Incidental Mutation 'R2171:Phc3'
ID 237465
Institutional Source Beutler Lab
Gene Symbol Phc3
Ensembl Gene ENSMUSG00000037652
Gene Name polyhomeotic 3
Synonyms EDR3, E030046K01Rik, HPH3
MMRRC Submission 040173-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2171 (G1)
Quality Score 225
Status Not validated
Chromosome 3
Chromosomal Location 30953520-31023564 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 31005078 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 172 (T172A)
Ref Sequence ENSEMBL: ENSMUSP00000037862 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046624] [ENSMUST00000064718] [ENSMUST00000099163] [ENSMUST00000108255] [ENSMUST00000129817] [ENSMUST00000152357] [ENSMUST00000168645] [ENSMUST00000177992]
AlphaFold Q8CHP6
Predicted Effect probably damaging
Transcript: ENSMUST00000046624
AA Change: T172A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000037862
Gene: ENSMUSG00000037652
AA Change: T172A

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 possibly damaging
Transcript: ENSMUST00000064718
AA Change: T172A

PolyPhen 2 Score 0.822 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000065617
Gene: ENSMUSG00000037652
AA Change: T172A

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 probably damaging
Transcript: ENSMUST00000099163
AA Change: T172A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000096767
Gene: ENSMUSG00000037652
AA Change: T172A

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 probably damaging
Transcript: ENSMUST00000108255
AA Change: T160A

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000103890
Gene: ENSMUSG00000037652
AA Change: T160A

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 probably damaging
Transcript: ENSMUST00000129817
AA Change: T160A

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000114916
Gene: ENSMUSG00000037652
AA Change: T160A

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 probably benign
Transcript: ENSMUST00000152357
AA Change: T172A

PolyPhen 2 Score 0.143 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000117614
Gene: ENSMUSG00000037652
AA Change: T172A

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 probably damaging
Transcript: ENSMUST00000168645
AA Change: T160A

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000130142
Gene: ENSMUSG00000037652
AA Change: T160A

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 probably damaging
Transcript: ENSMUST00000177992
AA Change: T160A

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000136820
Gene: ENSMUSG00000037652
AA Change: T160A

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
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.7%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abt1 A G 13: 23,606,387 (GRCm39) L189P probably damaging Het
Adgrl3 C A 5: 81,660,362 (GRCm39) S377* probably null Het
Adgrv1 A G 13: 81,419,037 (GRCm39) V5986A probably damaging Het
Arv1 T G 8: 125,455,094 (GRCm39) C102W probably damaging Het
Asb18 T C 1: 89,896,419 (GRCm39) H207R probably benign Het
Bach2 T C 4: 32,501,662 (GRCm39) V13A probably damaging Het
Bccip T C 7: 133,320,843 (GRCm39) S206P probably benign Het
Cdhr4 T C 9: 107,870,117 (GRCm39) S41P probably benign Het
Chd7 A G 4: 8,752,424 (GRCm39) Y307C probably damaging Het
Clec4f A T 6: 83,629,846 (GRCm39) S237R possibly damaging Het
Cntnap5a A G 1: 116,116,132 (GRCm39) D538G possibly damaging Het
Col9a2 T A 4: 120,902,198 (GRCm39) C173* probably null Het
Ctr9 T A 7: 110,646,117 (GRCm39) M703K possibly damaging Het
Cyp2a12 A G 7: 26,729,057 (GRCm39) Y83C probably damaging Het
Eef1akmt3 A C 10: 126,868,843 (GRCm39) D210E probably benign Het
Erbin A G 13: 103,971,466 (GRCm39) F717L probably benign Het
Gtf3a A G 5: 146,892,272 (GRCm39) N341S probably benign Het
Hltf T C 3: 20,113,245 (GRCm39) V6A probably damaging Het
Itga6 T A 2: 71,650,358 (GRCm39) Y135N probably damaging Het
Krt73 T C 15: 101,709,345 (GRCm39) Q154R possibly damaging Het
Lce1a1 C T 3: 92,554,048 (GRCm39) C142Y unknown Het
Lcorl A T 5: 45,904,493 (GRCm39) I112N probably damaging Het
Ltbp1 C T 17: 75,598,312 (GRCm39) H916Y probably damaging Het
Lypla2 T C 4: 135,697,915 (GRCm39) probably null Het
Man1c1 G C 4: 134,430,749 (GRCm39) P11R probably damaging Het
Mmp1a T A 9: 7,475,357 (GRCm39) D375E probably damaging Het
Nlrp14 T G 7: 106,781,709 (GRCm39) L302R probably damaging Het
Npy2r T G 3: 82,447,708 (GRCm39) T243P possibly damaging Het
Or11h4 A T 14: 50,973,876 (GRCm39) S248T probably benign Het
Or51k2 T C 7: 103,595,992 (GRCm39) V73A probably damaging Het
Paqr9 A T 9: 95,442,931 (GRCm39) H307L probably damaging Het
Pigs A G 11: 78,219,638 (GRCm39) T39A probably damaging Het
Pik3c2g C T 6: 139,801,012 (GRCm39) Q386* probably null Het
Pira2 T C 7: 3,847,417 (GRCm39) S91G probably benign Het
Plxna2 T A 1: 194,482,925 (GRCm39) N1539K probably damaging Het
Poc5 C T 13: 96,547,257 (GRCm39) H507Y probably damaging Het
Pou2f1 A T 1: 165,707,925 (GRCm39) probably benign Het
Pthlh T G 6: 147,158,694 (GRCm39) K89Q probably damaging Het
Rims4 A T 2: 163,706,046 (GRCm39) probably null Het
Rnf138 A G 18: 21,159,143 (GRCm39) N188D probably damaging Het
Rreb1 A G 13: 38,114,822 (GRCm39) D727G probably benign Het
Sc5d T G 9: 42,166,682 (GRCm39) K286Q probably benign Het
Slc10a5 C T 3: 10,400,342 (GRCm39) G106D possibly damaging Het
Smg6 A T 11: 74,929,472 (GRCm39) Q967L probably damaging Het
Spty2d1 C T 7: 46,644,361 (GRCm39) R636H probably damaging Het
Srms A T 2: 180,850,573 (GRCm39) Y195* probably null Het
Susd4 A G 1: 182,719,759 (GRCm39) D458G probably benign Het
Tecta T C 9: 42,270,220 (GRCm39) R1363G probably damaging Het
Thbs1 G A 2: 117,953,060 (GRCm39) G890D probably damaging Het
Tpp2 T C 1: 43,996,606 (GRCm39) V317A probably benign Het
Ttpa T C 4: 20,021,357 (GRCm39) V175A probably damaging Het
Vps13b G T 15: 35,887,343 (GRCm39) D3251Y probably benign Het
Vps54 A G 11: 21,248,810 (GRCm39) D441G probably benign Het
Zfp738 A T 13: 67,819,096 (GRCm39) Y298* probably null Het
Zfp804a G A 2: 82,087,527 (GRCm39) C452Y possibly damaging Het
Zxdc A G 6: 90,359,461 (GRCm39) K698E possibly damaging 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
R2419:Phc3 UTSW 3 31,005,027 (GRCm39) missense probably damaging 0.99
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'- GGCTAAGCATATGCACACAC -3'
(R):5'- AGTTGCCCACAGTAGAGGGTTC -3'

Sequencing Primer
(F):5'- GCATATGCACACACTTGTTAACTC -3'
(R):5'- AAGATCAGAGCCGCTCTTTG -3'
Posted On 2014-10-02