Incidental Mutation 'R4660:Ptpn9'
ID 352779
Institutional Source Beutler Lab
Gene Symbol Ptpn9
Ensembl Gene ENSMUSG00000032290
Gene Name protein tyrosine phosphatase, non-receptor type 9
Synonyms Meg2
MMRRC Submission 041920-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.531) question?
Stock # R4660 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 56902252-56970092 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 56943782 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Serine at position 105 (T105S)
Ref Sequence ENSEMBL: ENSMUSP00000150426 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034832] [ENSMUST00000216034]
AlphaFold O35239
Predicted Effect probably benign
Transcript: ENSMUST00000034832
AA Change: T219S

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000034832
Gene: ENSMUSG00000032290
AA Change: T219S

DomainStartEndE-ValueType
CRAL_TRIO_N 43 68 1.14e0 SMART
SEC14 90 240 7.33e-40 SMART
PTPc 302 576 1.01e-136 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000216034
AA Change: T105S

PolyPhen 2 Score 0.174 (Sensitivity: 0.92; Specificity: 0.87)
Meta Mutation Damage Score 0.0619 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 95.0%
Validation Efficiency 96% (102/106)
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 a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains an N-terminal domain that shares a significant similarity with yeast SEC14, which is a protein that has phosphatidylinositol transfer activity and is required for protein secretion through the Golgi complex in yeast. This PTP was found to be activated by polyphosphoinositide, and is thought to be involved in signaling events regulating phagocytosis. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele display hemorrhages, craniofacial anomalies, neural tube defects such as exencephaly and meningomyeloceles, cerebral infarctions, abnormal bone development, and >90% late embryonic lethality in addition to severe defectsin T lymphocyte and platelet activation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 92 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adra1d T C 2: 131,403,062 (GRCm39) T343A probably damaging Het
Angptl4 A T 17: 33,996,249 (GRCm39) probably benign Het
Antxr2 A T 5: 98,151,913 (GRCm39) probably null Het
Ap1b1 T A 11: 4,966,760 (GRCm39) V145E probably damaging Het
Asns G T 6: 7,678,012 (GRCm39) N355K probably benign Het
Asxl3 A G 18: 22,649,534 (GRCm39) T508A probably benign Het
B4galt7 T A 13: 55,752,111 (GRCm39) V54D possibly damaging Het
Bach2 C T 4: 32,562,777 (GRCm39) P415S probably benign Het
Bbs9 G A 9: 22,490,063 (GRCm39) R278Q probably benign Het
Blzf1 C T 1: 164,134,062 (GRCm39) probably benign Het
Btd A T 14: 31,389,760 (GRCm39) T494S probably benign Het
Casp9 C T 4: 141,540,934 (GRCm39) T434I probably benign Het
Cavin2 T C 1: 51,340,510 (GRCm39) S396P probably benign Het
Ccnk C T 12: 108,168,575 (GRCm39) probably benign Het
Cldn8 G A 16: 88,359,296 (GRCm39) H210Y probably benign Het
Clip1 G A 5: 123,717,437 (GRCm39) T1284I probably damaging Het
Coch T C 12: 51,642,268 (GRCm39) V80A probably benign Het
Cttnbp2 A G 6: 18,406,536 (GRCm39) S1052P probably benign Het
Cyp2j7 C T 4: 96,083,579 (GRCm39) R457K probably benign Het
Dalrd3 T C 9: 108,447,568 (GRCm39) S129P probably benign Het
Ddx10 A G 9: 53,147,698 (GRCm39) probably null Het
Dnah7b A T 1: 46,328,696 (GRCm39) T3143S probably damaging Het
Dynlt1b A G 17: 6,699,279 (GRCm39) T10A probably benign Het
Eif2s2 G A 2: 154,730,189 (GRCm39) T36I probably benign Het
Fam118b A T 9: 35,146,551 (GRCm39) H105Q possibly damaging Het
Galntl5 T A 5: 25,408,377 (GRCm39) I250N probably damaging Het
Gm11544 C T 11: 94,736,306 (GRCm39) noncoding transcript Het
Gm5709 C T 3: 59,526,124 (GRCm39) noncoding transcript Het
Golgb1 T A 16: 36,707,980 (GRCm39) I107N probably damaging Het
Gpld1 T C 13: 25,166,586 (GRCm39) probably null Het
Grik1 T A 16: 87,720,019 (GRCm39) T768S probably damaging Het
H2-T23 T G 17: 36,341,108 (GRCm39) Q349P probably damaging Het
Ing3 A T 6: 21,973,710 (GRCm39) probably benign Het
Iqgap3 T G 3: 88,027,483 (GRCm39) L702R probably damaging Het
Itga8 A G 2: 12,270,069 (GRCm39) V139A probably damaging Het
Jam2 G A 16: 84,609,840 (GRCm39) V151M probably damaging Het
Kbtbd12 T C 6: 88,594,772 (GRCm39) I353V probably benign Het
Kif27 T C 13: 58,471,730 (GRCm39) E786G probably damaging Het
Lingo4 T A 3: 94,310,672 (GRCm39) S537T probably benign Het
Lipo3 C T 19: 33,598,360 (GRCm39) probably benign Het
Lrrc3 G T 10: 77,729,866 (GRCm39) probably benign Het
Ltbp3 T A 19: 5,798,814 (GRCm39) probably null Het
Lyg1 T A 1: 37,985,942 (GRCm39) probably benign Het
Mcm9 T C 10: 53,424,623 (GRCm39) I656V probably benign Het
Mfsd8 T A 3: 40,776,372 (GRCm39) I427F probably benign Het
Mga T A 2: 119,769,104 (GRCm39) probably benign Het
Miga1 A G 3: 151,993,155 (GRCm39) L422P probably damaging Het
Msantd3 A G 4: 48,552,536 (GRCm39) I42V probably benign Het
Mybbp1a T C 11: 72,336,538 (GRCm39) V510A probably benign Het
Nccrp1 G T 7: 28,245,760 (GRCm39) P135T probably damaging Het
Neb T A 2: 52,145,600 (GRCm39) M2975L possibly damaging Het
Nfxl1 A T 5: 72,710,011 (GRCm39) I171N probably damaging Het
Odad2 A G 18: 7,211,609 (GRCm39) V755A possibly damaging Het
Or10q3 T C 19: 11,848,412 (GRCm39) H56R possibly damaging Het
Or12j5 A T 7: 140,083,933 (GRCm39) F146L probably benign Het
Or13a19 T C 7: 139,903,325 (GRCm39) F238L possibly damaging Het
Otop1 T G 5: 38,457,368 (GRCm39) S376A possibly damaging Het
Pdgfra T C 5: 75,322,932 (GRCm39) V10A possibly damaging Het
Pgs1 T C 11: 117,910,503 (GRCm39) V538A probably damaging Het
Ppa2 A T 3: 133,032,445 (GRCm39) T97S probably damaging Het
Pramel22 T A 4: 143,380,847 (GRCm39) Y392F probably benign Het
Pramel26 A G 4: 143,538,435 (GRCm39) S179P probably benign Het
Prdm10 G A 9: 31,238,624 (GRCm39) C172Y probably damaging Het
Prrc2c G A 1: 162,508,464 (GRCm39) P1091L probably damaging Het
Pthlh G A 6: 147,158,796 (GRCm39) R55C probably damaging Het
Rundc1 T A 11: 101,324,830 (GRCm39) V512E possibly damaging Het
Scrib G A 15: 75,937,185 (GRCm39) S307L probably damaging Het
Sec23ip A G 7: 128,352,010 (GRCm39) S26G probably null Het
Sec61a2 A G 2: 5,878,504 (GRCm39) probably benign Het
Sema3c T C 5: 17,877,511 (GRCm39) V206A probably damaging Het
Sgk2 C T 2: 162,839,763 (GRCm39) H124Y possibly damaging Het
Slc26a6 C T 9: 108,738,540 (GRCm39) T592I probably damaging Het
Slc5a11 T C 7: 122,864,486 (GRCm39) Y361H probably damaging Het
Smc6 T C 12: 11,324,008 (GRCm39) V51A probably damaging Het
Stab1 A T 14: 30,876,872 (GRCm39) N817K possibly damaging Het
Swt1 A T 1: 151,283,348 (GRCm39) D336E probably benign Het
Taf13 T A 3: 108,480,293 (GRCm39) probably benign Het
Tmub2 T C 11: 102,175,845 (GRCm39) probably benign Het
Tnf A G 17: 35,419,156 (GRCm39) S209P probably benign Het
Try10 A G 6: 41,334,761 (GRCm39) Y229C probably damaging Het
Ttbk1 G T 17: 46,788,714 (GRCm39) Y183* probably null Het
Ttc17 A T 2: 94,194,774 (GRCm39) I533N possibly damaging Het
Tubb6 C T 18: 67,535,016 (GRCm39) P305L probably damaging Het
Tulp3 G A 6: 128,300,017 (GRCm39) probably benign Het
Usp9x A G X: 12,989,747 (GRCm39) R776G possibly damaging Het
Virma T C 4: 11,513,505 (GRCm39) V453A probably damaging Het
Vmn2r103 A T 17: 20,032,077 (GRCm39) N617I probably damaging Het
Xirp1 G T 9: 119,846,058 (GRCm39) L942M probably damaging Het
Zc3h7b T G 15: 81,676,451 (GRCm39) V731G probably benign Het
Zfp534 C T 4: 147,759,175 (GRCm39) G498D probably benign Het
Zfp639 T C 3: 32,574,679 (GRCm39) Y435H probably damaging Het
Zxdc A G 6: 90,355,820 (GRCm39) H443R probably damaging Het
Other mutations in Ptpn9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01072:Ptpn9 APN 9 56,943,987 (GRCm39) missense possibly damaging 0.68
IGL01388:Ptpn9 APN 9 56,944,002 (GRCm39) missense probably benign 0.00
IGL01953:Ptpn9 APN 9 56,964,072 (GRCm39) missense possibly damaging 0.69
IGL02525:Ptpn9 APN 9 56,944,009 (GRCm39) nonsense probably null
IGL03294:Ptpn9 APN 9 56,934,671 (GRCm39) missense possibly damaging 0.79
BB009:Ptpn9 UTSW 9 56,943,900 (GRCm39) missense possibly damaging 0.48
BB019:Ptpn9 UTSW 9 56,943,900 (GRCm39) missense possibly damaging 0.48
PIT4486001:Ptpn9 UTSW 9 56,968,287 (GRCm39) missense probably damaging 0.99
R0530:Ptpn9 UTSW 9 56,968,417 (GRCm39) missense probably benign
R1617:Ptpn9 UTSW 9 56,934,692 (GRCm39) missense possibly damaging 0.79
R1964:Ptpn9 UTSW 9 56,967,196 (GRCm39) missense probably damaging 1.00
R2426:Ptpn9 UTSW 9 56,934,712 (GRCm39) missense possibly damaging 0.61
R4394:Ptpn9 UTSW 9 56,943,847 (GRCm39) missense possibly damaging 0.91
R4606:Ptpn9 UTSW 9 56,929,495 (GRCm39) missense possibly damaging 0.71
R4658:Ptpn9 UTSW 9 56,927,321 (GRCm39) missense probably benign 0.01
R5141:Ptpn9 UTSW 9 56,943,960 (GRCm39) missense possibly damaging 0.56
R5150:Ptpn9 UTSW 9 56,943,954 (GRCm39) missense probably benign
R5289:Ptpn9 UTSW 9 56,967,347 (GRCm39) critical splice donor site probably null
R5389:Ptpn9 UTSW 9 56,964,121 (GRCm39) intron probably benign
R5422:Ptpn9 UTSW 9 56,940,441 (GRCm39) missense probably damaging 1.00
R5437:Ptpn9 UTSW 9 56,927,321 (GRCm39) missense possibly damaging 0.80
R6075:Ptpn9 UTSW 9 56,968,430 (GRCm39) missense probably benign 0.00
R6084:Ptpn9 UTSW 9 56,940,447 (GRCm39) nonsense probably null
R6481:Ptpn9 UTSW 9 56,930,324 (GRCm39) missense probably damaging 1.00
R7120:Ptpn9 UTSW 9 56,967,166 (GRCm39) missense probably damaging 1.00
R7194:Ptpn9 UTSW 9 56,929,570 (GRCm39) missense probably damaging 1.00
R7195:Ptpn9 UTSW 9 56,929,533 (GRCm39) missense probably benign 0.02
R7349:Ptpn9 UTSW 9 56,951,660 (GRCm39) missense probably benign 0.16
R7439:Ptpn9 UTSW 9 56,934,717 (GRCm39) nonsense probably null
R7441:Ptpn9 UTSW 9 56,934,717 (GRCm39) nonsense probably null
R7801:Ptpn9 UTSW 9 56,968,297 (GRCm39) missense probably benign 0.36
R7879:Ptpn9 UTSW 9 56,964,010 (GRCm39) missense possibly damaging 0.50
R7932:Ptpn9 UTSW 9 56,943,900 (GRCm39) missense possibly damaging 0.48
R9323:Ptpn9 UTSW 9 56,934,701 (GRCm39) missense possibly damaging 0.93
R9433:Ptpn9 UTSW 9 56,964,010 (GRCm39) missense possibly damaging 0.50
R9614:Ptpn9 UTSW 9 56,944,005 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- GACCAACATTCTGGGCATTC -3'
(R):5'- CCTGGAACATGTACTGAGTCC -3'

Sequencing Primer
(F):5'- GGGCATTCTAACTTAGCTATCTGAG -3'
(R):5'- CTGGAACATGTACTGAGTCCCAGTC -3'
Posted On 2015-10-08