Incidental Mutation 'R2994:Nlgn1'
ID 257137
Institutional Source Beutler Lab
Gene Symbol Nlgn1
Ensembl Gene ENSMUSG00000063887
Gene Name neuroligin 1
Synonyms NL1, Nlg1, 6330415N05Rik
MMRRC Submission 040529-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2994 (G1)
Quality Score 225
Status Not validated
Chromosome 3
Chromosomal Location 25480379-26386609 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 25490162 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Asparagine at position 522 (D522N)
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: D522N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: D522N

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: D493N

PolyPhen 2 Score 0.936 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: D493N

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: D493N

PolyPhen 2 Score 0.936 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: D493N

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: D522N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: D522N

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: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 94.9%
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: 24 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca3 T C 17: 24,603,538 (GRCm39) S577P probably damaging Het
Agrn T C 4: 156,251,785 (GRCm39) T1826A possibly damaging Het
Arsi G A 18: 61,049,723 (GRCm39) G202E probably benign Het
Btnl6 C A 17: 34,734,498 (GRCm39) R88I possibly damaging Het
Cfap52 T A 11: 67,830,617 (GRCm39) Y281F probably benign Het
CK137956 T C 4: 127,845,300 (GRCm39) T148A probably benign Het
Fpr3 C T 17: 18,191,130 (GRCm39) Q134* probably null Het
Gbp4 A T 5: 105,284,886 (GRCm39) M1K probably null Het
Gpsm1 G A 2: 26,209,843 (GRCm39) probably benign Het
Nedd4 A G 9: 72,638,185 (GRCm39) D440G probably benign Het
Oprk1 T C 1: 5,672,955 (GRCm39) V364A probably benign Het
Or1e35 T C 11: 73,797,541 (GRCm39) Y259C probably damaging Het
Or5d18 A G 2: 87,865,301 (GRCm39) Y61H probably damaging Het
Polr1e T C 4: 45,027,473 (GRCm39) probably null Het
Psmd11 T C 11: 80,351,493 (GRCm39) Y239H probably damaging Het
Ripor2 A T 13: 24,885,610 (GRCm39) D576V probably damaging Het
Rundc3a C T 11: 102,291,489 (GRCm39) T327I probably damaging Het
Sh3rf1 A G 8: 61,825,609 (GRCm39) T535A probably benign Het
Slc13a2 T A 11: 78,295,563 (GRCm39) E101V probably damaging Het
Tg A T 15: 66,553,802 (GRCm39) T406S probably benign Het
Tjp2 T C 19: 24,090,215 (GRCm39) E609G probably damaging Het
Zfp459 G A 13: 67,556,853 (GRCm39) P77S possibly damaging Het
Zfp612 A G 8: 110,816,049 (GRCm39) K380E probably damaging Het
Zfp629 T C 7: 127,210,228 (GRCm39) E527G probably damaging 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
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'- GCAGAGTACTTTCCTGAGGTAC -3'
(R):5'- GCCAGTGATTTCGACTTTGC -3'

Sequencing Primer
(F):5'- AGAGTACTTTCCTGAGGTACTTACC -3'
(R):5'- ATACTGACTGGGCTGATCGC -3'
Posted On 2015-01-11