Incidental Mutation 'R6177:Phc3'
ID 487809
Institutional Source Beutler Lab
Gene Symbol Phc3
Ensembl Gene ENSMUSG00000037652
Gene Name polyhomeotic 3
Synonyms EDR3, E030046K01Rik, HPH3
MMRRC Submission 044319-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6177 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 30953520-31023564 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 30996714 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 219 (S219T)
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: S252T

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000037862
Gene: ENSMUSG00000037652
AA Change: S252T

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: S252T

PolyPhen 2 Score 0.165 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000065617
Gene: ENSMUSG00000037652
AA Change: S252T

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: S219T

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000096767
Gene: ENSMUSG00000037652
AA Change: S219T

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: S207T

PolyPhen 2 Score 0.788 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000103890
Gene: ENSMUSG00000037652
AA Change: S207T

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: S240T

PolyPhen 2 Score 0.745 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000114916
Gene: ENSMUSG00000037652
AA Change: S240T

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 possibly damaging
Transcript: ENSMUST00000168645
AA Change: S240T

PolyPhen 2 Score 0.745 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000130142
Gene: ENSMUSG00000037652
AA Change: S240T

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: S207T

PolyPhen 2 Score 0.788 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000136820
Gene: ENSMUSG00000037652
AA Change: S207T

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 0.0620 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.8%
  • 20x: 93.7%
Validation Efficiency 100% (65/65)
Allele List at MGI
Other mutations in this stock
Total: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcd2 T C 15: 91,074,896 (GRCm39) I306V probably damaging Het
Actrt3 A T 3: 30,652,316 (GRCm39) Y259* probably null Het
Ankfy1 G A 11: 72,645,285 (GRCm39) C788Y probably benign Het
Ano1 T A 7: 144,232,478 (GRCm39) M25L possibly damaging Het
Apol10b A T 15: 77,469,987 (GRCm39) D63E possibly damaging Het
Atp6v1c1 C A 15: 38,674,172 (GRCm39) S55* probably null Het
C1s2 T G 6: 124,606,960 (GRCm39) D296A probably damaging Het
Cabs1 C T 5: 88,127,613 (GRCm39) T88I possibly damaging Het
Cadm4 G A 7: 24,202,186 (GRCm39) V342M possibly damaging Het
Cat T C 2: 103,303,420 (GRCm39) E119G probably damaging Het
Cavin2 G T 1: 51,328,654 (GRCm39) S37I probably damaging Het
Cdhr18 T C 14: 13,868,002 (GRCm38) D229G probably benign Het
Cdk5rap2 G A 4: 70,199,719 (GRCm39) R802C probably damaging Het
Clip1 A G 5: 123,751,897 (GRCm39) probably benign Het
Dhx57 T C 17: 80,580,395 (GRCm39) N519S possibly damaging Het
Dpep2 T C 8: 106,712,831 (GRCm39) D260G probably damaging Het
Edem1 T A 6: 108,828,159 (GRCm39) probably null Het
Epb41l4a A T 18: 33,931,868 (GRCm39) probably null Het
Esp1 T C 17: 41,039,723 (GRCm39) S3P possibly damaging Het
Fam111a A G 19: 12,564,746 (GRCm39) Y165C probably damaging Het
Fstl4 A G 11: 53,059,031 (GRCm39) T497A probably benign Het
Gstcd T C 3: 132,787,834 (GRCm39) D288G probably damaging Het
Hmcn2 T A 2: 31,310,118 (GRCm39) L3264* probably null Het
Hyal4 T A 6: 24,766,089 (GRCm39) L481* probably null Het
Ighv2-7 A G 12: 113,771,055 (GRCm39) Y77H possibly damaging Het
Jdp2 G T 12: 85,685,614 (GRCm39) R125L probably benign Het
Lrp1b A T 2: 41,013,748 (GRCm39) probably null Het
Lrp2 AC A 2: 69,340,763 (GRCm39) probably null Het
Marveld2 C T 13: 100,733,886 (GRCm39) D250N probably damaging Het
Mast3 A G 8: 71,242,662 (GRCm39) S53P probably damaging Het
Ms4a20 A G 19: 11,083,114 (GRCm39) I102T possibly damaging Het
Myo3b T C 2: 70,143,707 (GRCm39) V1041A probably benign Het
Nkpd1 T A 7: 19,257,009 (GRCm39) F113I probably damaging Het
Obscn A G 11: 58,923,490 (GRCm39) S6470P probably damaging Het
Or1e16 AGCGGTCGTAGGC AGC 11: 73,286,480 (GRCm39) probably null Het
Or4a73 T C 2: 89,420,661 (GRCm39) D266G possibly damaging Het
Or9g4b C T 2: 85,616,004 (GRCm39) R50C probably damaging Het
Pdcd11 G T 19: 47,108,722 (GRCm39) G1246V probably damaging Het
Plxnb1 C T 9: 108,931,993 (GRCm39) probably null Het
Polh T C 17: 46,495,670 (GRCm39) D276G possibly damaging Het
Polq T A 16: 36,892,071 (GRCm39) V1991E probably damaging Het
Polr2g G A 19: 8,771,541 (GRCm39) R144C probably damaging Het
Pramel16 G A 4: 143,675,576 (GRCm39) H417Y possibly damaging Het
Prex2 A C 1: 11,207,001 (GRCm39) T520P possibly damaging Het
Psg21 T A 7: 18,386,279 (GRCm39) T236S possibly damaging Het
Ptpru A T 4: 131,520,836 (GRCm39) S761R probably benign Het
Rapgef6 G A 11: 54,510,842 (GRCm39) R253Q probably damaging Het
Rc3h2 C T 2: 37,279,658 (GRCm39) V524I probably benign Het
Sde2 T C 1: 180,685,784 (GRCm39) V112A probably damaging Het
Septin7 T C 9: 25,205,100 (GRCm39) probably null Het
Spef2 A G 15: 9,727,618 (GRCm39) V155A possibly damaging Het
St7 T C 6: 17,819,333 (GRCm39) probably null Het
Tmcc3 A T 10: 94,418,249 (GRCm39) Y339F probably damaging Het
Tmed6 T C 8: 107,792,083 (GRCm39) E54G probably damaging Het
Tnks1bp1 C T 2: 84,889,624 (GRCm39) probably benign Het
Trim43c T C 9: 88,722,600 (GRCm39) L82P possibly damaging Het
Txndc2 T C 17: 65,945,466 (GRCm39) D237G probably benign Het
Vmn1r91 T A 7: 19,835,404 (GRCm39) C108S possibly damaging Het
Vtn A T 11: 78,390,836 (GRCm39) D165V probably damaging Het
Wdr3 A T 3: 100,068,468 (GRCm39) S13R probably damaging Het
Zdhhc16 A G 19: 41,926,198 (GRCm39) Y31C probably benign Het
Zfp39 A T 11: 58,781,887 (GRCm39) W292R probably benign Het
Zfp612 A T 8: 110,816,606 (GRCm39) L604F 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
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'- CAACTGCTTGCCATGACTG -3'
(R):5'- AGTTGTCTCAGGAGCTTGGC -3'

Sequencing Primer
(F):5'- ATGACTGTGTACCCACCTGG -3'
(R):5'- GCCCTCCTTGTGTAGGCATAATG -3'
Posted On 2017-10-10