Incidental Mutation 'R2002:Nrxn3'
ID 223228
Institutional Source Beutler Lab
Gene Symbol Nrxn3
Ensembl Gene ENSMUSG00000066392
Gene Name neurexin III
Synonyms 4933401A11Rik, D12Bwg0831e, neurexin III alpha, neurexin III alpha, neurexin III beta, neurexin III beta, 9330112C09Rik
MMRRC Submission 040012-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2002 (G1)
Quality Score 225
Status Validated
Chromosome 12
Chromosomal Location 88689646-90301709 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 90299089 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Threonine at position 400 (A400T)
Ref Sequence ENSEMBL: ENSMUSP00000105760 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000057634] [ENSMUST00000110130] [ENSMUST00000110133] [ENSMUST00000163134] [ENSMUST00000167103] [ENSMUST00000167887] [ENSMUST00000190626]
AlphaFold Q6P9K9
Predicted Effect probably damaging
Transcript: ENSMUST00000057634
AA Change: A1070T

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000050075
Gene: ENSMUSG00000066392
AA Change: A1070T

DomainStartEndE-ValueType
LamG 94 246 3.28e-41 SMART
EGF 273 307 4.1e-2 SMART
LamG 332 470 4.87e-26 SMART
LamG 518 654 7.08e-37 SMART
EGF 688 722 1.99e1 SMART
LamG 750 907 1.14e-17 SMART
low complexity region 948 964 N/A INTRINSIC
low complexity region 1028 1043 N/A INTRINSIC
4.1m 1046 1064 4.38e-5 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000110130
AA Change: A537T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000105757
Gene: ENSMUSG00000066392
AA Change: A537T

DomainStartEndE-ValueType
signal peptide 1 35 N/A INTRINSIC
LamG 107 264 1.14e-17 SMART
Blast:LamG 294 410 6e-47 BLAST
low complexity region 492 507 N/A INTRINSIC
4.1m 510 528 4.38e-5 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000110133
AA Change: A400T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000105760
Gene: ENSMUSG00000066392
AA Change: A400T

DomainStartEndE-ValueType
signal peptide 1 35 N/A INTRINSIC
LamG 107 234 1.8e-20 SMART
Blast:LamG 264 330 1e-19 BLAST
low complexity region 358 373 N/A INTRINSIC
4.1m 376 394 4.38e-5 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000163134
AA Change: A1541T

PolyPhen 2 Score 0.912 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000129678
Gene: ENSMUSG00000066392
AA Change: A1541T

DomainStartEndE-ValueType
LamG 47 184 9.8e-31 SMART
EGF 201 235 8.07e-1 SMART
LamG 279 413 7.19e-38 SMART
LamG 467 619 3.28e-41 SMART
EGF 646 680 4.1e-2 SMART
LamG 705 843 4.87e-26 SMART
LamG 891 1027 7.08e-37 SMART
EGF 1052 1086 1.99e1 SMART
LamG 1114 1271 1.14e-17 SMART
low complexity region 1312 1328 N/A INTRINSIC
low complexity region 1395 1406 N/A INTRINSIC
low complexity region 1499 1514 N/A INTRINSIC
4.1m 1517 1535 4.38e-5 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000167103
SMART Domains Protein: ENSMUSP00000127407
Gene: ENSMUSG00000066392

DomainStartEndE-ValueType
LamG 47 184 9.8e-31 SMART
EGF 201 235 8.07e-1 SMART
LamG 279 413 7.19e-38 SMART
LamG 467 619 3.28e-41 SMART
EGF 646 680 4.1e-2 SMART
LamG 705 834 5.76e-28 SMART
LamG 882 1018 7.08e-37 SMART
EGF 1043 1077 1.99e1 SMART
LamG 1105 1262 1.14e-17 SMART
low complexity region 1303 1319 N/A INTRINSIC
low complexity region 1354 1382 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000167887
AA Change: A1070T

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000127926
Gene: ENSMUSG00000066392
AA Change: A1070T

DomainStartEndE-ValueType
LamG 94 246 3.28e-41 SMART
EGF 273 307 4.1e-2 SMART
LamG 332 470 4.87e-26 SMART
LamG 518 654 7.08e-37 SMART
EGF 688 722 1.99e1 SMART
LamG 750 907 1.14e-17 SMART
low complexity region 948 964 N/A INTRINSIC
low complexity region 1028 1043 N/A INTRINSIC
4.1m 1046 1064 4.38e-5 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000190626
SMART Domains Protein: ENSMUSP00000139879
Gene: ENSMUSG00000066392

DomainStartEndE-ValueType
LamG 94 246 2.1e-43 SMART
EGF 273 307 2e-4 SMART
LamG 332 470 3.1e-28 SMART
LamG 518 654 4.4e-39 SMART
EGF 688 722 9.6e-2 SMART
LamG 750 877 1.1e-22 SMART
low complexity region 918 934 N/A INTRINSIC
low complexity region 972 1000 N/A INTRINSIC
Meta Mutation Damage Score 0.1108 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.2%
  • 20x: 91.6%
Validation Efficiency 97% (72/74)
MGI Phenotype FUNCTION: This gene encodes a member of a family of proteins that function in the nervous system as receptors and cell adhesion molecules. Extensive alternative splicing and the use of alternative promoters results in multiple transcript variants for this gene, but the full-length nature of many of these variants has not been determined. Transcripts that initiate from an upstream promoter encode alpha isoforms, which contain epidermal growth factor-like (EGF-like) sequences and laminin G domains. Transcripts initiating from the downstream promoter encode beta isoforms, which lack EGF-like sequences. [provided by RefSeq, Dec 2012]
PHENOTYPE: Twenty percent of mice homozygous for a knock-out allele die postnatally prior to 20 days of age. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930548G14Rik T C 15: 46,489,002 (GRCm39) noncoding transcript Het
Abcb4 T A 5: 8,955,989 (GRCm39) S98T probably benign Het
Acan T C 7: 78,750,541 (GRCm39) S1771P probably damaging Het
Acvr1c T A 2: 58,205,987 (GRCm39) Q41L probably benign Het
Ak2 T A 4: 128,902,022 (GRCm39) S232T probably benign Het
Akr1e1 T A 13: 4,657,564 (GRCm39) probably benign Het
Ano7 T C 1: 93,328,303 (GRCm39) probably benign Het
Aox1 T A 1: 58,086,300 (GRCm39) H68Q possibly damaging Het
Apaf1 A G 10: 90,897,676 (GRCm39) V269A possibly damaging Het
Apba2 A T 7: 64,383,290 (GRCm39) I368F probably damaging Het
Armc3 A G 2: 19,293,747 (GRCm39) M513V probably benign Het
Asb5 G A 8: 55,036,655 (GRCm39) V116M probably damaging Het
Atg16l2 A G 7: 100,944,127 (GRCm39) S280P possibly damaging Het
Atp6v0c G T 17: 24,383,835 (GRCm39) T40K probably damaging Het
Cdk2ap2 A G 19: 4,147,903 (GRCm39) M57V possibly damaging Het
Cip2a T C 16: 48,826,214 (GRCm39) probably benign Het
Ctnnd1 T C 2: 84,450,704 (GRCm39) N172S probably benign Het
Ddx55 T A 5: 124,704,503 (GRCm39) V370E probably damaging Het
Ddx6 A G 9: 44,518,831 (GRCm39) T48A probably benign Het
Dnah10 C T 5: 124,911,052 (GRCm39) R4490W probably damaging Het
Dspp T A 5: 104,326,425 (GRCm39) S929R unknown Het
Erbb3 T C 10: 128,422,094 (GRCm39) Y50C probably benign Het
Fam209 C A 2: 172,314,689 (GRCm39) N59K probably benign Het
Fgd3 T C 13: 49,449,931 (GRCm39) E106G probably benign Het
Frmd4a A C 2: 4,577,176 (GRCm39) K344T probably damaging Het
Gbe1 A G 16: 70,325,814 (GRCm39) E617G probably damaging Het
Gm5089 T A 14: 122,673,686 (GRCm39) I12F unknown Het
Gm7052 T A 17: 22,258,920 (GRCm39) probably benign Het
Gria1 A T 11: 56,902,930 (GRCm39) N24I possibly damaging Het
Grin2b T C 6: 135,710,243 (GRCm39) E1101G probably damaging Het
Hjurp GT GTT 1: 88,194,246 (GRCm39) probably null Het
Kcnma1 A C 14: 23,387,097 (GRCm39) S982A probably damaging Het
Khdrbs3 T A 15: 68,885,328 (GRCm39) probably benign Het
Kif23 A T 9: 61,834,666 (GRCm39) C426* probably null Het
Lmo7 G T 14: 102,124,497 (GRCm39) A319S probably benign Het
Ly6c1 T A 15: 74,920,342 (GRCm39) T7S possibly damaging Het
Magel2 G A 7: 62,028,844 (GRCm39) V583I unknown Het
Mamdc4 A T 2: 25,457,244 (GRCm39) W548R probably damaging Het
Mfsd2a C T 4: 122,850,609 (GRCm39) R88Q probably damaging Het
Mkrn1 T C 6: 39,382,737 (GRCm39) T158A probably benign Het
Mroh2b G T 15: 4,955,166 (GRCm39) D720Y probably damaging Het
Mycbp2 A G 14: 103,485,839 (GRCm39) V1041A probably damaging Het
Ncam2 A T 16: 81,386,586 (GRCm39) H655L possibly damaging Het
Npas2 T C 1: 39,377,276 (GRCm39) V546A probably benign Het
Oog3 G T 4: 143,884,675 (GRCm39) H420Q possibly damaging Het
Or3a10 A T 11: 73,935,865 (GRCm39) S78R possibly damaging Het
Or5ap2 T A 2: 85,680,744 (GRCm39) V316E probably benign Het
Or8k28 T C 2: 86,285,817 (GRCm39) H266R probably benign Het
Pak5 T A 2: 135,958,557 (GRCm39) H177L probably benign Het
Pcca A G 14: 123,124,477 (GRCm39) I683V probably benign Het
Pea15a T C 1: 172,026,252 (GRCm39) I90V probably benign Het
Plagl1 C A 10: 13,004,402 (GRCm39) probably benign Het
Prmt1 A G 7: 44,628,148 (GRCm39) V237A probably damaging Het
Ptprz1 T A 6: 23,027,833 (GRCm39) Y910* probably null Het
Rasal3 T A 17: 32,612,585 (GRCm39) T757S probably damaging Het
Rbbp8 T C 18: 11,860,223 (GRCm39) probably benign Het
S1pr1 A G 3: 115,506,544 (GRCm39) S17P probably benign Het
Scel G A 14: 103,779,421 (GRCm39) V131M probably damaging Het
Scn2a G A 2: 65,512,427 (GRCm39) R188Q probably null Het
Snap29 T A 16: 17,224,190 (GRCm39) Y68* probably null Het
Spdl1 T C 11: 34,713,473 (GRCm39) T199A probably benign Het
Srbd1 T C 17: 86,449,828 (GRCm39) N14D probably benign Het
Ston1 G A 17: 88,942,957 (GRCm39) G121D probably benign Het
Syt16 G A 12: 74,281,977 (GRCm39) G367E possibly damaging Het
Tdpoz1 T C 3: 93,578,710 (GRCm39) T25A possibly damaging Het
Tmem182 T A 1: 40,845,355 (GRCm39) Y77N probably damaging Het
Tmprss11f A T 5: 86,687,627 (GRCm39) probably benign Het
Trp73 T C 4: 154,165,902 (GRCm39) T56A probably damaging Het
Trpm3 A G 19: 22,959,947 (GRCm39) K1194R probably damaging Het
Ttc39c T A 18: 12,830,935 (GRCm39) probably null Het
Ube4b T C 4: 149,468,254 (GRCm39) D174G probably benign Het
Vmn1r211 A T 13: 23,035,953 (GRCm39) M238K probably damaging Het
Wsb2 T A 5: 117,508,798 (GRCm39) N77K probably benign Het
Xkr4 C T 1: 3,741,318 (GRCm39) R85Q probably benign Het
Zmynd11 T A 13: 9,739,514 (GRCm39) probably null Het
Other mutations in Nrxn3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00911:Nrxn3 APN 12 90,171,366 (GRCm39) missense probably damaging 1.00
IGL00961:Nrxn3 APN 12 90,171,320 (GRCm39) missense possibly damaging 0.95
IGL01073:Nrxn3 APN 12 89,221,510 (GRCm39) missense probably benign 0.25
IGL01338:Nrxn3 APN 12 89,221,804 (GRCm39) missense possibly damaging 0.86
IGL01377:Nrxn3 APN 12 89,499,782 (GRCm39) critical splice donor site probably null
IGL01409:Nrxn3 APN 12 89,477,128 (GRCm39) missense probably damaging 1.00
IGL01764:Nrxn3 APN 12 90,171,524 (GRCm39) missense possibly damaging 0.48
IGL02063:Nrxn3 APN 12 88,762,565 (GRCm39) missense possibly damaging 0.86
IGL02171:Nrxn3 APN 12 89,159,933 (GRCm39) missense probably damaging 1.00
IGL02309:Nrxn3 APN 12 89,943,175 (GRCm39) missense probably damaging 0.99
IGL02340:Nrxn3 APN 12 90,171,402 (GRCm39) missense possibly damaging 0.82
IGL02343:Nrxn3 APN 12 88,762,123 (GRCm39) missense probably damaging 1.00
IGL02600:Nrxn3 APN 12 89,478,682 (GRCm39) splice site probably benign
IGL02735:Nrxn3 APN 12 89,221,624 (GRCm39) missense probably benign 0.16
IGL03061:Nrxn3 APN 12 89,478,698 (GRCm39) nonsense probably null
IGL03206:Nrxn3 APN 12 89,227,278 (GRCm39) missense possibly damaging 0.88
IGL03337:Nrxn3 APN 12 89,221,790 (GRCm39) missense probably damaging 1.00
R0098:Nrxn3 UTSW 12 89,226,971 (GRCm39) missense probably damaging 1.00
R0098:Nrxn3 UTSW 12 89,226,971 (GRCm39) missense probably damaging 1.00
R0144:Nrxn3 UTSW 12 89,315,162 (GRCm39) missense probably damaging 1.00
R0334:Nrxn3 UTSW 12 89,780,412 (GRCm39) critical splice donor site probably null
R0531:Nrxn3 UTSW 12 88,762,112 (GRCm39) missense probably damaging 1.00
R0840:Nrxn3 UTSW 12 90,298,567 (GRCm39) missense possibly damaging 0.68
R1324:Nrxn3 UTSW 12 89,221,466 (GRCm39) missense possibly damaging 0.89
R1438:Nrxn3 UTSW 12 90,298,909 (GRCm39) missense probably damaging 1.00
R1484:Nrxn3 UTSW 12 89,221,547 (GRCm39) missense probably damaging 0.99
R1621:Nrxn3 UTSW 12 88,762,480 (GRCm39) missense probably benign
R1637:Nrxn3 UTSW 12 89,321,238 (GRCm39) missense possibly damaging 0.94
R1659:Nrxn3 UTSW 12 90,299,165 (GRCm39) missense probably damaging 1.00
R1746:Nrxn3 UTSW 12 89,221,789 (GRCm39) missense possibly damaging 0.63
R1801:Nrxn3 UTSW 12 90,250,356 (GRCm39) missense probably damaging 1.00
R1912:Nrxn3 UTSW 12 88,762,112 (GRCm39) missense probably damaging 1.00
R1940:Nrxn3 UTSW 12 89,227,151 (GRCm39) missense probably damaging 0.98
R1993:Nrxn3 UTSW 12 89,227,181 (GRCm39) missense possibly damaging 0.59
R2125:Nrxn3 UTSW 12 89,227,290 (GRCm39) splice site probably null
R2179:Nrxn3 UTSW 12 89,221,448 (GRCm39) missense probably damaging 1.00
R2207:Nrxn3 UTSW 12 89,315,082 (GRCm39) missense probably damaging 1.00
R2284:Nrxn3 UTSW 12 89,477,135 (GRCm39) missense probably damaging 1.00
R2433:Nrxn3 UTSW 12 89,943,160 (GRCm39) missense probably damaging 1.00
R2969:Nrxn3 UTSW 12 89,321,241 (GRCm39) missense probably damaging 1.00
R3053:Nrxn3 UTSW 12 89,221,871 (GRCm39) missense probably damaging 0.99
R3076:Nrxn3 UTSW 12 89,227,186 (GRCm39) missense probably damaging 1.00
R3078:Nrxn3 UTSW 12 89,227,186 (GRCm39) missense probably damaging 1.00
R4033:Nrxn3 UTSW 12 89,499,771 (GRCm39) missense probably damaging 1.00
R4222:Nrxn3 UTSW 12 89,499,762 (GRCm39) nonsense probably null
R4321:Nrxn3 UTSW 12 90,166,005 (GRCm39) missense probably damaging 1.00
R4470:Nrxn3 UTSW 12 90,171,515 (GRCm39) missense probably damaging 1.00
R4471:Nrxn3 UTSW 12 90,171,515 (GRCm39) missense probably damaging 1.00
R4472:Nrxn3 UTSW 12 90,171,515 (GRCm39) missense probably damaging 1.00
R4686:Nrxn3 UTSW 12 89,477,421 (GRCm39) missense probably damaging 0.99
R4776:Nrxn3 UTSW 12 90,298,730 (GRCm39) missense possibly damaging 0.55
R4821:Nrxn3 UTSW 12 90,171,483 (GRCm39) missense probably damaging 0.99
R4869:Nrxn3 UTSW 12 88,762,352 (GRCm39) missense possibly damaging 0.95
R4910:Nrxn3 UTSW 12 89,227,130 (GRCm39) missense possibly damaging 0.72
R4960:Nrxn3 UTSW 12 88,761,971 (GRCm39) missense possibly damaging 0.79
R4990:Nrxn3 UTSW 12 89,227,244 (GRCm39) missense probably damaging 1.00
R4991:Nrxn3 UTSW 12 89,227,244 (GRCm39) missense probably damaging 1.00
R5057:Nrxn3 UTSW 12 89,221,804 (GRCm39) missense probably damaging 0.99
R5329:Nrxn3 UTSW 12 89,780,354 (GRCm39) missense possibly damaging 0.92
R5888:Nrxn3 UTSW 12 89,478,855 (GRCm39) missense possibly damaging 0.91
R6249:Nrxn3 UTSW 12 89,221,448 (GRCm39) missense probably damaging 1.00
R6264:Nrxn3 UTSW 12 90,299,011 (GRCm39) missense probably damaging 1.00
R6373:Nrxn3 UTSW 12 89,943,237 (GRCm39) missense probably damaging 1.00
R6401:Nrxn3 UTSW 12 89,221,770 (GRCm39) missense possibly damaging 0.46
R6434:Nrxn3 UTSW 12 88,762,285 (GRCm39) missense probably benign 0.32
R6528:Nrxn3 UTSW 12 89,479,819 (GRCm39) missense probably damaging 1.00
R6612:Nrxn3 UTSW 12 89,780,102 (GRCm39) intron probably benign
R6632:Nrxn3 UTSW 12 89,159,924 (GRCm39) missense probably damaging 1.00
R6874:Nrxn3 UTSW 12 90,298,964 (GRCm39) missense probably damaging 0.99
R7122:Nrxn3 UTSW 12 89,477,377 (GRCm39) missense probably damaging 1.00
R7328:Nrxn3 UTSW 12 88,762,345 (GRCm39) missense probably benign
R7352:Nrxn3 UTSW 12 88,817,063 (GRCm39) missense probably benign
R7425:Nrxn3 UTSW 12 89,479,870 (GRCm39) nonsense probably null
R7444:Nrxn3 UTSW 12 89,477,464 (GRCm39) missense probably damaging 1.00
R7483:Nrxn3 UTSW 12 89,477,232 (GRCm39) missense probably damaging 1.00
R7599:Nrxn3 UTSW 12 89,478,832 (GRCm39) missense probably benign
R7738:Nrxn3 UTSW 12 88,817,074 (GRCm39) missense possibly damaging 0.68
R7765:Nrxn3 UTSW 12 89,780,254 (GRCm39) missense probably benign 0.03
R8139:Nrxn3 UTSW 12 90,171,438 (GRCm39) missense probably benign 0.01
R8192:Nrxn3 UTSW 12 90,171,569 (GRCm39) missense probably benign 0.08
R8351:Nrxn3 UTSW 12 89,477,413 (GRCm39) missense probably damaging 1.00
R8368:Nrxn3 UTSW 12 90,298,815 (GRCm39) nonsense probably null
R8397:Nrxn3 UTSW 12 90,298,583 (GRCm39) missense probably benign 0.17
R8426:Nrxn3 UTSW 12 88,762,097 (GRCm39) missense possibly damaging 0.91
R8451:Nrxn3 UTSW 12 89,477,413 (GRCm39) missense probably damaging 1.00
R8777:Nrxn3 UTSW 12 89,227,234 (GRCm39) missense probably damaging 1.00
R8777-TAIL:Nrxn3 UTSW 12 89,227,234 (GRCm39) missense probably damaging 1.00
R8844:Nrxn3 UTSW 12 89,153,920 (GRCm39) missense possibly damaging 0.88
R8870:Nrxn3 UTSW 12 90,171,560 (GRCm39) missense probably benign 0.00
R9043:Nrxn3 UTSW 12 89,227,252 (GRCm39) missense probably damaging 1.00
R9102:Nrxn3 UTSW 12 90,298,924 (GRCm39) missense probably benign 0.01
R9167:Nrxn3 UTSW 12 89,154,068 (GRCm39) missense probably damaging 1.00
R9445:Nrxn3 UTSW 12 89,499,737 (GRCm39) nonsense probably null
R9447:Nrxn3 UTSW 12 89,221,678 (GRCm39) missense probably benign 0.35
X0019:Nrxn3 UTSW 12 90,165,995 (GRCm39) missense probably damaging 1.00
Z1176:Nrxn3 UTSW 12 89,484,679 (GRCm39) missense possibly damaging 0.45
Z1176:Nrxn3 UTSW 12 89,153,825 (GRCm39) nonsense probably null
Z1177:Nrxn3 UTSW 12 90,298,619 (GRCm39) missense probably benign 0.05
Z1177:Nrxn3 UTSW 12 89,227,082 (GRCm39) missense probably damaging 1.00
Z1177:Nrxn3 UTSW 12 88,762,458 (GRCm39) missense probably benign 0.00
Z1177:Nrxn3 UTSW 12 90,298,888 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- CCATGTTCCGTAATGTGCCC -3'
(R):5'- CTCATTGTCAAAGTATTCAGGTGTG -3'

Sequencing Primer
(F):5'- GTTCCGTAATGTGCCCACAGC -3'
(R):5'- GTCAAAGTATTCAGGTGTGTGTATAG -3'
Posted On 2014-08-25