Incidental Mutation 'R6454:Plekhm1'
ID 519491
Institutional Source Beutler Lab
Gene Symbol Plekhm1
Ensembl Gene ENSMUSG00000034247
Gene Name pleckstrin homology domain containing, family M (with RUN domain) member 1
Synonyms AP162, B2, D330036J23Rik
MMRRC Submission 044590-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6454 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 103255101-103303513 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 103268208 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Cysteine at position 588 (R588C)
Ref Sequence ENSEMBL: ENSMUSP00000047327 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041272]
AlphaFold Q7TSI1
Predicted Effect probably damaging
Transcript: ENSMUST00000041272
AA Change: R588C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000047327
Gene: ENSMUSG00000034247
AA Change: R588C

DomainStartEndE-ValueType
RUN 117 180 3.36e-20 SMART
low complexity region 246 273 N/A INTRINSIC
low complexity region 336 350 N/A INTRINSIC
low complexity region 361 373 N/A INTRINSIC
Blast:DUF4206 448 543 2e-11 BLAST
PH 552 644 2.16e-9 SMART
low complexity region 658 674 N/A INTRINSIC
PH 702 797 2.15e-4 SMART
DUF4206 864 1068 7.51e-103 SMART
C1 1005 1058 2.72e-3 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000184350
Meta Mutation Damage Score 0.6329 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.1%
  • 20x: 94.1%
Validation Efficiency 100% (63/63)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is essential for bone resorption, and may play a critical role in vesicular transport in the osteoclast. Mutations in this gene are associated with autosomal recessive osteopetrosis type 6 (OPTB6). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2009]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit increased trabecular bone mass and decreased bone resorption capacity of osteoclasts caused by defects in the peripheral positioning and secretion of lysosomes. Mice homozygous for a gene trap insertion do not exhibit any detectable phenotype. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam34l G T 8: 44,079,845 (GRCm39) N126K probably damaging Het
Arid2 C T 15: 96,270,294 (GRCm39) T1469I probably benign Het
Atp12a A G 14: 56,608,290 (GRCm39) T93A probably benign Het
Atp8a2 A T 14: 60,245,948 (GRCm39) probably null Het
Casz1 A T 4: 149,035,952 (GRCm39) I1405F probably damaging Het
Chrnb3 T C 8: 27,883,403 (GRCm39) S100P probably damaging Het
Creld2 T A 15: 88,707,274 (GRCm39) C197* probably null Het
Csmd1 A T 8: 15,971,150 (GRCm39) F3055Y probably damaging Het
Dnah11 T A 12: 117,880,590 (GRCm39) E3843D probably benign Het
Dnah14 T C 1: 181,611,270 (GRCm39) S3799P probably damaging Het
Dpp9 A T 17: 56,513,808 (GRCm39) L102Q probably damaging Het
Eipr1 T G 12: 28,914,761 (GRCm39) I305S probably damaging Het
Enpp5 G A 17: 44,396,155 (GRCm39) G356S probably damaging Het
Faf1 G T 4: 109,699,531 (GRCm39) A359S probably benign Het
Fam13b A G 18: 34,590,715 (GRCm39) probably null Het
Gm14496 A T 2: 181,638,015 (GRCm39) N363I probably damaging Het
Grm8 T G 6: 27,363,775 (GRCm39) H580P possibly damaging Het
Itih5 T C 2: 10,245,479 (GRCm39) F523L probably benign Het
Klhl1 A T 14: 96,517,527 (GRCm39) M383K possibly damaging Het
Lgi4 A T 7: 30,759,557 (GRCm39) T38S probably benign Het
Myh13 T A 11: 67,241,191 (GRCm39) M856K probably benign Het
Myo7a C T 7: 97,722,374 (GRCm39) V1184M probably benign Het
Nlrp9c G A 7: 26,085,199 (GRCm39) R127C possibly damaging Het
Notch2 T C 3: 98,044,722 (GRCm39) I1548T possibly damaging Het
Nphs2 T A 1: 156,146,337 (GRCm39) H179Q probably damaging Het
Nup153 T C 13: 46,863,136 (GRCm39) probably null Het
Nup50l T G 6: 96,142,609 (GRCm39) H145P possibly damaging Het
Odf2l C A 3: 144,859,181 (GRCm39) Q517K possibly damaging Het
Omd A T 13: 49,743,345 (GRCm39) I132F probably damaging Het
Or10d1b A G 9: 39,613,130 (GRCm39) *312Q probably null Het
Or4a81 T C 2: 89,619,522 (GRCm39) Y58C probably damaging Het
Or5b12 T A 19: 12,897,395 (GRCm39) N93Y probably benign Het
Or9g19 A G 2: 85,600,717 (GRCm39) K191E probably benign Het
Otog A G 7: 45,955,241 (GRCm39) N544D probably damaging Het
Ovol3 A G 7: 29,934,800 (GRCm39) Y29H probably damaging Het
Papolb T C 5: 142,515,353 (GRCm39) K97E possibly damaging Het
Pcdhb19 G T 18: 37,632,322 (GRCm39) V706L probably benign Het
Pira1 C G 7: 3,740,319 (GRCm39) A301P probably damaging Het
Pnpla6 G T 8: 3,587,986 (GRCm39) V1062L probably damaging Het
Ppp1r9a T A 6: 4,905,827 (GRCm39) F127L probably damaging Het
Rigi T A 4: 40,220,456 (GRCm39) I476F probably damaging Het
Rnf5 A C 17: 34,821,283 (GRCm39) C47W probably damaging Het
Sbno1 A T 5: 124,538,910 (GRCm39) M517K probably damaging Het
Slc44a5 C T 3: 153,948,796 (GRCm39) T188M probably benign Het
Smco1 A G 16: 32,092,041 (GRCm39) T40A possibly damaging Het
Speer4f2 A T 5: 17,579,431 (GRCm39) I77F probably damaging Het
Spem2 A G 11: 69,708,254 (GRCm39) L237P probably damaging Het
Spg7 A G 8: 123,806,162 (GRCm39) K291E possibly damaging Het
Tent5b A G 4: 133,207,720 (GRCm39) D37G probably damaging Het
Tiam2 A T 17: 3,488,938 (GRCm39) T749S probably benign Het
Tln1 T C 4: 43,533,866 (GRCm39) K2291E probably damaging Het
Tm6sf1 A G 7: 81,525,801 (GRCm39) M294V probably damaging Het
Tmem35b T C 4: 127,022,811 (GRCm39) *138R probably null Het
Tpst1 A G 5: 130,130,892 (GRCm39) K121E possibly damaging Het
Tsc22d2 T A 3: 58,323,261 (GRCm39) V51D possibly damaging Het
Tshr C A 12: 91,505,323 (GRCm39) Q754K probably benign Het
Ttc38 T A 15: 85,723,023 (GRCm39) M157K probably damaging Het
Ube2g2 T G 10: 77,470,580 (GRCm39) probably benign Het
Ugt2b37 T G 5: 87,388,836 (GRCm39) D459A probably damaging Het
Usp35 A T 7: 96,960,851 (GRCm39) Y858* probably null Het
Usp35 A T 7: 96,960,767 (GRCm39) N886K probably damaging Het
Wdr33 T C 18: 31,963,028 (GRCm39) V125A possibly damaging Het
Xpnpep1 G A 19: 52,986,310 (GRCm39) T506I possibly damaging Het
Other mutations in Plekhm1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01517:Plekhm1 APN 11 103,285,609 (GRCm39) missense possibly damaging 0.54
IGL01876:Plekhm1 APN 11 103,267,577 (GRCm39) missense probably damaging 1.00
IGL02159:Plekhm1 APN 11 103,271,057 (GRCm39) missense probably benign 0.04
IGL02404:Plekhm1 APN 11 103,285,824 (GRCm39) missense probably benign 0.18
IGL02537:Plekhm1 APN 11 103,288,018 (GRCm39) missense probably damaging 1.00
IGL02568:Plekhm1 APN 11 103,285,876 (GRCm39) missense probably damaging 1.00
IGL02660:Plekhm1 APN 11 103,264,920 (GRCm39) splice site probably benign
IGL03130:Plekhm1 APN 11 103,268,207 (GRCm39) missense probably benign 0.17
IGL03208:Plekhm1 APN 11 103,267,596 (GRCm39) missense probably benign 0.00
R0442:Plekhm1 UTSW 11 103,288,000 (GRCm39) missense possibly damaging 0.45
R0491:Plekhm1 UTSW 11 103,285,602 (GRCm39) missense probably benign 0.05
R0520:Plekhm1 UTSW 11 103,285,770 (GRCm39) missense probably benign 0.17
R0964:Plekhm1 UTSW 11 103,285,908 (GRCm39) nonsense probably null
R1189:Plekhm1 UTSW 11 103,277,888 (GRCm39) missense probably benign 0.00
R1501:Plekhm1 UTSW 11 103,277,888 (GRCm39) missense probably benign 0.00
R1697:Plekhm1 UTSW 11 103,267,710 (GRCm39) missense probably damaging 1.00
R1781:Plekhm1 UTSW 11 103,285,682 (GRCm39) missense probably damaging 1.00
R1873:Plekhm1 UTSW 11 103,264,824 (GRCm39) missense probably benign 0.01
R2087:Plekhm1 UTSW 11 103,287,851 (GRCm39) critical splice donor site probably null
R2215:Plekhm1 UTSW 11 103,267,811 (GRCm39) missense probably damaging 1.00
R2271:Plekhm1 UTSW 11 103,277,948 (GRCm39) missense probably benign 0.00
R4256:Plekhm1 UTSW 11 103,261,760 (GRCm39) missense probably damaging 0.98
R4393:Plekhm1 UTSW 11 103,267,791 (GRCm39) missense possibly damaging 0.51
R4526:Plekhm1 UTSW 11 103,286,130 (GRCm39) missense probably damaging 0.97
R5119:Plekhm1 UTSW 11 103,278,141 (GRCm39) missense possibly damaging 0.62
R5975:Plekhm1 UTSW 11 103,267,517 (GRCm39) missense possibly damaging 0.49
R6389:Plekhm1 UTSW 11 103,257,720 (GRCm39) missense probably benign 0.21
R6755:Plekhm1 UTSW 11 103,278,069 (GRCm39) missense possibly damaging 0.65
R6830:Plekhm1 UTSW 11 103,267,715 (GRCm39) missense probably damaging 0.97
R7039:Plekhm1 UTSW 11 103,286,054 (GRCm39) missense probably damaging 1.00
R7066:Plekhm1 UTSW 11 103,261,814 (GRCm39) missense possibly damaging 0.47
R7149:Plekhm1 UTSW 11 103,285,742 (GRCm39) missense probably damaging 0.98
R7349:Plekhm1 UTSW 11 103,278,160 (GRCm39) missense probably damaging 0.98
R7505:Plekhm1 UTSW 11 103,270,855 (GRCm39) splice site probably null
R7792:Plekhm1 UTSW 11 103,287,886 (GRCm39) missense probably damaging 0.99
R7867:Plekhm1 UTSW 11 103,271,153 (GRCm39) missense probably damaging 1.00
R8124:Plekhm1 UTSW 11 103,257,775 (GRCm39) missense probably benign 0.02
R8194:Plekhm1 UTSW 11 103,285,886 (GRCm39) missense possibly damaging 0.68
R8725:Plekhm1 UTSW 11 103,258,444 (GRCm39) missense probably damaging 1.00
R8727:Plekhm1 UTSW 11 103,258,444 (GRCm39) missense probably damaging 1.00
R8734:Plekhm1 UTSW 11 103,285,778 (GRCm39) missense probably damaging 1.00
R8927:Plekhm1 UTSW 11 103,268,039 (GRCm39) missense probably benign 0.04
R8928:Plekhm1 UTSW 11 103,268,039 (GRCm39) missense probably benign 0.04
R9681:Plekhm1 UTSW 11 103,258,950 (GRCm39) missense possibly damaging 0.82
X0058:Plekhm1 UTSW 11 103,268,192 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- CACTCATCTTCCTGCTGAGG -3'
(R):5'- ACTCTCCCACAGAACATTGG -3'

Sequencing Primer
(F):5'- TTCCTGCTGAGGGCGCAC -3'
(R):5'- CCAGTTGTGGCTTTGAACTAAAAAGG -3'
Posted On 2018-05-24