Incidental Mutation 'R5840:Phc3'
ID 450362
Institutional Source Beutler Lab
Gene Symbol Phc3
Ensembl Gene ENSMUSG00000037652
Gene Name polyhomeotic 3
Synonyms EDR3, E030046K01Rik, HPH3
MMRRC Submission 044060-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5840 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 30953520-31023564 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 30990732 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Leucine at position 495 (S495L)
Ref Sequence ENSEMBL: ENSMUSP00000037862 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046624] [ENSMUST00000064718] [ENSMUST00000099163] [ENSMUST00000108255] [ENSMUST00000129817] [ENSMUST00000168645] [ENSMUST00000177992] [ENSMUST00000152357]
AlphaFold Q8CHP6
Predicted Effect possibly damaging
Transcript: ENSMUST00000046624
AA Change: S495L

PolyPhen 2 Score 0.950 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000037862
Gene: ENSMUSG00000037652
AA Change: S495L

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 benign
Transcript: ENSMUST00000064718
AA Change: S453L

PolyPhen 2 Score 0.054 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000065617
Gene: ENSMUSG00000037652
AA Change: S453L

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: S462L

PolyPhen 2 Score 0.782 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000096767
Gene: ENSMUSG00000037652
AA Change: S462L

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 benign
Transcript: ENSMUST00000108255
AA Change: S450L

PolyPhen 2 Score 0.128 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000103890
Gene: ENSMUSG00000037652
AA Change: S450L

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 benign
Transcript: ENSMUST00000129817
AA Change: S483L

PolyPhen 2 Score 0.128 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000114916
Gene: ENSMUSG00000037652
AA Change: S483L

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: ENSMUST00000168645
AA Change: S483L

PolyPhen 2 Score 0.128 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000130142
Gene: ENSMUSG00000037652
AA Change: S483L

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 benign
Transcript: ENSMUST00000177992
AA Change: S450L

PolyPhen 2 Score 0.128 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000136820
Gene: ENSMUSG00000037652
AA Change: S450L

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 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
Meta Mutation Damage Score 0.0607 question?
Coding Region Coverage
  • 1x: 99.8%
  • 3x: 99.3%
  • 10x: 96.5%
  • 20x: 88.1%
Validation Efficiency 99% (75/76)
Allele List at MGI
Other mutations in this stock
Total: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca2 G A 2: 25,323,371 (GRCm39) R113Q probably benign Het
Aip G A 19: 4,166,010 (GRCm39) P147L possibly damaging Het
Anapc1 A C 2: 128,448,957 (GRCm39) probably benign Het
Arhgap42 C T 9: 9,046,518 (GRCm39) V240I possibly damaging Het
Axdnd1 T C 1: 156,176,528 (GRCm39) E684G probably damaging Het
BC005624 G A 2: 30,871,869 (GRCm39) R2W probably benign Het
Cd177 T G 7: 24,457,495 (GRCm39) Q182P probably damaging Het
Cdca5 G A 19: 6,140,399 (GRCm39) E187K possibly damaging Het
Chmp1a T C 8: 123,934,839 (GRCm39) Q39R probably benign Het
Dab2ip A G 2: 35,617,511 (GRCm39) I1079V probably damaging Het
Dip2c A T 13: 9,556,712 (GRCm39) E85D possibly damaging Het
Elmo2 A T 2: 165,137,472 (GRCm39) S497R possibly damaging Het
Ephb6 C T 6: 41,592,507 (GRCm39) A339V possibly damaging Het
Foxred1 T C 9: 35,121,435 (GRCm39) K38E probably damaging Het
Frem2 T A 3: 53,555,342 (GRCm39) T1732S probably damaging Het
Fto A G 8: 92,393,068 (GRCm39) probably benign Het
Gm17430 T A 18: 9,726,528 (GRCm39) Q48L probably damaging Het
Gng2 A G 14: 19,925,882 (GRCm39) I70T probably damaging Het
Gtf2a2 A G 9: 69,922,575 (GRCm39) probably benign Het
Invs A G 4: 48,396,284 (GRCm39) D263G probably damaging Het
Itga2b C T 11: 102,352,157 (GRCm39) V475M probably damaging Het
Kansl1l A G 1: 66,809,374 (GRCm39) probably benign Het
Klhl25 T C 7: 75,516,440 (GRCm39) F449L possibly damaging Het
Lamb1 T A 12: 31,316,755 (GRCm39) C83S probably damaging Het
Loxl4 G T 19: 42,587,154 (GRCm39) T648K probably damaging Het
Lrit2 T C 14: 36,790,962 (GRCm39) F214L possibly damaging Het
N4bp2 T G 5: 65,965,437 (GRCm39) L1162R probably damaging Het
Naa40 A T 19: 7,207,373 (GRCm39) I117N probably benign Het
Ncapd3 T C 9: 27,006,054 (GRCm39) S1492P probably benign Het
Nf2 T A 11: 4,766,146 (GRCm39) D128V probably benign Het
Nox4 T C 7: 87,010,001 (GRCm39) S401P probably benign Het
Nt5c1b T C 12: 10,427,171 (GRCm39) V323A probably damaging Het
Or52a33 C T 7: 103,288,463 (GRCm39) V295I probably benign Het
Or52s19 T A 7: 103,007,576 (GRCm39) H275L probably damaging Het
Or5b118 G A 19: 13,449,242 (GRCm39) V303I probably benign Het
Pcdhb14 T C 18: 37,581,803 (GRCm39) V303A probably benign Het
Pde8a C A 7: 80,863,713 (GRCm39) H17Q probably benign Het
Pfkl C T 10: 77,824,558 (GRCm39) V716I probably benign Het
Psg18 A G 7: 18,080,527 (GRCm39) probably benign Het
Rcc2 T G 4: 140,439,449 (GRCm39) N175K possibly damaging Het
Rhot2 G A 17: 26,059,032 (GRCm39) T276I probably benign Het
Rnase9 A T 14: 51,276,445 (GRCm39) Y178N probably benign Het
Sema4b T C 7: 79,868,697 (GRCm39) C297R probably damaging Het
Slc35d2 T C 13: 64,266,227 (GRCm39) probably null Het
Sptlc3 A T 2: 139,389,126 (GRCm39) N169Y probably damaging Het
Srsf9 T G 5: 115,469,524 (GRCm39) M29R probably benign Het
Stip1 C A 19: 6,999,436 (GRCm39) D449Y possibly damaging Het
Syne2 T A 12: 75,927,065 (GRCm39) probably null Het
Tgm5 A G 2: 120,916,141 (GRCm39) probably null Het
Thbs2 A T 17: 14,901,692 (GRCm39) probably null Het
Trak2 T C 1: 58,958,432 (GRCm39) E283G probably damaging Het
Trbv21 A G 6: 41,179,792 (GRCm39) Y36C probably damaging Het
Trpm7 A T 2: 126,664,531 (GRCm39) Y949* probably null Het
Ubqln5 T C 7: 103,778,161 (GRCm39) D221G possibly damaging Het
Ubxn4 T A 1: 128,187,262 (GRCm39) V85D possibly damaging Het
Vmn1r172 T A 7: 23,359,600 (GRCm39) W162R probably benign Het
Vrk2 A G 11: 26,484,314 (GRCm39) probably benign Het
Zc3h8 A C 2: 128,771,824 (GRCm39) D276E probably benign Het
Zfp369 C T 13: 65,445,092 (GRCm39) T745I possibly damaging Het
Zfp608 T C 18: 55,031,978 (GRCm39) K654R probably 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
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
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'- GCAACTGGACCAAAGCTTCTG -3'
(R):5'- GTGTCTTCAGCTCTTCAAACAGG -3'

Sequencing Primer
(F):5'- GGTAGCTCCTCTTCTGACACCAAAG -3'
(R):5'- GCTCTTCAAACAGGGCCAAATTTG -3'
Posted On 2016-12-20