 11: 97,568,048 (GRCm39) S826P probably damaging Het
Mlst8 AT ATT 17: 24,696,987 (GRCm39) probably null Het
Myrfl C T 10: 116,658,716 (GRCm39) V414I probably benign Het
Nbeal1 T C 1: 60,273,999 (GRCm39) V409A probably damaging Het
Nin T A 12: 70,077,700 (GRCm39) Q1035L probably damaging Het
Nlrp10 A G 7: 108,523,770 (GRCm39) V570A probably benign Het
Olfm3 A T 3: 114,895,589 (GRCm39) E157V probably null Het
Or8g24 T A 9: 38,989,580 (GRCm39) I154F probably benign Het
Or8g37 T C 9: 39,731,363 (GRCm39) S143P probably benign Het
Otud7a A G 7: 63,300,624 (GRCm39) D21G probably damaging Het
Pax2 A G 19: 44,777,271 (GRCm39) T155A probably benign Het
Pcf11 A T 7: 92,310,546 (GRCm39) S481T probably damaging Het
Prkab2 T C 3: 97,573,943 (GRCm39) V194A probably benign Het
Prl3a1 G A 13: 27,454,136 (GRCm39) G38E possibly damaging Het
Psmb8 T C 17: 34,419,884 (GRCm39) V246A probably damaging Het
Ptpn12 A T 5: 21,203,308 (GRCm39) V490E probably benign Het
Ptprm A T 17: 67,247,575 (GRCm39) S587T probably benign Het
Qars1 G A 9: 108,390,380 (GRCm39) R427H probably benign Het
R3hdml T C 2: 163,340,216 (GRCm39) F128L probably benign Het
Rapgef4 A G 2: 72,038,471 (GRCm39) M541V probably benign Het
Rhbdf1 G A 11: 32,164,277 (GRCm39) R234* probably null Het
Rufy1 A T 11: 50,297,233 (GRCm39) D406E probably benign Het
Satb1 A T 17: 52,047,173 (GRCm39) L683Q probably damaging Het
Satb2 T C 1: 56,938,229 (GRCm39) T132A probably damaging Het
Sbspon A G 1: 15,930,519 (GRCm39) S156P probably damaging Het
Shb A T 4: 45,458,347 (GRCm39) probably null Het
She A G 3: 89,756,792 (GRCm39) K282R possibly damaging Het
Slc25a13 A G 6: 6,152,482 (GRCm39) L85P probably damaging Het
Slc7a13 A T 4: 19,841,578 (GRCm39) H475L probably benign Het
Sorl1 C T 9: 41,957,920 (GRCm39) V575I probably benign Het
Spag9 T A 11: 93,988,184 (GRCm39) C833S possibly damaging Het
Speer2 A C 16: 69,654,052 (GRCm39) N232K probably damaging Het
Syncrip A T 9: 88,358,927 (GRCm39) M194K probably damaging Het
Sytl3 A C 17: 6,995,732 (GRCm39) T171P probably damaging Het
Taar7f T A 10: 23,925,747 (GRCm39) Y114N probably damaging Het
Tamalin T C 15: 101,122,381 (GRCm39) Y67H probably benign Het
Tap1 C G 17: 34,412,481 (GRCm39) P506R probably damaging Het
Tle6 T C 10: 81,431,319 (GRCm39) D212G possibly damaging Het
Trim80 G T 11: 115,332,155 (GRCm39) E116* probably null Het
Ttll4 A G 1: 74,726,718 (GRCm39) R745G probably damaging Het
Vdac2 A T 14: 21,887,947 (GRCm39) I85F possibly damaging Het
Vmn1r188 A G 13: 22,272,309 (GRCm39) R88G probably damaging Het
Washc2 T C 6: 116,232,052 (GRCm39) S821P possibly damaging Het
Wdhd1 T C 14: 47,507,647 (GRCm39) Y213C probably damaging Het
Wdr55 C A 18: 36,893,437 (GRCm39) P33Q probably damaging Het
Yrdc C T 4: 124,745,739 (GRCm39) A32V probably benign Het
Zfp608 T A 18: 55,030,851 (GRCm39) K1030* probably null Het
Zfp618 T A 4: 63,050,555 (GRCm39) probably null Het
Other mutations in Nlgn1
AlleleSourceChrCoordTypePredicted EffectPPH 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
G1citation:Nlgn1 UTSW 3 26,187,796 (GRCm39) missense probably benign 0.00
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
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'- CTACCCATTGATGGTCCGTAAAC -3'
(R):5'- TGCCTGCAGAAGAAGCCTTAC -3'

Sequencing Primer
(F):5'- TTGATGGTCCGTAAACAAAGCC -3'
(R):5'- GAAGCCTTACAAAGAACTTGTTGATC -3'
Posted On 2014-08-01