Incidental Mutation 'R2198:Nlgn1'
ID 238478
Institutional Source Beutler Lab
Gene Symbol Nlgn1
Ensembl Gene ENSMUSG00000063887
Gene Name neuroligin 1
Synonyms NL1, Nlg1, 6330415N05Rik
MMRRC Submission 040200-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2198 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 25480379-26386609 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 25487925 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Isoleucine at position 803 (M803I)
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: M803I

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: M803I

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: M774I

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: M774I

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: M774I

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: M774I

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: M803I

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: M803I

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
Meta Mutation Damage Score 0.1443 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
Validation Efficiency 98% (60/61)
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adra1a T C 14: 66,875,385 (GRCm39) I120T probably damaging Het
Akr1c21 C T 13: 4,627,464 (GRCm39) P186L probably damaging Het
Alpk2 T C 18: 65,483,255 (GRCm39) K251R probably benign Het
Ank2 T C 3: 126,728,226 (GRCm39) E789G possibly damaging Het
Bag3 AAAGG AAAGGAAGG 7: 128,147,493 (GRCm39) probably null Het
Cacna2d4 T C 6: 119,324,220 (GRCm39) probably benign Het
Carf G A 1: 60,180,643 (GRCm39) R355H probably damaging Het
Cdh20 A T 1: 104,875,047 (GRCm39) probably null Het
Celf6 G T 9: 59,510,622 (GRCm39) L169F possibly damaging Het
Cep295nl A T 11: 118,223,419 (GRCm39) I475N probably benign Het
Chdh T A 14: 29,753,489 (GRCm39) S133T possibly damaging Het
Cnot6l C T 5: 96,227,800 (GRCm39) D478N possibly damaging Het
Ctnna3 C A 10: 64,838,524 (GRCm39) T867K probably benign Het
Ctse T G 1: 131,600,185 (GRCm39) Y311* probably null Het
Ddx60 T A 8: 62,411,097 (GRCm39) M453K possibly damaging Het
Dnah9 A G 11: 65,750,325 (GRCm39) F3927L possibly damaging Het
Dsg4 T C 18: 20,594,499 (GRCm39) S543P probably benign Het
Dspp A T 5: 104,323,567 (GRCm39) T237S probably benign Het
Eml6 T G 11: 29,800,935 (GRCm39) H357P probably benign Het
Epha3 T C 16: 63,664,507 (GRCm39) I38V possibly damaging Het
Erap1 C T 13: 74,794,806 (GRCm39) T155I probably damaging Het
Erh T C 12: 80,689,559 (GRCm39) probably benign Het
F5 A T 1: 164,034,603 (GRCm39) K1834M probably damaging Het
Fyn A G 10: 39,405,541 (GRCm39) E269G probably benign Het
Gm4884 A G 7: 40,690,229 (GRCm39) T42A probably benign Het
Grm1 T G 10: 10,658,520 (GRCm39) R323S probably damaging Het
Gstt4 T C 10: 75,658,235 (GRCm39) D8G probably damaging Het
Gvin-ps3 T A 7: 105,682,758 (GRCm39) M166L probably benign Het
Ldlr A G 9: 21,643,698 (GRCm39) D94G probably damaging Het
Mrpl54 G A 10: 81,101,575 (GRCm39) probably null Het
Naip2 A T 13: 100,289,100 (GRCm39) F1210Y probably damaging Het
Nifk A G 1: 118,257,130 (GRCm39) R88G probably benign Het
Or2r11 A G 6: 42,437,950 (GRCm39) M1T probably null Het
Or2y16 C T 11: 49,334,786 (GRCm39) S36F probably benign Het
Or6c88 T A 10: 129,406,915 (GRCm39) Y130* probably null Het
Or8g18 G A 9: 39,149,048 (GRCm39) T224I possibly damaging Het
Pip4k2a A T 2: 18,852,466 (GRCm39) M272K probably damaging Het
Ppp1cb G T 5: 32,640,704 (GRCm39) C139F probably damaging Het
Rad23b G A 4: 55,385,497 (GRCm39) G345R possibly damaging Het
Shc4 A T 2: 125,481,266 (GRCm39) V548E possibly damaging Het
Slc26a9 A G 1: 131,691,001 (GRCm39) probably benign Het
Slc8a1 T A 17: 81,715,685 (GRCm39) K783* probably null Het
Sobp A C 10: 42,898,520 (GRCm39) I355S possibly damaging Het
Thbs4 A G 13: 92,899,779 (GRCm39) Y491H possibly damaging Het
Tle2 T C 10: 81,426,147 (GRCm39) V727A probably damaging Het
Tmprss9 C T 10: 80,723,293 (GRCm39) P251L probably damaging Het
Tnks A T 8: 35,315,803 (GRCm39) D994E probably benign Het
Tnks C T 8: 35,340,221 (GRCm39) D466N probably benign Het
Tonsl A G 15: 76,520,872 (GRCm39) F394L probably benign Het
Trpa1 T A 1: 14,980,970 (GRCm39) Y144F probably benign Het
Usp22 A G 11: 61,050,163 (GRCm39) F324S probably damaging Het
Vmn1r78 G T 7: 11,886,487 (GRCm39) V33F probably benign Het
Wdr81 C T 11: 75,336,907 (GRCm39) R1494Q probably benign Het
Wdr87-ps G T 7: 29,226,697 (GRCm39) noncoding transcript Het
Zc3h14 G A 12: 98,719,068 (GRCm39) M144I probably damaging Het
Zc3h14 G A 12: 98,719,069 (GRCm39) V145M possibly damaging Het
Zfp82 T C 7: 29,756,936 (GRCm39) T49A 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
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'- TGAGAGTCTTCCGAGTTGAAAGC -3'
(R):5'- AACCCATGCTCCAGAAGAGG -3'

Sequencing Primer
(F):5'- TCTTCCGAGTTGAAAGCCAAGG -3'
(R):5'- GCTCCAGAAGAGGAAATTATGTCTC -3'
Posted On 2014-10-02