Incidental Mutation 'R1221:Nrxn1'
ID 100153
Institutional Source Beutler Lab
Gene Symbol Nrxn1
Ensembl Gene ENSMUSG00000024109
Gene Name neurexin I
Synonyms alpha-latrotoxin receptor (calcium-dependent), 1700062G21Rik, neurexin I alpha, neurexin I alpha, 9330127H16Rik, neurexin I beta, neurexin I beta, A230068P09Rik, neurexin I alpha, neurexin I beta
MMRRC Submission 039290-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1221 (G1)
Quality Score 225
Status Not validated
Chromosome 17
Chromosomal Location 90341059-91400499 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 90950722 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Serine at position 478 (T478S)
Ref Sequence ENSEMBL: ENSMUSP00000057294 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000054059] [ENSMUST00000072671] [ENSMUST00000160800] [ENSMUST00000160844] [ENSMUST00000161402] [ENSMUST00000174331]
AlphaFold Q9CS84
PDB Structure Structure of mouse beta-neurexin 1 [X-RAY DIFFRACTION]
Crystal structure of beta-neurexin 1 with the splice insert 4 [X-RAY DIFFRACTION]
Predicted Effect probably damaging
Transcript: ENSMUST00000054059
AA Change: T478S

PolyPhen 2 Score 0.971 (Sensitivity: 0.77; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000057294
Gene: ENSMUSG00000024109
AA Change: T478S

DomainStartEndE-ValueType
low complexity region 9 23 N/A INTRINSIC
LamG 50 192 2.29e-31 SMART
EGF 216 256 4.26e0 SMART
LamG 304 438 2.3e-36 SMART
LamG 492 644 2.74e-43 SMART
EGF 671 705 1.58e-3 SMART
LamG 730 869 7.27e-25 SMART
LamG 917 1053 8.46e-35 SMART
EGF 1078 1112 1.87e1 SMART
LamG 1140 1297 7.74e-20 SMART
low complexity region 1324 1355 N/A INTRINSIC
low complexity region 1426 1441 N/A INTRINSIC
4.1m 1444 1462 1.19e-6 SMART
low complexity region 1481 1493 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000072671
AA Change: T478S

PolyPhen 2 Score 0.784 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000072458
Gene: ENSMUSG00000024109
AA Change: T478S

DomainStartEndE-ValueType
low complexity region 9 23 N/A INTRINSIC
LamG 50 192 2.29e-31 SMART
EGF 216 256 4.26e0 SMART
LamG 304 438 2.3e-36 SMART
LamG 492 644 2.74e-43 SMART
EGF 671 705 1.58e-3 SMART
LamG 730 869 7.27e-25 SMART
LamG 917 1053 8.46e-35 SMART
EGF 1078 1112 1.87e1 SMART
LamG 1140 1297 7.74e-20 SMART
low complexity region 1324 1355 N/A INTRINSIC
low complexity region 1423 1438 N/A INTRINSIC
4.1m 1441 1459 1.19e-6 SMART
low complexity region 1478 1490 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000160800
AA Change: T474S

PolyPhen 2 Score 0.790 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000124561
Gene: ENSMUSG00000024109
AA Change: T474S

DomainStartEndE-ValueType
low complexity region 9 23 N/A INTRINSIC
LamG 50 192 2.29e-31 SMART
EGF 216 256 4.26e0 SMART
LamG 300 434 2.3e-36 SMART
LamG 488 640 2.74e-43 SMART
EGF 667 701 1.58e-3 SMART
LamG 726 865 7.27e-25 SMART
LamG 913 1049 8.46e-35 SMART
EGF 1074 1108 1.87e1 SMART
LamG 1136 1293 7.74e-20 SMART
low complexity region 1320 1351 N/A INTRINSIC
low complexity region 1422 1437 N/A INTRINSIC
4.1m 1440 1458 1.19e-6 SMART
low complexity region 1477 1489 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000160844
AA Change: T486S

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000125407
Gene: ENSMUSG00000024109
AA Change: T486S

DomainStartEndE-ValueType
low complexity region 9 23 N/A INTRINSIC
LamG 50 192 2.29e-31 SMART
EGF 216 256 4.26e0 SMART
LamG 304 446 1.24e-32 SMART
LamG 500 652 2.74e-43 SMART
EGF 679 713 1.58e-3 SMART
LamG 738 877 7.27e-25 SMART
LamG 925 1061 8.46e-35 SMART
EGF 1086 1120 1.87e1 SMART
LamG 1148 1305 7.74e-20 SMART
low complexity region 1332 1363 N/A INTRINSIC
low complexity region 1434 1449 N/A INTRINSIC
4.1m 1452 1470 1.19e-6 SMART
low complexity region 1489 1501 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161102
Predicted Effect probably benign
Transcript: ENSMUST00000161402
AA Change: T493S

PolyPhen 2 Score 0.152 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000124116
Gene: ENSMUSG00000024109
AA Change: T493S

DomainStartEndE-ValueType
low complexity region 9 23 N/A INTRINSIC
LamG 50 192 2.29e-31 SMART
EGF 216 256 4.26e0 SMART
LamG 304 453 3.46e-31 SMART
LamG 507 659 2.74e-43 SMART
EGF 686 720 1.58e-3 SMART
LamG 745 884 7.27e-25 SMART
LamG 932 1068 8.46e-35 SMART
EGF 1093 1127 1.87e1 SMART
LamG 1155 1312 7.74e-20 SMART
low complexity region 1339 1370 N/A INTRINSIC
low complexity region 1441 1456 N/A INTRINSIC
4.1m 1459 1477 1.19e-6 SMART
low complexity region 1496 1508 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000197224
AA Change: T56S
Predicted Effect probably benign
Transcript: ENSMUST00000174331
AA Change: T486S

PolyPhen 2 Score 0.301 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000133491
Gene: ENSMUSG00000024109
AA Change: T486S

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
LamG 50 192 2.29e-31 SMART
EGF 216 256 4.26e0 SMART
LamG 304 446 1.24e-32 SMART
LamG 500 652 2.74e-43 SMART
EGF 679 713 1.58e-3 SMART
LamG 738 877 7.27e-25 SMART
LamG 925 1061 8.46e-35 SMART
EGF 1086 1120 1.87e1 SMART
LamG 1148 1275 3.29e-23 SMART
low complexity region 1302 1333 N/A INTRINSIC
low complexity region 1404 1419 N/A INTRINSIC
4.1m 1422 1440 1.19e-6 SMART
low complexity region 1459 1471 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161637
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 94.0%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a single-pass type I membrane protein that belongs to the neurexin family. Neurexins are synaptic transmembrane receptors that bind endogenous ligands that include neuroligins, dystroglycan, and neurexophilins. Neurexin complexes are required for efficient neurotransmission and are involved in synaptogenesis. In vertebrates, alternate promoter usage results in multiple isoform classes, of which the alpha and beta classes are the best characterized. In humans, allelic variants in this gene are associated with Pitt-Hopkins-like syndrome-2, while deletions have been associated with autism and schizophrenia. Mouse knockouts display decreased spontaneous and evoked vesicle release resulting in impaired synaptic transmission. In addition, knockout mice show altered social approach, reduced social investigation, reduced locomotor activity, and in males, increased aggression. Alternative splicing and promoter usage result in multiple transcript variants. [provided by RefSeq, Nov 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit reduced Ca(2+)-dependent binding of alpha-latrotoxin to brain membranes. Isolated synaptosomes display only a small reduction in alpha-latrotoxin -triggered glutamate release in the absence of Ca(2+) but show a major decrease in the presence of Ca(2+). [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aak1 T C 6: 86,942,460 (GRCm39) S668P unknown Het
Anks1 A G 17: 28,269,616 (GRCm39) Q770R possibly damaging Het
Apc2 G A 10: 80,142,214 (GRCm39) V378I probably damaging Het
Apeh A G 9: 107,969,808 (GRCm39) V184A probably benign Het
AU018091 A G 7: 3,208,717 (GRCm39) F404S probably damaging Het
Bap1 T C 14: 30,979,608 (GRCm39) L537P probably damaging Het
Bhlha15 A G 5: 144,128,341 (GRCm39) Y151C probably damaging Het
Bmp8b A T 4: 123,008,504 (GRCm39) T157S probably damaging Het
Btbd1 G T 7: 81,468,005 (GRCm39) H172N possibly damaging Het
C1rl A G 6: 124,470,940 (GRCm39) R83G probably benign Het
Cep104 A G 4: 154,072,902 (GRCm39) T387A probably benign Het
Cfi A T 3: 129,666,618 (GRCm39) Q447L probably damaging Het
Cimap1a G T 7: 140,428,296 (GRCm39) W10L probably damaging Het
Coq6 A G 12: 84,418,301 (GRCm39) E295G possibly damaging Het
Dclre1a T C 19: 56,519,700 (GRCm39) T978A possibly damaging Het
Dlc1 T C 8: 37,051,985 (GRCm39) D582G probably benign Het
Dlgap2 A G 8: 14,776,952 (GRCm39) T65A probably benign Het
Dock5 G A 14: 67,996,610 (GRCm39) S1711L probably benign Het
Drc3 A C 11: 60,275,052 (GRCm39) I338L probably benign Het
Dsc1 A T 18: 20,247,599 (GRCm39) C5* probably null Het
F5 A G 1: 163,989,368 (GRCm39) Y90C probably damaging Het
Gdf10 G A 14: 33,654,710 (GRCm39) A406T probably benign Het
Gm136 G T 4: 34,744,127 (GRCm39) A239E possibly damaging Het
Gm4952 A T 19: 12,601,059 (GRCm39) D93V possibly damaging Het
Gramd1c T C 16: 43,810,227 (GRCm39) T454A possibly damaging Het
Gstm6 A G 3: 107,848,418 (GRCm39) I58T probably damaging Het
Kdm3b C T 18: 34,941,298 (GRCm39) S263L possibly damaging Het
Kdm5b G C 1: 134,526,829 (GRCm39) S317T probably damaging Het
Myo15b A G 11: 115,777,546 (GRCm39) R71G possibly damaging Het
Nlrp1b G A 11: 71,072,290 (GRCm39) P518S probably benign Het
Nme5 A T 18: 34,704,575 (GRCm39) I90N probably damaging Het
Or8g22 A C 9: 38,958,483 (GRCm39) D77E probably damaging Het
Osmr G A 15: 6,853,042 (GRCm39) Q617* probably null Het
Pcsk5 T C 19: 17,814,512 (GRCm39) D2G possibly damaging Het
Pdpn G A 4: 143,000,608 (GRCm39) R75C probably damaging Het
Pidd1 A T 7: 141,018,725 (GRCm39) F842Y probably damaging Het
Resf1 T A 6: 149,227,719 (GRCm39) V255E probably benign Het
Sema3a A G 5: 13,566,190 (GRCm39) Q158R probably benign Het
Setbp1 T A 18: 78,899,798 (GRCm39) R1290W probably damaging Het
Slc20a1 G A 2: 129,050,324 (GRCm39) G494D probably benign Het
Spag17 A G 3: 99,889,584 (GRCm39) E151G possibly damaging Het
Stt3b A G 9: 115,086,567 (GRCm39) F351L probably benign Het
Tas1r2 A G 4: 139,396,436 (GRCm39) M592V probably benign Het
Tbcd A G 11: 121,387,909 (GRCm39) T347A probably benign Het
Tmem109 C A 19: 10,851,733 (GRCm39) R37L possibly damaging Het
Tmem67 G A 4: 12,045,871 (GRCm39) S862L possibly damaging Het
Ttn T A 2: 76,781,857 (GRCm39) D1017V probably damaging Het
Zfp646 G A 7: 127,482,292 (GRCm39) G1490S probably benign Het
Zfyve16 T C 13: 92,644,813 (GRCm39) S1130G possibly damaging Het
Other mutations in Nrxn1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01310:Nrxn1 APN 17 90,366,902 (GRCm39) critical splice donor site probably null
IGL01644:Nrxn1 APN 17 90,928,301 (GRCm39) missense possibly damaging 0.94
IGL01820:Nrxn1 APN 17 90,950,531 (GRCm39) missense probably damaging 0.98
IGL01902:Nrxn1 APN 17 91,395,919 (GRCm39) splice site probably null
IGL02079:Nrxn1 APN 17 90,950,511 (GRCm39) missense probably damaging 0.99
IGL02089:Nrxn1 APN 17 91,395,829 (GRCm39) missense probably benign 0.01
IGL02133:Nrxn1 APN 17 90,950,671 (GRCm39) missense probably damaging 1.00
IGL02179:Nrxn1 APN 17 90,937,511 (GRCm39) missense probably damaging 0.99
IGL02199:Nrxn1 APN 17 90,344,686 (GRCm39) missense probably damaging 1.00
IGL02262:Nrxn1 APN 17 91,011,636 (GRCm39) missense probably damaging 1.00
IGL02941:Nrxn1 APN 17 90,515,811 (GRCm39) missense probably damaging 1.00
PIT4449001:Nrxn1 UTSW 17 90,905,007 (GRCm39) missense probably damaging 1.00
PIT4791001:Nrxn1 UTSW 17 90,762,931 (GRCm39) intron probably benign
R0123:Nrxn1 UTSW 17 91,302,915 (GRCm39) splice site probably null
R0212:Nrxn1 UTSW 17 90,670,186 (GRCm39) unclassified probably benign
R0277:Nrxn1 UTSW 17 91,008,170 (GRCm39) critical splice donor site probably null
R0323:Nrxn1 UTSW 17 91,008,170 (GRCm39) critical splice donor site probably null
R0384:Nrxn1 UTSW 17 90,515,775 (GRCm39) missense probably damaging 1.00
R0395:Nrxn1 UTSW 17 91,395,742 (GRCm39) missense possibly damaging 0.90
R0606:Nrxn1 UTSW 17 90,872,801 (GRCm39) missense probably damaging 1.00
R0616:Nrxn1 UTSW 17 90,670,285 (GRCm39) missense probably damaging 1.00
R0624:Nrxn1 UTSW 17 91,396,117 (GRCm39) missense unknown
R0633:Nrxn1 UTSW 17 91,011,609 (GRCm39) missense probably damaging 1.00
R0927:Nrxn1 UTSW 17 90,344,758 (GRCm39) missense probably damaging 1.00
R1035:Nrxn1 UTSW 17 90,471,302 (GRCm39) missense probably damaging 0.96
R1403:Nrxn1 UTSW 17 90,950,481 (GRCm39) missense probably benign 0.11
R1403:Nrxn1 UTSW 17 90,950,481 (GRCm39) missense probably benign 0.11
R1691:Nrxn1 UTSW 17 90,469,717 (GRCm39) missense probably damaging 0.98
R1703:Nrxn1 UTSW 17 90,515,845 (GRCm39) missense probably damaging 1.00
R1709:Nrxn1 UTSW 17 90,344,615 (GRCm39) missense probably damaging 1.00
R1721:Nrxn1 UTSW 17 90,469,832 (GRCm39) missense probably damaging 1.00
R1792:Nrxn1 UTSW 17 90,896,252 (GRCm39) missense probably damaging 0.96
R1980:Nrxn1 UTSW 17 91,395,746 (GRCm39) missense probably benign 0.01
R2116:Nrxn1 UTSW 17 91,011,705 (GRCm39) missense probably damaging 1.00
R2117:Nrxn1 UTSW 17 91,011,705 (GRCm39) missense probably damaging 1.00
R2162:Nrxn1 UTSW 17 90,469,859 (GRCm39) missense probably damaging 1.00
R3119:Nrxn1 UTSW 17 90,904,947 (GRCm39) nonsense probably null
R3409:Nrxn1 UTSW 17 90,515,795 (GRCm39) missense probably damaging 1.00
R3683:Nrxn1 UTSW 17 90,930,880 (GRCm39) missense probably damaging 1.00
R3885:Nrxn1 UTSW 17 90,930,899 (GRCm39) missense probably damaging 1.00
R3939:Nrxn1 UTSW 17 90,515,849 (GRCm39) missense probably damaging 1.00
R4475:Nrxn1 UTSW 17 91,009,410 (GRCm39) missense probably damaging 0.98
R4640:Nrxn1 UTSW 17 90,868,196 (GRCm39) missense probably damaging 1.00
R4678:Nrxn1 UTSW 17 90,930,850 (GRCm39) missense probably damaging 1.00
R4690:Nrxn1 UTSW 17 90,344,509 (GRCm39) missense probably damaging 1.00
R4790:Nrxn1 UTSW 17 90,762,477 (GRCm39) missense possibly damaging 0.86
R4877:Nrxn1 UTSW 17 91,395,605 (GRCm39) missense probably benign 0.33
R4989:Nrxn1 UTSW 17 90,928,274 (GRCm39) intron probably benign
R5204:Nrxn1 UTSW 17 90,469,792 (GRCm39) missense probably damaging 1.00
R5205:Nrxn1 UTSW 17 90,471,302 (GRCm39) missense probably damaging 0.96
R5239:Nrxn1 UTSW 17 91,011,537 (GRCm39) missense probably damaging 1.00
R5250:Nrxn1 UTSW 17 90,842,869 (GRCm39) intron probably benign
R5473:Nrxn1 UTSW 17 90,897,520 (GRCm39) missense probably damaging 1.00
R5629:Nrxn1 UTSW 17 90,897,460 (GRCm39) missense possibly damaging 0.75
R5743:Nrxn1 UTSW 17 90,950,652 (GRCm39) missense probably damaging 1.00
R5910:Nrxn1 UTSW 17 91,011,746 (GRCm39) nonsense probably null
R5961:Nrxn1 UTSW 17 90,762,371 (GRCm39) missense probably damaging 0.99
R5979:Nrxn1 UTSW 17 91,395,631 (GRCm39) missense possibly damaging 0.54
R5992:Nrxn1 UTSW 17 90,930,935 (GRCm39) missense probably benign 0.01
R6024:Nrxn1 UTSW 17 90,897,526 (GRCm39) missense possibly damaging 0.88
R6031:Nrxn1 UTSW 17 90,896,218 (GRCm39) missense probably damaging 1.00
R6031:Nrxn1 UTSW 17 90,896,218 (GRCm39) missense probably damaging 1.00
R6185:Nrxn1 UTSW 17 90,344,564 (GRCm39) missense probably damaging 1.00
R6220:Nrxn1 UTSW 17 91,395,904 (GRCm39) missense probably benign 0.14
R6306:Nrxn1 UTSW 17 90,872,874 (GRCm39) missense possibly damaging 0.55
R6621:Nrxn1 UTSW 17 90,469,610 (GRCm39) missense probably damaging 1.00
R6669:Nrxn1 UTSW 17 90,366,991 (GRCm39) missense probably damaging 0.98
R6770:Nrxn1 UTSW 17 90,344,607 (GRCm39) missense probably damaging 1.00
R6798:Nrxn1 UTSW 17 90,937,378 (GRCm39) missense probably damaging 1.00
R6923:Nrxn1 UTSW 17 91,395,661 (GRCm39) missense probably benign 0.06
R7140:Nrxn1 UTSW 17 91,396,192 (GRCm39) start gained probably benign
R7374:Nrxn1 UTSW 17 90,896,097 (GRCm39) critical splice donor site probably null
R7564:Nrxn1 UTSW 17 90,670,334 (GRCm39) missense possibly damaging 0.64
R7570:Nrxn1 UTSW 17 90,469,807 (GRCm39) missense probably benign 0.35
R7800:Nrxn1 UTSW 17 91,396,635 (GRCm39) unclassified probably benign
R7828:Nrxn1 UTSW 17 90,366,979 (GRCm39) missense probably damaging 0.99
R7974:Nrxn1 UTSW 17 91,008,207 (GRCm39) missense probably damaging 1.00
R8001:Nrxn1 UTSW 17 91,395,964 (GRCm39) missense possibly damaging 0.49
R8189:Nrxn1 UTSW 17 91,011,637 (GRCm39) missense probably damaging 0.96
R8258:Nrxn1 UTSW 17 90,471,249 (GRCm39) missense probably damaging 0.99
R8259:Nrxn1 UTSW 17 90,471,249 (GRCm39) missense probably damaging 0.99
R8298:Nrxn1 UTSW 17 91,011,597 (GRCm39) missense probably damaging 1.00
R8801:Nrxn1 UTSW 17 91,009,393 (GRCm39) critical splice donor site probably benign
R8814:Nrxn1 UTSW 17 90,937,529 (GRCm39) missense probably damaging 1.00
R8873:Nrxn1 UTSW 17 90,872,821 (GRCm39) nonsense probably null
R8954:Nrxn1 UTSW 17 90,897,615 (GRCm39) missense probably damaging 1.00
R9086:Nrxn1 UTSW 17 90,469,792 (GRCm39) missense probably damaging 1.00
R9110:Nrxn1 UTSW 17 90,869,233 (GRCm39) nonsense probably null
R9498:Nrxn1 UTSW 17 90,897,397 (GRCm39) missense probably damaging 1.00
R9499:Nrxn1 UTSW 17 90,937,450 (GRCm39) missense probably damaging 1.00
R9552:Nrxn1 UTSW 17 90,937,450 (GRCm39) missense probably damaging 1.00
R9780:Nrxn1 UTSW 17 90,931,042 (GRCm39) missense possibly damaging 0.54
RF005:Nrxn1 UTSW 17 90,670,304 (GRCm39) missense probably damaging 1.00
RF024:Nrxn1 UTSW 17 90,670,304 (GRCm39) missense probably damaging 1.00
X0021:Nrxn1 UTSW 17 90,897,640 (GRCm39) missense probably damaging 1.00
X0063:Nrxn1 UTSW 17 90,670,259 (GRCm39) missense possibly damaging 0.54
Z1088:Nrxn1 UTSW 17 90,366,933 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TGACCGTCCATCCCGTTGGAAATC -3'
(R):5'- TGGTGAATTTCAGCACACCGACTTC -3'

Sequencing Primer
(F):5'- GTACCTGATCCCATGTCTAAGAGG -3'
(R):5'- ACTTCAAAATTCCATGAGCTGC -3'
Posted On 2014-01-15