Incidental Mutation 'R9209:Nlgn1'
ID 698686
Institutional Source Beutler Lab
Gene Symbol Nlgn1
Ensembl Gene ENSMUSG00000063887
Gene Name neuroligin 1
Synonyms NL1, Nlg1, 6330415N05Rik
MMRRC Submission
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R9209 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 25480379-26386609 bp(-) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) A to G at 25966804 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000142200 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000075054] [ENSMUST00000108308] [ENSMUST00000191835] [ENSMUST00000193603] [ENSMUST00000193603] [ENSMUST00000193603]
AlphaFold Q99K10
PDB Structure Crystal structure of a synaptic adhesion complex [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000075054
SMART Domains Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887

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 probably benign
Transcript: ENSMUST00000108308
SMART Domains Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887

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 benign
Transcript: ENSMUST00000191835
SMART Domains Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887

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 null
Transcript: ENSMUST00000193603
SMART Domains Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887

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
Predicted Effect probably null
Transcript: ENSMUST00000193603
SMART Domains Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887

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
Predicted Effect probably null
Transcript: ENSMUST00000193603
SMART Domains Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887

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: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
Validation Efficiency 96% (73/76)
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: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610021A01Rik T A 7: 41,275,837 (GRCm39) N513K possibly damaging Het
Actl6a T A 3: 32,779,469 (GRCm39) I399N probably damaging Het
Adamts5 A G 16: 85,666,971 (GRCm39) V507A probably damaging Het
Ap3d1 A G 10: 80,554,918 (GRCm39) V469A probably benign Het
Arhgef4 G T 1: 34,764,241 (GRCm39) probably null Het
Arhgef4 A T 1: 34,849,576 (GRCm39) Q389L probably benign Het
Atad2 A G 15: 57,980,194 (GRCm39) V106A possibly damaging Het
Azin2 T C 4: 128,841,341 (GRCm39) E275G probably damaging Het
Bhlhe23 A G 2: 180,418,143 (GRCm39) S132P probably damaging Het
Capn12 A G 7: 28,581,243 (GRCm39) Y32C probably damaging Het
Celsr2 A T 3: 108,321,349 (GRCm39) S488T probably benign Het
Cenpx A G 11: 120,602,582 (GRCm39) V27A possibly damaging Het
Clca3a2 G A 3: 144,778,005 (GRCm39) P760L probably benign Het
Clstn3 T C 6: 124,408,571 (GRCm39) S951G probably benign Het
Clybl C A 14: 122,621,670 (GRCm39) P286Q probably benign Het
Cmya5 T A 13: 93,226,866 (GRCm39) M2741L probably benign Het
Cntnap2 G A 6: 47,026,183 (GRCm39) G944E probably damaging Het
Col8a1 A C 16: 57,447,283 (GRCm39) Y742* probably null Het
Crb1 T C 1: 139,171,051 (GRCm39) K780E probably damaging Het
Crygc T A 1: 65,112,376 (GRCm39) Y66F probably benign Het
Cyp2b9 G A 7: 25,873,004 (GRCm39) G49E possibly damaging Het
D130043K22Rik T C 13: 25,041,090 (GRCm39) S171P possibly damaging Het
Dhx36 T C 3: 62,378,895 (GRCm39) I890V probably benign Het
Dpp9 C T 17: 56,512,765 (GRCm39) G148S probably damaging Het
Eml6 G T 11: 29,781,175 (GRCm39) S619Y probably damaging Het
Enpp4 A T 17: 44,412,252 (GRCm39) L319* probably null Het
Esyt1 T C 10: 128,361,356 (GRCm39) S113G probably benign Het
Fat1 A G 8: 45,404,791 (GRCm39) D514G possibly damaging Het
Fbxo16 G A 14: 65,524,594 (GRCm39) R38Q probably damaging Het
Fchsd1 A T 18: 38,092,706 (GRCm39) M668K unknown Het
Gpr149 C T 3: 62,511,093 (GRCm39) S302N probably benign Het
Gsap A G 5: 21,433,064 (GRCm39) K258E probably benign Het
Helq C A 5: 100,939,218 (GRCm39) V443F probably benign Het
Helq T A 5: 100,939,219 (GRCm39) K442N probably damaging Het
Ighv1-37 T C 12: 114,860,123 (GRCm39) E29G possibly damaging Het
Ighv1-9 C A 12: 114,547,620 (GRCm39) M1I probably null Het
Itga6 T G 2: 71,671,477 (GRCm39) F743V probably benign Het
Lpin1 C A 12: 16,588,548 (GRCm39) D881Y Het
Lypd8 T A 11: 58,273,640 (GRCm39) C40S possibly damaging Het
Macf1 C T 4: 123,326,227 (GRCm39) R5092Q probably damaging Het
Mcm7 A G 5: 138,166,593 (GRCm39) probably null Het
Micall2 G A 5: 139,696,170 (GRCm39) T831I unknown Het
Myo18b A T 5: 113,022,927 (GRCm39) M155K unknown Het
Nckap5 T A 1: 125,867,928 (GRCm39) H201L unknown Het
Ndst2 A T 14: 20,779,240 (GRCm39) D333E possibly damaging Het
Nup188 T G 2: 30,232,397 (GRCm39) Y1483D probably benign Het
Or4c109 A C 2: 88,818,057 (GRCm39) L163* probably null Het
Or52ae9 T A 7: 103,390,319 (GRCm39) S43C probably benign Het
Or52n4b A C 7: 108,144,664 (GRCm39) I311L probably benign Het
Or5p66 T A 7: 107,885,526 (GRCm39) Y269F probably benign Het
Or8g33 T A 9: 39,337,635 (GRCm39) H244L probably damaging Het
Peg3 A C 7: 6,711,226 (GRCm39) I1332S possibly damaging Het
Piezo2 T C 18: 63,154,372 (GRCm39) K2469R probably damaging Het
Pik3cg T C 12: 32,247,312 (GRCm39) M804V probably damaging Het
Polq A T 16: 36,869,011 (GRCm39) I794F possibly damaging Het
Rasgef1b A G 5: 99,370,191 (GRCm39) V437A probably benign Het
Rdm1 T A 11: 101,518,857 (GRCm39) D21E probably benign Het
Ripk4 G T 16: 97,551,311 (GRCm39) Q219K possibly damaging Het
Ropn1l T C 15: 31,441,471 (GRCm39) I217V Het
Sdf2 T C 11: 78,136,858 (GRCm39) S13P unknown Het
Selenbp1 A G 3: 94,847,079 (GRCm39) T202A probably benign Het
Slfn5 T C 11: 82,850,933 (GRCm39) F410S possibly damaging Het
Srrm2 A G 17: 24,039,880 (GRCm39) T2175A probably benign Het
St6galnac3 T C 3: 153,117,360 (GRCm39) Y121C possibly damaging Het
Stat1 A G 1: 52,184,337 (GRCm39) N417S probably benign Het
Tead1 T C 7: 112,475,378 (GRCm39) F276L probably damaging Het
Teddm3 A T 16: 20,971,737 (GRCm39) S277R probably benign Het
Tmc2 A G 2: 130,103,317 (GRCm39) probably null Het
Tmem156 G A 5: 65,231,127 (GRCm39) L248F probably damaging Het
Tnn T C 1: 159,953,986 (GRCm39) S590G probably benign Het
Trmt44 A G 5: 35,731,422 (GRCm39) probably null Het
Upp2 T A 2: 58,668,022 (GRCm39) Y238* probably null Het
Usp32 T C 11: 84,930,838 (GRCm39) T531A probably damaging Het
Vmn2r78 A T 7: 86,569,431 (GRCm39) D108V probably benign Het
Wdfy3 G T 5: 102,078,830 (GRCm39) A824E probably benign Het
Xylt1 T C 7: 117,255,870 (GRCm39) V814A probably benign Het
Zfy1 C T Y: 732,990 (GRCm39) R281H unknown 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
R1952:Nlgn1 UTSW 3 25,490,464 (GRCm39) missense probably damaging 1.00
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
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'- CATCAGTGATCAGTGCCTTCATTAC -3'
(R):5'- GTTGGGGATAACTATAATTGCCAACC -3'

Sequencing Primer
(F):5'- AGTGATCAGTGCCTTCATTACCTTTC -3'
(R):5'- CCATTTATTTTGCAGATATTCGGGAC -3'
Posted On 2022-02-07