Incidental Mutation 'R9596:Nlgn1'
ID 723256
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 # R9596 (G1)
Quality Score 225.009
Status Not validated
Chromosome 3
Chromosomal Location 25480379-26386609 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 25488587 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 583 (I583F)
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: I583F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: I583F

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 damaging
Transcript: ENSMUST00000108308
AA Change: I554F

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: I554F

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: ENSMUST00000191835
AA Change: I554F

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: I554F

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: I583F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: I583F

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: 99.7%
  • 20x: 99.1%
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. [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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aamp G T 1: 74,320,262 (GRCm39) Q355K probably benign Het
Acte1 G T 7: 143,434,902 (GRCm39) probably null Het
AI661453 T C 17: 47,780,411 (GRCm39) S188P unknown Het
Atp10a A G 7: 58,477,553 (GRCm39) S1251G probably damaging Het
Ccr10 A G 11: 101,065,018 (GRCm39) F171L probably benign Het
Clec10a A T 11: 70,059,973 (GRCm39) D65V probably damaging Het
Clybl A T 14: 122,548,768 (GRCm39) I57L probably benign Het
Col5a1 G T 2: 27,819,551 (GRCm39) E218* probably null Het
Diaph1 G A 18: 38,024,111 (GRCm39) P576S unknown Het
Dsg1c T A 18: 20,416,361 (GRCm39) I754N probably benign Het
Fam47e G C 5: 92,726,395 (GRCm39) R111P probably benign Het
Fastkd3 G A 13: 68,735,806 (GRCm39) V519M probably damaging Het
Fhod3 T A 18: 25,193,392 (GRCm39) Y634* probably null Het
Frem3 G A 8: 81,341,951 (GRCm39) V1415I probably benign Het
Herc2 G A 7: 55,834,595 (GRCm39) S3191N Het
Kif19a A T 11: 114,676,752 (GRCm39) E527V probably benign Het
Lmbr1 C A 5: 29,440,105 (GRCm39) G420* probably null Het
Map3k9 A G 12: 81,777,404 (GRCm39) S526P probably damaging Het
Mink1 T A 11: 70,497,915 (GRCm39) L506Q possibly damaging Het
Mroh9 T C 1: 162,893,576 (GRCm39) I200V probably damaging Het
Mrps14 T C 1: 160,027,122 (GRCm39) V110A possibly damaging Het
Mta1 A G 12: 113,090,470 (GRCm39) Q209R probably damaging Het
Mtss2 G A 8: 111,458,689 (GRCm39) S195N Het
Ntng1 T C 3: 110,042,956 (GRCm39) probably benign Het
Or10w1 A G 19: 13,632,002 (GRCm39) S70G probably damaging Het
Or1p1c C T 11: 74,160,289 (GRCm39) H25Y probably benign Het
Or2ag13 A T 7: 106,313,412 (GRCm39) Y159N probably benign Het
Or5ac25 A G 16: 59,181,942 (GRCm39) I213T possibly damaging Het
Or6c65 A G 10: 129,603,988 (GRCm39) T208A probably damaging Het
Pcdha12 A T 18: 37,154,302 (GRCm39) L340F probably benign Het
Pdk4 T A 6: 5,491,842 (GRCm39) M173L probably benign Het
Pds5a A G 5: 65,772,830 (GRCm39) S1258P probably benign Het
Plcd1 A T 9: 118,917,183 (GRCm39) L22Q probably benign Het
Prag1 A G 8: 36,570,113 (GRCm39) D232G probably damaging Het
Rest C T 5: 77,423,141 (GRCm39) T315M probably damaging Het
Scrn2 G A 11: 96,923,907 (GRCm39) V264M probably damaging Het
Sipa1l3 C A 7: 29,031,691 (GRCm39) V1513F probably benign Het
Skic3 T C 13: 76,330,968 (GRCm39) V1466A possibly damaging Het
Slc44a1 T A 4: 53,544,553 (GRCm39) N421K probably benign Het
Smc6 G T 12: 11,345,045 (GRCm39) R662I probably damaging Het
Spata31e5 C A 1: 28,815,688 (GRCm39) M781I probably benign Het
Srcap T A 7: 127,131,036 (GRCm39) W751R probably damaging Het
Sv2b A G 7: 74,767,462 (GRCm39) F645L probably damaging Het
Sycp2 A G 2: 177,990,212 (GRCm39) probably null Het
Syne4 A G 7: 30,014,504 (GRCm39) T41A probably benign Het
Tns3 G A 11: 8,401,142 (GRCm39) T1052M possibly damaging Het
Trap1 A T 16: 3,871,374 (GRCm39) I381N probably damaging Het
Tshz1 A G 18: 84,031,904 (GRCm39) S835P possibly damaging Het
Ube3b T A 5: 114,527,171 (GRCm39) W130R probably damaging Het
Ubr5 G A 15: 37,986,213 (GRCm39) T2207I Het
Vmn1r43 G A 6: 89,846,877 (GRCm39) T203M probably damaging Het
Vmn2r11 T G 5: 109,201,563 (GRCm39) I314L possibly damaging Het
Vmn2r15 T A 5: 109,440,791 (GRCm39) I356L probably benign Het
Vmn2r31 G T 7: 7,397,292 (GRCm39) T322N probably benign Het
Vmn2r8 A T 5: 108,947,196 (GRCm39) F519I possibly damaging Het
Wdr35 T C 12: 9,036,092 (GRCm39) F288L probably benign Het
Xab2 A T 8: 3,663,018 (GRCm39) V521D probably damaging Het
Zfp639 T C 3: 32,574,269 (GRCm39) F298S probably damaging Het
Zfp786 G A 6: 47,797,406 (GRCm39) R511* probably null Het
Zfp936 T A 7: 42,839,834 (GRCm39) C434S probably damaging Het
Zranb1 T C 7: 132,552,146 (GRCm39) F266L probably benign 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
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
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'- TCCGTGGATGGCACTTTAG -3'
(R):5'- TCTCTAAATGAACAGGGATCCAG -3'

Sequencing Primer
(F):5'- TGTCGAGGTATACTGAGAAATGTC -3'
(R):5'- CTCCCGAGTGCTGGGATTAAAATC -3'
Posted On 2022-08-09