Incidental Mutation 'R4222:Phc3'
ID 319384
Institutional Source Beutler Lab
Gene Symbol Phc3
Ensembl Gene ENSMUSG00000037652
Gene Name polyhomeotic 3
Synonyms EDR3, E030046K01Rik, HPH3
MMRRC Submission 041042-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4222 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 30953520-31023564 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 30990968 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 383 (S383R)
Ref Sequence ENSEMBL: ENSMUSP00000096767 (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: S416R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000037862
Gene: ENSMUSG00000037652
AA Change: S416R

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: S416R

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000065617
Gene: ENSMUSG00000037652
AA Change: S416R

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: S383R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000096767
Gene: ENSMUSG00000037652
AA Change: S383R

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: S371R

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000103890
Gene: ENSMUSG00000037652
AA Change: S371R

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 noncoding transcript
Transcript: ENSMUST00000124472
Predicted Effect probably damaging
Transcript: ENSMUST00000129817
AA Change: S404R

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000114916
Gene: ENSMUSG00000037652
AA Change: S404R

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
SMART Domains Protein: ENSMUSP00000117614
Gene: ENSMUSG00000037652

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: S404R

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000130142
Gene: ENSMUSG00000037652
AA Change: S404R

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: S371R

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000136820
Gene: ENSMUSG00000037652
AA Change: S371R

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 0.0722 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.2%
  • 20x: 95.3%
Validation Efficiency 91% (49/54)
Allele List at MGI
Other mutations in this stock
Total: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgre4 A G 17: 56,092,121 (GRCm39) Y127C probably damaging Het
Aif1l A T 2: 31,852,251 (GRCm39) S40C probably damaging Het
Alkal1 A G 1: 6,458,839 (GRCm39) K76R probably damaging Het
Atm T C 9: 53,391,969 (GRCm39) S1807G probably benign Het
Bhmt-ps1 T A 4: 26,369,352 (GRCm39) noncoding transcript Het
Brd10 A T 19: 29,696,149 (GRCm39) S1115T probably benign Het
Cyp3a11 A T 5: 145,797,276 (GRCm39) Y368N probably damaging Het
Gar1 A T 3: 129,624,455 (GRCm39) probably benign Het
Gm5265 A T 1: 169,281,370 (GRCm39) noncoding transcript Het
Gm7964 T G 7: 83,406,030 (GRCm39) N281K probably damaging Het
Grin1 T C 2: 25,187,332 (GRCm39) probably benign Het
H1f5 A T 13: 21,964,147 (GRCm39) probably benign Het
Hapln4 T A 8: 70,539,610 (GRCm39) W214R probably damaging Het
Ift56 A G 6: 38,372,010 (GRCm39) Y200C probably damaging Het
Irgq C A 7: 24,233,050 (GRCm39) A297D possibly damaging Het
Kri1 T C 9: 21,192,359 (GRCm39) E145G probably benign Het
Lama3 T C 18: 12,583,460 (GRCm39) C683R probably damaging Het
Mrpl22 T A 11: 58,062,693 (GRCm39) probably benign Het
Myo7a T A 7: 97,722,436 (GRCm39) Q1163L possibly damaging Het
Nipsnap3a T A 4: 52,997,251 (GRCm39) D172E probably benign Het
Nrxn3 G T 12: 89,499,762 (GRCm39) G718* probably null Het
Olfm3 C T 3: 114,883,820 (GRCm39) Q41* probably null Het
Or52z12 A G 7: 103,233,966 (GRCm39) T246A probably damaging Het
Or8u8 G T 2: 86,012,341 (GRCm39) T38K probably damaging Het
Parm1 G A 5: 91,741,726 (GRCm39) M31I probably benign Het
Pkn2 A T 3: 142,499,627 (GRCm39) L950* probably null Het
Plec C T 15: 76,061,519 (GRCm39) R2671H probably damaging Het
Ptbp1 T C 10: 79,695,047 (GRCm39) I125T probably benign Het
Ptch1 C T 13: 63,682,143 (GRCm39) R537H probably damaging Het
Ptk7 A T 17: 46,885,389 (GRCm39) M679K probably benign Het
Ptx3 C T 3: 66,132,127 (GRCm39) T216I probably damaging Het
Rrp8 T C 7: 105,383,229 (GRCm39) I346V possibly damaging Het
Rsrc1 A G 3: 66,901,900 (GRCm39) K17E unknown Het
Ryr2 T A 13: 11,752,759 (GRCm39) E1854V possibly damaging Het
Semp2l2a T C 8: 13,888,061 (GRCm39) E10G probably benign Het
Slc25a45 A T 19: 5,930,146 (GRCm39) I39F probably damaging Het
Spag5 G A 11: 78,195,337 (GRCm39) V215I probably damaging Het
Ston1 A G 17: 88,944,199 (GRCm39) Y535C probably damaging Het
Tbc1d14 A T 5: 36,650,452 (GRCm39) S395T probably benign Het
Tlr11 C T 14: 50,599,306 (GRCm39) P431S probably damaging Het
Trerf1 G T 17: 47,625,727 (GRCm39) noncoding transcript Het
Trim43b T A 9: 88,972,692 (GRCm39) Q154L probably benign Het
Vmn1r49 A G 6: 90,049,228 (GRCm39) F258S probably benign Het
Vmn1r-ps103 C A 13: 22,626,198 (GRCm39) noncoding transcript Het
Vmn2r14 A G 5: 109,364,149 (GRCm39) M589T probably benign Het
Vmn2r60 A T 7: 41,765,952 (GRCm39) T20S probably benign Het
Zbtb5 A G 4: 44,993,855 (GRCm39) probably null Het
Zfp35 T G 18: 24,136,246 (GRCm39) F197V 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
R2171:Phc3 UTSW 3 31,005,078 (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
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'- CCAATGTGTACAACAGGGGATG -3'
(R):5'- TTCAGCCAATCACCCTTCAGAG -3'

Sequencing Primer
(F):5'- TACAACAGGGGATGCTGGAAGTG -3'
(R):5'- TTCAGAGTCCAAGTCAAGATCC -3'
Posted On 2015-06-10