Incidental Mutation 'R2419:Phc3'
ID 249125
Institutional Source Beutler Lab
Gene Symbol Phc3
Ensembl Gene ENSMUSG00000037652
Gene Name polyhomeotic 3
Synonyms EDR3, E030046K01Rik, HPH3
MMRRC Submission 040381-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2419 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 30953520-31023564 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 31005027 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Valine at position 189 (M189V)
Ref Sequence ENSEMBL: ENSMUSP00000065617 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046624] [ENSMUST00000064718] [ENSMUST00000099163] [ENSMUST00000108255] [ENSMUST00000129817] [ENSMUST00000152357] [ENSMUST00000168645] [ENSMUST00000177992]
AlphaFold Q8CHP6
Predicted Effect possibly damaging
Transcript: ENSMUST00000046624
AA Change: M189V

PolyPhen 2 Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000037862
Gene: ENSMUSG00000037652
AA Change: M189V

DomainStartEndE-ValueType
low complexity region 18 40 N/A INTRINSIC
low complexity region 72 89 N/A INTRINSIC
low complexity region 92 142 N/A INTRINSIC
low complexity region 152 166 N/A INTRINSIC
low complexity region 206 224 N/A INTRINSIC
low complexity region 333 359 N/A INTRINSIC
low complexity region 393 419 N/A INTRINSIC
low complexity region 512 538 N/A INTRINSIC
low complexity region 564 578 N/A INTRINSIC
low complexity region 583 594 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000064718
AA Change: M189V

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000065617
Gene: ENSMUSG00000037652
AA Change: M189V

DomainStartEndE-ValueType
low complexity region 18 40 N/A INTRINSIC
low complexity region 72 89 N/A INTRINSIC
low complexity region 92 142 N/A INTRINSIC
low complexity region 152 166 N/A INTRINSIC
low complexity region 206 224 N/A INTRINSIC
low complexity region 333 359 N/A INTRINSIC
low complexity region 393 419 N/A INTRINSIC
low complexity region 470 496 N/A INTRINSIC
low complexity region 522 536 N/A INTRINSIC
low complexity region 541 571 N/A INTRINSIC
low complexity region 610 618 N/A INTRINSIC
low complexity region 628 656 N/A INTRINSIC
PDB:2L8E|A 745 781 1e-8 PDB
low complexity region 849 868 N/A INTRINSIC
SAM 884 951 4.04e-13 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000099163
AA Change: M189V

PolyPhen 2 Score 0.886 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000096767
Gene: ENSMUSG00000037652
AA Change: M189V

DomainStartEndE-ValueType
low complexity region 18 40 N/A INTRINSIC
low complexity region 72 89 N/A INTRINSIC
low complexity region 92 142 N/A INTRINSIC
low complexity region 152 166 N/A INTRINSIC
low complexity region 300 326 N/A INTRINSIC
low complexity region 360 386 N/A INTRINSIC
low complexity region 479 505 N/A INTRINSIC
low complexity region 531 545 N/A INTRINSIC
low complexity region 550 580 N/A INTRINSIC
low complexity region 619 627 N/A INTRINSIC
low complexity region 637 665 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000108255
AA Change: M177V

PolyPhen 2 Score 0.894 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000103890
Gene: ENSMUSG00000037652
AA Change: M177V

DomainStartEndE-ValueType
low complexity region 6 28 N/A INTRINSIC
low complexity region 60 77 N/A INTRINSIC
low complexity region 80 130 N/A INTRINSIC
low complexity region 140 154 N/A INTRINSIC
low complexity region 288 314 N/A INTRINSIC
low complexity region 348 374 N/A INTRINSIC
low complexity region 467 493 N/A INTRINSIC
low complexity region 519 533 N/A INTRINSIC
low complexity region 538 568 N/A INTRINSIC
low complexity region 607 615 N/A INTRINSIC
low complexity region 625 653 N/A INTRINSIC
PDB:2L8E|A 742 778 8e-9 PDB
low complexity region 846 865 N/A INTRINSIC
SAM 881 948 4.04e-13 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000129817
AA Change: M177V

PolyPhen 2 Score 0.894 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000114916
Gene: ENSMUSG00000037652
AA Change: M177V

DomainStartEndE-ValueType
low complexity region 6 28 N/A INTRINSIC
low complexity region 60 77 N/A INTRINSIC
low complexity region 80 130 N/A INTRINSIC
low complexity region 140 154 N/A INTRINSIC
low complexity region 194 212 N/A INTRINSIC
low complexity region 321 347 N/A INTRINSIC
low complexity region 381 407 N/A INTRINSIC
low complexity region 500 526 N/A INTRINSIC
low complexity region 552 566 N/A INTRINSIC
low complexity region 571 601 N/A INTRINSIC
low complexity region 640 648 N/A INTRINSIC
low complexity region 658 686 N/A INTRINSIC
PDB:2L8E|A 775 811 7e-9 PDB
low complexity region 879 898 N/A INTRINSIC
SAM 914 980 1.7e-11 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000152357
AA Change: M189V

PolyPhen 2 Score 0.886 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000117614
Gene: ENSMUSG00000037652
AA Change: M189V

DomainStartEndE-ValueType
low complexity region 18 40 N/A INTRINSIC
low complexity region 72 89 N/A INTRINSIC
low complexity region 92 142 N/A INTRINSIC
low complexity region 152 166 N/A INTRINSIC
low complexity region 201 222 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000168645
AA Change: M177V

PolyPhen 2 Score 0.894 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000130142
Gene: ENSMUSG00000037652
AA Change: M177V

DomainStartEndE-ValueType
low complexity region 6 28 N/A INTRINSIC
low complexity region 60 77 N/A INTRINSIC
low complexity region 80 130 N/A INTRINSIC
low complexity region 140 154 N/A INTRINSIC
low complexity region 194 212 N/A INTRINSIC
low complexity region 321 347 N/A INTRINSIC
low complexity region 381 407 N/A INTRINSIC
low complexity region 500 526 N/A INTRINSIC
low complexity region 552 566 N/A INTRINSIC
low complexity region 571 601 N/A INTRINSIC
low complexity region 640 648 N/A INTRINSIC
low complexity region 658 686 N/A INTRINSIC
PDB:2L8E|A 775 811 7e-9 PDB
low complexity region 879 898 N/A INTRINSIC
SAM 914 980 1.6e-11 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000177992
AA Change: M177V

PolyPhen 2 Score 0.894 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000136820
Gene: ENSMUSG00000037652
AA Change: M177V

DomainStartEndE-ValueType
low complexity region 6 28 N/A INTRINSIC
low complexity region 60 77 N/A INTRINSIC
low complexity region 80 130 N/A INTRINSIC
low complexity region 140 154 N/A INTRINSIC
low complexity region 288 314 N/A INTRINSIC
low complexity region 348 374 N/A INTRINSIC
low complexity region 467 493 N/A INTRINSIC
low complexity region 519 533 N/A INTRINSIC
low complexity region 538 568 N/A INTRINSIC
low complexity region 607 615 N/A INTRINSIC
low complexity region 625 653 N/A INTRINSIC
PDB:2L8E|A 742 778 8e-9 PDB
low complexity region 846 865 N/A INTRINSIC
SAM 881 948 4.04e-13 SMART
Meta Mutation Damage Score 0.1585 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 94.9%
Validation Efficiency 98% (57/58)
Allele List at MGI
Other mutations in this stock
Total: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca2 G A 2: 25,328,001 (GRCm39) A768T probably benign Het
Acyp2 T C 11: 30,582,316 (GRCm39) Y33C probably benign Het
Ampd3 A G 7: 110,367,576 (GRCm39) probably benign Het
Arap3 T C 18: 38,122,997 (GRCm39) D501G probably damaging Het
Arl4d A T 11: 101,557,714 (GRCm39) Q80L probably damaging Het
Bcorl1 A G X: 47,459,418 (GRCm39) T425A probably damaging Het
Ccdc38 T A 10: 93,384,837 (GRCm39) V35D probably benign Het
Cd6 G A 19: 10,770,216 (GRCm39) P492S probably damaging Het
Cdh20 G A 1: 104,902,740 (GRCm39) S477N possibly damaging Het
Cnmd G A 14: 79,875,488 (GRCm39) P311S probably damaging Het
Cnot8 G A 11: 58,006,136 (GRCm39) G222R probably damaging Het
Dnah9 A T 11: 65,986,241 (GRCm39) L1131* probably null Het
Dscc1 G A 15: 54,946,820 (GRCm39) R302* probably null Het
Dusp18 T C 11: 3,847,018 (GRCm39) S3P possibly damaging Het
Eml2 A G 7: 18,910,620 (GRCm39) probably benign Het
Foxb2 G C 19: 16,850,325 (GRCm39) A227G probably damaging Het
Hey1 A G 3: 8,731,003 (GRCm39) probably null Het
Itk A G 11: 46,229,044 (GRCm39) F379L probably damaging Het
Kcna2 G A 3: 107,011,469 (GRCm39) G17R probably benign Het
Kif7 C A 7: 79,348,441 (GRCm39) R1300L probably benign Het
Klkb1 A T 8: 45,742,149 (GRCm39) D43E possibly damaging Het
Leng9 A G 7: 4,151,626 (GRCm39) V350A probably benign Het
Lmbr1l A C 15: 98,805,418 (GRCm39) F361C possibly damaging Het
Lrat A G 3: 82,810,992 (GRCm39) S10P probably damaging Het
Lrrk2 C A 15: 91,681,729 (GRCm39) probably benign Het
Mcur1 C T 13: 43,703,013 (GRCm39) V241M possibly damaging Het
Met T C 6: 17,535,829 (GRCm39) probably benign Het
Mical3 A G 6: 120,936,884 (GRCm39) V342A probably benign Het
Nup210 G A 6: 90,994,538 (GRCm39) probably benign Het
Or1i2 T A 10: 78,448,221 (GRCm39) I85F probably benign Het
Or1j12 T A 2: 36,343,338 (GRCm39) V247E probably damaging Het
Or4c107 A G 2: 88,789,380 (GRCm39) N190S probably benign Het
Pcdhac1 T C 18: 37,224,381 (GRCm39) L398P probably benign Het
Plcb1 A G 2: 135,104,020 (GRCm39) probably benign Het
Plcxd3 G T 15: 4,604,245 (GRCm39) K284N probably benign Het
Plxnb2 A G 15: 89,045,272 (GRCm39) V1058A possibly damaging Het
Rbbp5 T C 1: 132,421,564 (GRCm39) I88T possibly damaging Het
Rfpl4b T C 10: 38,697,368 (GRCm39) R78G probably benign Het
Rsf1 CG CGACGGCGGGG 7: 97,229,115 (GRCm39) probably benign Het
Samt2 A T X: 153,358,223 (GRCm39) probably null Het
Sdad1 T C 5: 92,453,677 (GRCm39) H37R possibly damaging Het
Setd2 T A 9: 110,378,065 (GRCm39) F627I possibly damaging Het
Ski A G 4: 155,245,350 (GRCm39) S293P probably benign Het
Slc27a1 A G 8: 72,032,560 (GRCm39) E191G possibly damaging Het
Snx18 T C 13: 113,753,755 (GRCm39) M393V possibly damaging Het
Spata31g1 A G 4: 42,974,146 (GRCm39) T1160A possibly damaging Het
Tacc1 A G 8: 25,672,829 (GRCm39) V42A possibly damaging Het
Tbc1d8 A G 1: 39,415,983 (GRCm39) F897L probably damaging Het
Tenm3 C T 8: 48,729,693 (GRCm39) D1438N possibly damaging Het
Tmem62 G A 2: 120,837,586 (GRCm39) G501E probably damaging Het
Tmem94 A G 11: 115,687,641 (GRCm39) K1167E probably damaging Het
Trap1 A G 16: 3,886,194 (GRCm39) S88P probably benign Het
Ugt2b38 T C 5: 87,571,591 (GRCm39) D147G probably damaging Het
Vmn1r168 A T 7: 23,240,824 (GRCm39) N227I probably benign Het
Vmn1r203 T A 13: 22,709,004 (GRCm39) S262T possibly damaging Het
Vmn1r204 T G 13: 22,740,420 (GRCm39) L17R probably damaging Het
Zcchc14 T A 8: 122,330,675 (GRCm39) Q896L probably damaging Het
Zfp619 A G 7: 39,185,307 (GRCm39) K446E possibly damaging Het
Zpr1 T C 9: 46,187,490 (GRCm39) probably benign Het
Other mutations in Phc3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00924:Phc3 APN 3 30,990,624 (GRCm39) missense probably damaging 0.98
IGL00985:Phc3 APN 3 30,968,346 (GRCm39) missense probably benign 0.13
IGL01340:Phc3 APN 3 30,984,033 (GRCm39) missense possibly damaging 0.85
IGL01450:Phc3 APN 3 30,968,653 (GRCm39) missense probably damaging 1.00
IGL01546:Phc3 APN 3 31,015,888 (GRCm39) missense probably damaging 1.00
IGL01918:Phc3 APN 3 30,968,565 (GRCm39) critical splice donor site probably null
IGL02178:Phc3 APN 3 30,984,012 (GRCm39) missense possibly damaging 0.47
IGL02210:Phc3 APN 3 30,990,858 (GRCm39) missense probably damaging 0.99
IGL02330:Phc3 APN 3 30,990,530 (GRCm39) missense probably damaging 1.00
IGL02516:Phc3 APN 3 31,002,942 (GRCm39) missense probably damaging 1.00
IGL03030:Phc3 APN 3 30,991,002 (GRCm39) missense probably damaging 1.00
See_saw UTSW 3 30,991,198 (GRCm39) nonsense probably null
R1228:Phc3 UTSW 3 30,976,404 (GRCm39) missense possibly damaging 0.71
R1239:Phc3 UTSW 3 30,968,279 (GRCm39) missense probably damaging 1.00
R1319:Phc3 UTSW 3 30,984,018 (GRCm39) missense probably damaging 0.97
R1521:Phc3 UTSW 3 30,990,724 (GRCm39) missense possibly damaging 0.89
R1772:Phc3 UTSW 3 31,015,969 (GRCm39) missense probably damaging 1.00
R1793:Phc3 UTSW 3 31,002,865 (GRCm39) missense probably damaging 1.00
R1879:Phc3 UTSW 3 30,968,607 (GRCm39) missense probably damaging 1.00
R2171:Phc3 UTSW 3 31,005,078 (GRCm39) missense probably damaging 1.00
R2863:Phc3 UTSW 3 30,968,277 (GRCm39) missense probably damaging 0.99
R2864:Phc3 UTSW 3 30,968,277 (GRCm39) missense probably damaging 0.99
R3700:Phc3 UTSW 3 30,968,277 (GRCm39) missense probably damaging 1.00
R3980:Phc3 UTSW 3 30,991,080 (GRCm39) missense probably damaging 0.99
R4222:Phc3 UTSW 3 30,990,968 (GRCm39) missense probably damaging 1.00
R4223:Phc3 UTSW 3 30,990,968 (GRCm39) missense probably damaging 1.00
R4584:Phc3 UTSW 3 31,020,031 (GRCm39) missense possibly damaging 0.46
R4928:Phc3 UTSW 3 31,005,068 (GRCm39) missense probably damaging 1.00
R5100:Phc3 UTSW 3 30,976,348 (GRCm39) missense possibly damaging 0.71
R5340:Phc3 UTSW 3 30,961,616 (GRCm39) missense probably damaging 1.00
R5656:Phc3 UTSW 3 31,020,015 (GRCm39) missense probably damaging 0.98
R5840:Phc3 UTSW 3 30,990,732 (GRCm39) missense possibly damaging 0.95
R6022:Phc3 UTSW 3 30,984,174 (GRCm39) missense probably damaging 1.00
R6061:Phc3 UTSW 3 30,968,678 (GRCm39) missense probably damaging 1.00
R6177:Phc3 UTSW 3 30,996,714 (GRCm39) missense probably damaging 1.00
R6188:Phc3 UTSW 3 30,991,198 (GRCm39) nonsense probably null
R6866:Phc3 UTSW 3 30,968,680 (GRCm39) nonsense probably null
R6870:Phc3 UTSW 3 30,990,910 (GRCm39) missense probably damaging 1.00
R7155:Phc3 UTSW 3 30,968,346 (GRCm39) missense probably benign 0.01
R7603:Phc3 UTSW 3 30,961,601 (GRCm39) missense probably damaging 0.97
R7874:Phc3 UTSW 3 30,990,863 (GRCm39) missense probably benign 0.00
R8422:Phc3 UTSW 3 30,984,039 (GRCm39) nonsense probably null
R8877:Phc3 UTSW 3 30,968,271 (GRCm39) missense probably damaging 1.00
R8972:Phc3 UTSW 3 31,015,926 (GRCm39) missense possibly damaging 0.95
R9003:Phc3 UTSW 3 31,020,007 (GRCm39) missense possibly damaging 0.86
R9042:Phc3 UTSW 3 30,983,916 (GRCm39) missense unknown
R9155:Phc3 UTSW 3 30,968,691 (GRCm39) missense probably benign 0.01
R9168:Phc3 UTSW 3 30,961,544 (GRCm39) missense probably benign
X0025:Phc3 UTSW 3 31,020,035 (GRCm39) missense probably damaging 0.96
Z1176:Phc3 UTSW 3 30,990,746 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- AGGCTTCCTACTTCAAGGTGG -3'
(R):5'- ATCAGAGCCGCTCTTTGAG -3'

Sequencing Primer
(F):5'- ATGCCTCGCTTTATCCAG -3'
(R):5'- CTGGAAGCATCTGACCTGTTACG -3'
Posted On 2014-11-12