Incidental Mutation 'R6870:Phc3'
ID 536128
Institutional Source Beutler Lab
Gene Symbol Phc3
Ensembl Gene ENSMUSG00000037652
Gene Name polyhomeotic 3
Synonyms EDR3, E030046K01Rik, HPH3
MMRRC Submission 044967-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6870 (G1)
Quality Score 225.009
Status Not validated
Chromosome 3
Chromosomal Location 30953520-31023564 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 30990910 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 403 (S403P)
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 benign
Transcript: ENSMUST00000046624
AA Change: S436P

PolyPhen 2 Score 0.048 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000037862
Gene: ENSMUSG00000037652
AA Change: S436P

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: S436P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000065617
Gene: ENSMUSG00000037652
AA Change: S436P

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: S403P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000096767
Gene: ENSMUSG00000037652
AA Change: S403P

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: S391P

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000103890
Gene: ENSMUSG00000037652
AA Change: S391P

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: ENSMUST00000129817
AA Change: S424P

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000114916
Gene: ENSMUSG00000037652
AA Change: S424P

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 benign
Transcript: ENSMUST00000168645
AA Change: S424P

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000130142
Gene: ENSMUSG00000037652
AA Change: S424P

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: S391P

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000136820
Gene: ENSMUSG00000037652
AA Change: S391P

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: 100.0%
  • 3x: 99.9%
  • 10x: 99.2%
  • 20x: 97.4%
Validation Efficiency 72% (39/54)
Allele List at MGI
Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700088E04Rik T C 15: 79,020,608 (GRCm39) Y62C probably benign Het
A1bg T C 15: 60,791,564 (GRCm39) T291A probably damaging Het
Abcb11 A G 2: 69,115,642 (GRCm39) I574T possibly damaging Het
Abcb5 T A 12: 118,929,000 (GRCm39) Y17F possibly damaging Het
Arfgef3 A T 10: 18,522,478 (GRCm39) L516* probably null Het
Arhgap21 A G 2: 20,885,321 (GRCm39) S619P probably damaging Het
Atp2c1 A G 9: 105,347,261 (GRCm39) V65A probably benign Het
Calm3 T A 7: 16,653,568 (GRCm39) Q9L probably benign Het
Cd300c2 C T 11: 114,891,503 (GRCm39) D124N probably damaging Het
Celsr3 A G 9: 108,706,390 (GRCm39) T958A probably benign Het
Cemip2 T C 19: 21,809,487 (GRCm39) S956P possibly damaging Het
Cfap69 T C 5: 5,671,958 (GRCm39) T317A probably benign Het
Cluh T A 11: 74,556,210 (GRCm39) I887K probably damaging Het
Dag1 A T 9: 108,086,457 (GRCm39) V228E probably damaging Het
Dhtkd1 T C 2: 5,924,248 (GRCm39) probably null Het
Dnah1 T A 14: 30,993,018 (GRCm39) K2959* probably null Het
Dnttip2 T A 3: 122,069,457 (GRCm39) V224E probably damaging Het
Drosha C T 15: 12,907,479 (GRCm39) P1071L probably benign Het
E030025P04Rik T A 11: 109,030,993 (GRCm39) H84L unknown Het
Elac2 A T 11: 64,890,589 (GRCm39) S698C probably null Het
Elf2 A T 3: 51,201,586 (GRCm39) *88R probably null Het
Fastkd1 T A 2: 69,538,958 (GRCm39) I143L probably benign Het
Fbxw10 C T 11: 62,746,193 (GRCm39) R366C probably damaging Het
Frg2f1 T C 4: 119,388,329 (GRCm39) M57V probably benign Het
Gbp4 T C 5: 105,273,444 (GRCm39) S129G probably damaging Het
Gnat2 A C 3: 108,002,947 (GRCm39) probably benign Het
Golgb1 C A 16: 36,738,565 (GRCm39) F2301L probably damaging Het
Il18bp T C 7: 101,666,518 (GRCm39) T2A possibly damaging Het
Kpna2 T C 11: 106,883,520 (GRCm39) probably null Het
Lrrfip2 A T 9: 111,045,187 (GRCm39) probably benign Het
Map4k1 T G 7: 28,701,096 (GRCm39) probably null Het
Mcm3ap T C 10: 76,306,049 (GRCm39) V54A probably benign Het
Nup133 A G 8: 124,626,246 (GRCm39) I1112T probably benign Het
Or8b1 A C 9: 38,399,382 (GRCm39) D19A probably benign Het
Pcdhac1 T A 18: 37,225,140 (GRCm39) V651D probably damaging Het
Pde10a A G 17: 9,186,356 (GRCm39) T571A possibly damaging Het
Prl7b1 T C 13: 27,788,516 (GRCm39) E113G probably damaging Het
Psmd2 T G 16: 20,480,593 (GRCm39) M744R probably benign Het
Qrich2 T C 11: 116,346,156 (GRCm39) D1556G probably damaging Het
Septin1 C T 7: 126,816,876 (GRCm39) V46M probably benign Het
Shank2 C A 7: 143,606,197 (GRCm39) Q127K probably damaging Het
Siah1a A G 8: 87,451,653 (GRCm39) V277A possibly damaging Het
Slc4a7 T A 14: 14,733,846 (GRCm38) D85E probably damaging Het
Slc5a12 A T 2: 110,472,155 (GRCm39) I526F probably damaging Het
Svil T C 18: 5,063,231 (GRCm39) V834A possibly damaging Het
Sycp1 T A 3: 102,842,919 (GRCm39) S17C probably damaging Het
Tssk6 G A 8: 70,355,673 (GRCm39) R239Q probably benign Het
Txnrd1 A G 10: 82,709,042 (GRCm39) D80G probably benign Het
Tyk2 A G 9: 21,036,250 (GRCm39) F79S probably damaging Het
Tyrp1 T C 4: 80,769,014 (GRCm39) S503P probably benign Het
Upf1 A T 8: 70,794,211 (GRCm39) C232S probably benign Het
Zeb2 G A 2: 44,878,922 (GRCm39) T1080I 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
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
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'- GACTGTAGGGCTGAATACTGC -3'
(R):5'- TTCTCCGGCTCCCAGTAATG -3'

Sequencing Primer
(F):5'- AGGGCTGAATACTGCTGGTG -3'
(R):5'- AGTAATGCCCAGCCGCAG -3'
Posted On 2018-10-18