Incidental Mutation 'R5992:Plxnd1'
ID 480884
Institutional Source Beutler Lab
Gene Symbol Plxnd1
Ensembl Gene ENSMUSG00000030123
Gene Name plexin D1
Synonyms b2b553Clo, 6230425C21Rik, b2b1863Clo
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5992 (G1)
Quality Score 225.009
Status Not validated
Chromosome 6
Chromosomal Location 115954811-115995005 bp(-) (GRCm38)
Type of Mutation critical splice acceptor site
DNA Base Change (assembly) C to A at 115967787 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change
Gene Model predicted gene model for transcript(s): [ENSMUST00000015511]
AlphaFold Q3UH93
Predicted Effect probably benign
Transcript: ENSMUST00000015511
AA Change: Q1015H

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000015511
Gene: ENSMUSG00000030123
AA Change: Q1015H

DomainStartEndE-ValueType
signal peptide 1 48 N/A INTRINSIC
Sema 61 531 6.52e-90 SMART
PSI 550 603 6.06e-12 SMART
PSI 703 755 1.06e-2 SMART
Blast:PSI 850 891 9e-20 BLAST
IPT 892 981 4.43e-20 SMART
IPT 982 1068 6.61e-19 SMART
IPT 1070 1149 6.13e-14 SMART
transmembrane domain 1271 1293 N/A INTRINSIC
Pfam:Plexin_cytopl 1345 1888 5e-238 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000131590
SMART Domains Protein: ENSMUSP00000115650
Gene: ENSMUSG00000030123

DomainStartEndE-ValueType
Blast:PSI 2 34 1e-13 BLAST
IPT 35 124 4.43e-20 SMART
Blast:IPT 125 177 3e-30 BLAST
Pfam:TIG 180 233 4.6e-6 PFAM
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.4%
  • 20x: 91.9%
Validation Efficiency
MGI Phenotype PHENOTYPE: Homozygous null mice display neonatal lethality, thin-walled atria, and vascular abnormalities including abnormal branchial arch artery development, cardiac outflow tract abnormalities, and reduced vascular smooth muscle around some vessels. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aars2 T A 17: 45,508,623 (GRCm38) L188* probably null Het
Acod1 C T 14: 103,055,035 (GRCm38) R332C probably damaging Het
Adamts3 T A 5: 89,691,335 (GRCm38) K852M probably damaging Het
Adm A T 7: 110,627,696 (GRCm38) probably benign Het
Aff4 A G 11: 53,373,010 (GRCm38) S286G probably damaging Het
Ank2 A G 3: 126,959,651 (GRCm38) probably null Het
Aqr A T 2: 114,143,049 (GRCm38) Y427* probably null Het
Arid1b C A 17: 4,994,956 (GRCm38) probably benign Het
Arpp21 T A 9: 112,143,485 (GRCm38) R259* probably null Het
Cep290 C T 10: 100,543,321 (GRCm38) A55V possibly damaging Het
Chsy3 GT G 18: 59,176,166 (GRCm38) 163 probably null Het
Clcn2 T C 16: 20,713,654 (GRCm38) E68G possibly damaging Het
Corin T A 5: 72,316,389 (GRCm38) H699L probably benign Het
Cyld T C 8: 88,733,053 (GRCm38) Y446H probably damaging Het
Dcst1 T A 3: 89,352,576 (GRCm38) E613V probably damaging Het
Dlk1 T C 12: 109,455,581 (GRCm38) C74R probably damaging Het
Dnah12 A C 14: 26,697,341 (GRCm38) K128T probably benign Het
Dspp T A 5: 104,178,451 (GRCm38) S893R unknown Het
Dtl A T 1: 191,568,572 (GRCm38) probably null Het
F2rl1 T A 13: 95,514,270 (GRCm38) S35C probably benign Het
Fcgbp A T 7: 28,120,534 (GRCm38) Y2562F probably benign Het
Fgf10 A T 13: 118,715,508 (GRCm38) D42V probably benign Het
Gm10271 A T 10: 116,972,592 (GRCm38) F6L probably damaging Het
Gm21190 T A 5: 15,524,851 (GRCm38) E256D probably damaging Het
Gm5157 A G 7: 21,185,421 (GRCm38) S66P probably damaging Het
Gm884 A T 11: 103,613,792 (GRCm38) M2450K possibly damaging Het
Hal T G 10: 93,490,916 (GRCm38) L138R probably damaging Het
Hsd17b3 T C 13: 64,059,470 (GRCm38) probably null Het
Lrsam1 T C 2: 32,955,222 (GRCm38) T94A probably benign Het
Macc1 T C 12: 119,447,585 (GRCm38) V696A probably damaging Het
Magi2 G A 5: 19,227,291 (GRCm38) M1I probably null Het
March7 C A 2: 60,245,220 (GRCm38) N674K probably benign Het
Mfap1b A G 2: 121,470,295 (GRCm38) V34A probably benign Het
Mob3b G A 4: 35,084,069 (GRCm38) S40L probably benign Het
Ndufs2 A T 1: 171,236,418 (GRCm38) V386E probably damaging Het
Nfic C T 10: 81,420,747 (GRCm38) A19T probably damaging Het
Nfs1 G A 2: 156,134,453 (GRCm38) R174W probably damaging Het
Nin G T 12: 70,045,524 (GRCm38) S670R possibly damaging Het
Nrxn1 T C 17: 90,623,507 (GRCm38) I754V probably benign Het
Nwd1 T C 8: 72,653,573 (GRCm38) probably null Het
Olfr1231 T A 2: 89,303,359 (GRCm38) T78S possibly damaging Het
Olfr1238 T A 2: 89,406,879 (GRCm38) M67L probably benign Het
Olfr575 G T 7: 102,955,009 (GRCm38) N197K probably benign Het
Pcdhgb8 A G 18: 37,763,449 (GRCm38) E524G probably damaging Het
Phlpp1 A T 1: 106,318,993 (GRCm38) R638* probably null Het
Pkmyt1 G C 17: 23,735,326 (GRCm38) W360S probably benign Het
Poldip3 A T 15: 83,129,229 (GRCm38) N322K probably damaging Het
Prmt3 A T 7: 49,828,947 (GRCm38) I419L probably benign Het
Prss36 A T 7: 127,944,830 (GRCm38) V123E probably damaging Het
Prss58 A G 6: 40,897,769 (GRCm38) I46T probably damaging Het
Rac1 T C 5: 143,506,998 (GRCm38) probably benign Het
Rb1cc1 A G 1: 6,233,996 (GRCm38) Y36C probably damaging Het
Rif1 C G 2: 52,095,844 (GRCm38) L614V probably damaging Het
Rnd2 C T 11: 101,468,999 (GRCm38) L57F probably damaging Het
Rp1 A T 1: 4,148,703 (GRCm38) F951L unknown Het
Rps6ka5 G T 12: 100,575,250 (GRCm38) P417T possibly damaging Het
Ryr1 A G 7: 29,067,637 (GRCm38) W2967R probably damaging Het
Sacs T A 14: 61,205,543 (GRCm38) S1679R probably damaging Het
Scn1a A C 2: 66,335,456 (GRCm38) W153G probably damaging Het
Serpinb7 A G 1: 107,445,996 (GRCm38) Y114C probably damaging Het
Son T C 16: 91,658,904 (GRCm38) M1513T probably benign Het
Spag8 C T 4: 43,651,534 (GRCm38) V447M probably benign Het
St3gal2 T A 8: 110,969,553 (GRCm38) Y257N probably damaging Het
Tars A T 15: 11,397,196 (GRCm38) D40E probably damaging Het
Tlr3 T C 8: 45,397,814 (GRCm38) H158R probably benign Het
Tppp2 G T 14: 51,918,935 (GRCm38) V50L probably benign Het
Trrap T C 5: 144,810,184 (GRCm38) S1503P probably benign Het
Ttll4 T G 1: 74,685,391 (GRCm38) S573R probably damaging Het
Vmn2r104 A T 17: 20,029,485 (GRCm38) N841K probably damaging Het
Vmn2r3 A T 3: 64,259,647 (GRCm38) C688S probably damaging Het
Vps16 T C 2: 130,424,449 (GRCm38) probably null Het
Zfp608 G A 18: 54,899,248 (GRCm38) T540I probably benign Het
Zfp775 G A 6: 48,619,816 (GRCm38) R208Q probably damaging Het
Other mutations in Plxnd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00764:Plxnd1 APN 6 115,967,972 (GRCm38) missense possibly damaging 0.51
IGL01099:Plxnd1 APN 6 115,969,945 (GRCm38) missense probably benign
IGL01323:Plxnd1 APN 6 115,966,799 (GRCm38) missense possibly damaging 0.81
IGL01382:Plxnd1 APN 6 115,960,527 (GRCm38) missense probably damaging 1.00
IGL01786:Plxnd1 APN 6 115,959,935 (GRCm38) missense probably damaging 1.00
IGL02244:Plxnd1 APN 6 115,978,257 (GRCm38) missense probably benign 0.39
IGL02272:Plxnd1 APN 6 115,993,628 (GRCm38) missense probably damaging 1.00
IGL02293:Plxnd1 APN 6 115,963,913 (GRCm38) missense probably damaging 1.00
IGL02465:Plxnd1 APN 6 115,955,742 (GRCm38) makesense probably null
IGL02873:Plxnd1 APN 6 115,959,976 (GRCm38) missense probably damaging 1.00
IGL03209:Plxnd1 APN 6 115,962,357 (GRCm38) missense probably damaging 1.00
Hiss UTSW 6 115,969,929 (GRCm38) missense possibly damaging 0.94
murmer UTSW 6 115,968,793 (GRCm38) missense probably benign 0.00
mutter UTSW 6 115,968,044 (GRCm38) missense probably benign 0.27
rattle UTSW 6 115,959,794 (GRCm38) missense probably damaging 0.96
R0238:Plxnd1 UTSW 6 115,968,793 (GRCm38) missense probably benign 0.00
R0238:Plxnd1 UTSW 6 115,968,793 (GRCm38) missense probably benign 0.00
R0239:Plxnd1 UTSW 6 115,968,793 (GRCm38) missense probably benign 0.00
R0239:Plxnd1 UTSW 6 115,968,793 (GRCm38) missense probably benign 0.00
R0357:Plxnd1 UTSW 6 115,969,460 (GRCm38) missense probably benign 0.00
R0646:Plxnd1 UTSW 6 115,958,699 (GRCm38) splice site probably benign
R0648:Plxnd1 UTSW 6 115,994,001 (GRCm38) missense possibly damaging 0.86
R0718:Plxnd1 UTSW 6 115,966,638 (GRCm38) missense possibly damaging 0.68
R1116:Plxnd1 UTSW 6 115,967,005 (GRCm38) splice site probably null
R1292:Plxnd1 UTSW 6 115,962,683 (GRCm38) unclassified probably benign
R1715:Plxnd1 UTSW 6 115,968,681 (GRCm38) missense probably benign 0.02
R1760:Plxnd1 UTSW 6 115,967,779 (GRCm38) missense possibly damaging 0.95
R1799:Plxnd1 UTSW 6 115,994,057 (GRCm38) missense probably damaging 1.00
R1817:Plxnd1 UTSW 6 115,980,601 (GRCm38) missense possibly damaging 0.83
R1848:Plxnd1 UTSW 6 115,966,546 (GRCm38) missense probably damaging 1.00
R1851:Plxnd1 UTSW 6 115,963,914 (GRCm38) missense probably damaging 1.00
R1864:Plxnd1 UTSW 6 115,969,441 (GRCm38) splice site probably null
R1865:Plxnd1 UTSW 6 115,969,441 (GRCm38) splice site probably null
R1875:Plxnd1 UTSW 6 115,978,084 (GRCm38) splice site probably null
R1899:Plxnd1 UTSW 6 115,969,363 (GRCm38) missense probably benign
R1913:Plxnd1 UTSW 6 115,978,017 (GRCm38) missense possibly damaging 0.50
R1970:Plxnd1 UTSW 6 115,962,517 (GRCm38) missense probably damaging 1.00
R2007:Plxnd1 UTSW 6 115,967,255 (GRCm38) missense probably damaging 1.00
R2134:Plxnd1 UTSW 6 115,957,548 (GRCm38) missense probably damaging 1.00
R2202:Plxnd1 UTSW 6 115,962,764 (GRCm38) missense probably benign 0.45
R2230:Plxnd1 UTSW 6 115,964,144 (GRCm38) missense probably damaging 1.00
R2267:Plxnd1 UTSW 6 115,962,743 (GRCm38) missense probably benign 0.29
R2427:Plxnd1 UTSW 6 115,967,748 (GRCm38) critical splice donor site probably null
R4108:Plxnd1 UTSW 6 115,959,315 (GRCm38) missense probably damaging 1.00
R4233:Plxnd1 UTSW 6 115,965,953 (GRCm38) missense probably benign 0.30
R4280:Plxnd1 UTSW 6 115,956,095 (GRCm38) splice site probably null
R4280:Plxnd1 UTSW 6 115,956,094 (GRCm38) splice site probably benign
R4346:Plxnd1 UTSW 6 115,977,980 (GRCm38) missense probably benign 0.16
R4439:Plxnd1 UTSW 6 115,993,976 (GRCm38) missense probably damaging 0.99
R4572:Plxnd1 UTSW 6 115,955,756 (GRCm38) missense probably damaging 1.00
R4576:Plxnd1 UTSW 6 115,968,044 (GRCm38) missense probably benign 0.27
R4599:Plxnd1 UTSW 6 115,994,276 (GRCm38) missense probably damaging 1.00
R4614:Plxnd1 UTSW 6 115,972,525 (GRCm38) missense possibly damaging 0.83
R4700:Plxnd1 UTSW 6 115,958,615 (GRCm38) missense probably damaging 1.00
R4705:Plxnd1 UTSW 6 115,958,620 (GRCm38) missense probably damaging 1.00
R4806:Plxnd1 UTSW 6 115,960,855 (GRCm38) missense probably damaging 1.00
R4944:Plxnd1 UTSW 6 115,955,765 (GRCm38) missense probably damaging 1.00
R4977:Plxnd1 UTSW 6 115,994,376 (GRCm38) missense probably damaging 1.00
R5069:Plxnd1 UTSW 6 115,965,901 (GRCm38) missense probably damaging 0.98
R5155:Plxnd1 UTSW 6 115,958,988 (GRCm38) critical splice donor site probably null
R5460:Plxnd1 UTSW 6 115,957,648 (GRCm38) missense probably damaging 1.00
R5729:Plxnd1 UTSW 6 115,965,877 (GRCm38) missense probably damaging 1.00
R5909:Plxnd1 UTSW 6 115,968,688 (GRCm38) missense probably benign 0.00
R6129:Plxnd1 UTSW 6 115,978,174 (GRCm38) missense probably damaging 1.00
R6254:Plxnd1 UTSW 6 115,977,960 (GRCm38) missense probably benign 0.01
R6273:Plxnd1 UTSW 6 115,978,492 (GRCm38) missense probably damaging 1.00
R6310:Plxnd1 UTSW 6 115,976,736 (GRCm38) missense possibly damaging 0.94
R6732:Plxnd1 UTSW 6 115,969,929 (GRCm38) missense possibly damaging 0.94
R6857:Plxnd1 UTSW 6 115,993,763 (GRCm38) missense probably benign 0.05
R7243:Plxnd1 UTSW 6 115,972,507 (GRCm38) missense probably benign 0.00
R7282:Plxnd1 UTSW 6 115,960,837 (GRCm38) missense probably damaging 1.00
R7632:Plxnd1 UTSW 6 115,976,639 (GRCm38) missense probably benign
R7699:Plxnd1 UTSW 6 115,959,794 (GRCm38) missense probably damaging 0.96
R7915:Plxnd1 UTSW 6 115,966,918 (GRCm38) missense probably benign 0.00
R8090:Plxnd1 UTSW 6 115,956,617 (GRCm38) missense probably damaging 1.00
R8382:Plxnd1 UTSW 6 115,972,472 (GRCm38) missense probably benign
R8507:Plxnd1 UTSW 6 115,966,905 (GRCm38) missense probably damaging 0.97
R8539:Plxnd1 UTSW 6 115,962,807 (GRCm38) missense possibly damaging 0.94
R8548:Plxnd1 UTSW 6 115,957,597 (GRCm38) missense probably damaging 1.00
R8963:Plxnd1 UTSW 6 115,972,545 (GRCm38) nonsense probably null
R9119:Plxnd1 UTSW 6 115,955,871 (GRCm38) splice site probably benign
R9177:Plxnd1 UTSW 6 115,966,508 (GRCm38) missense probably benign 0.00
R9182:Plxnd1 UTSW 6 115,993,785 (GRCm38) missense probably damaging 0.98
R9185:Plxnd1 UTSW 6 115,957,565 (GRCm38) missense probably damaging 1.00
R9226:Plxnd1 UTSW 6 115,957,563 (GRCm38) missense probably damaging 1.00
R9433:Plxnd1 UTSW 6 115,968,793 (GRCm38) missense probably benign 0.00
R9449:Plxnd1 UTSW 6 115,955,769 (GRCm38) missense probably damaging 1.00
R9451:Plxnd1 UTSW 6 115,963,316 (GRCm38) missense possibly damaging 0.72
R9599:Plxnd1 UTSW 6 115,963,313 (GRCm38) missense possibly damaging 0.78
R9627:Plxnd1 UTSW 6 115,963,313 (GRCm38) missense possibly damaging 0.78
R9644:Plxnd1 UTSW 6 115,963,313 (GRCm38) missense possibly damaging 0.78
R9672:Plxnd1 UTSW 6 115,963,313 (GRCm38) missense possibly damaging 0.78
X0024:Plxnd1 UTSW 6 115,963,310 (GRCm38) missense probably benign 0.02
X0026:Plxnd1 UTSW 6 115,966,784 (GRCm38) missense possibly damaging 0.88
Z1088:Plxnd1 UTSW 6 115,967,510 (GRCm38) missense probably benign 0.02
Predicted Primers PCR Primer
(F):5'- TTGTTCACCCACTGCAGGTC -3'
(R):5'- TCTCCTATGTGGTAAGTAGGCC -3'

Sequencing Primer
(F):5'- AGGTCCCTCAGCCTTGTG -3'
(R):5'- TGGTAAGTAGGCCACCACCTC -3'
Posted On 2017-06-26