Incidental Mutation 'R1522:Phf3'
ID 167482
Institutional Source Beutler Lab
Gene Symbol Phf3
Ensembl Gene ENSMUSG00000048874
Gene Name PHD finger protein 3
Synonyms AU020177, 2310061N19Rik
MMRRC Submission 040871-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1522 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 30841417-30912989 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 30844729 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 1410 (T1410I)
Ref Sequence ENSEMBL: ENSMUSP00000139610 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000088310] [ENSMUST00000186733] [ENSMUST00000191329]
AlphaFold B2RQG2
Predicted Effect probably benign
Transcript: ENSMUST00000088310
AA Change: T1410I

PolyPhen 2 Score 0.048 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000085650
Gene: ENSMUSG00000048874
AA Change: T1410I

DomainStartEndE-ValueType
low complexity region 212 223 N/A INTRINSIC
low complexity region 337 344 N/A INTRINSIC
low complexity region 600 611 N/A INTRINSIC
low complexity region 651 660 N/A INTRINSIC
PHD 697 748 3.82e-10 SMART
low complexity region 847 859 N/A INTRINSIC
low complexity region 876 887 N/A INTRINSIC
TFS2M 908 1008 1.28e-47 SMART
Pfam:SPOC 1188 1294 4.2e-26 PFAM
low complexity region 1367 1373 N/A INTRINSIC
low complexity region 1516 1529 N/A INTRINSIC
low complexity region 1597 1620 N/A INTRINSIC
low complexity region 1796 1811 N/A INTRINSIC
low complexity region 1813 1846 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000186733
AA Change: T1410I

PolyPhen 2 Score 0.048 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000139610
Gene: ENSMUSG00000048874
AA Change: T1410I

DomainStartEndE-ValueType
low complexity region 212 223 N/A INTRINSIC
low complexity region 337 344 N/A INTRINSIC
low complexity region 600 611 N/A INTRINSIC
low complexity region 651 660 N/A INTRINSIC
PHD 697 748 3.82e-10 SMART
low complexity region 847 859 N/A INTRINSIC
low complexity region 876 887 N/A INTRINSIC
TFS2M 908 1008 1.28e-47 SMART
Pfam:SPOC 1188 1294 4.2e-26 PFAM
low complexity region 1367 1373 N/A INTRINSIC
low complexity region 1516 1529 N/A INTRINSIC
low complexity region 1597 1620 N/A INTRINSIC
low complexity region 1796 1811 N/A INTRINSIC
low complexity region 1813 1846 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000190190
Predicted Effect probably benign
Transcript: ENSMUST00000191329
SMART Domains Protein: ENSMUSP00000139662
Gene: ENSMUSG00000048874

DomainStartEndE-ValueType
Pfam:SPOC 1 88 1.9e-17 PFAM
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.1%
  • 10x: 95.8%
  • 20x: 91.1%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
Allele List at MGI
Other mutations in this stock
Total: 99 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700003E16Rik T C 6: 83,139,568 (GRCm39) S498P probably damaging Het
3100002H09Rik A G 4: 124,504,487 (GRCm39) W22R probably damaging Het
AA986860 A G 1: 130,670,831 (GRCm39) E351G probably damaging Het
Acsl5 T C 19: 55,268,924 (GRCm39) V195A probably benign Het
Actmap A G 7: 26,902,105 (GRCm39) H244R probably damaging Het
Adamts10 A G 17: 33,756,293 (GRCm39) D312G probably benign Het
Adgrb1 A G 15: 74,452,466 (GRCm39) M211V probably damaging Het
Ankfy1 C T 11: 72,646,693 (GRCm39) R859* probably null Het
Atp8b1 T A 18: 64,683,503 (GRCm39) I742L probably benign Het
B3galnt2 T A 13: 14,145,354 (GRCm39) V89E probably damaging Het
Brinp3 A C 1: 146,777,628 (GRCm39) T692P probably damaging Het
C9 T A 15: 6,516,243 (GRCm39) F349I probably damaging Het
Cacna1a T A 8: 85,360,062 (GRCm39) M1976K probably benign Het
Castor2 T G 5: 134,154,726 (GRCm39) S43R probably damaging Het
Ccdc180 T C 4: 45,927,975 (GRCm39) V1170A possibly damaging Het
Celsr1 A G 15: 85,815,477 (GRCm39) V1846A probably benign Het
Ces1f A T 8: 93,998,517 (GRCm39) Y160N possibly damaging Het
Cfap45 A G 1: 172,368,139 (GRCm39) E377G probably damaging Het
Clca3a1 T A 3: 144,460,932 (GRCm39) M240L probably benign Het
Clnk G A 5: 38,952,309 (GRCm39) T10M probably damaging Het
Cntrl T A 2: 35,045,291 (GRCm39) I781K possibly damaging Het
Col11a2 G A 17: 34,274,228 (GRCm39) G375S probably damaging Het
Col6a5 T A 9: 105,817,193 (GRCm39) I373F unknown Het
Dmxl1 C T 18: 49,985,434 (GRCm39) A227V probably benign Het
Dok5 A G 2: 170,574,052 (GRCm39) N4D probably benign Het
Dpysl3 A T 18: 43,496,622 (GRCm39) V138D probably damaging Het
Efs A T 14: 55,157,172 (GRCm39) Y380N probably damaging Het
Eme2 G A 17: 25,111,892 (GRCm39) S263F probably damaging Het
Farp2 A G 1: 93,546,275 (GRCm39) Q855R possibly damaging Het
Fcrl2 A C 3: 87,164,014 (GRCm39) S372A possibly damaging Het
Gadl1 C T 9: 115,773,297 (GRCm39) A113V probably damaging Het
Gda T A 19: 21,389,903 (GRCm39) E219D probably benign Het
Gli1 A T 10: 127,168,446 (GRCm39) M469K probably damaging Het
Gm4847 A T 1: 166,469,219 (GRCm39) S148R probably damaging Het
Golga2 T C 2: 32,192,216 (GRCm39) V325A probably benign Het
Hpf1 A G 8: 61,349,783 (GRCm39) D137G probably damaging Het
Htr2a C G 14: 74,943,293 (GRCm39) S291* probably null Het
Itga5 G A 15: 103,265,209 (GRCm39) Q233* probably null Het
Jazf1 C A 6: 52,789,168 (GRCm39) R102L probably damaging Het
Kif6 T G 17: 50,021,141 (GRCm39) L322R probably damaging Het
Ktn1 A C 14: 47,904,873 (GRCm39) K217T probably damaging Het
Lig4 A T 8: 10,023,012 (GRCm39) V256E possibly damaging Het
Lrp1 G T 10: 127,403,233 (GRCm39) D2113E probably damaging Het
Lrp1 A T 10: 127,411,155 (GRCm39) D1399E probably benign Het
Mmel1 A G 4: 154,979,443 (GRCm39) E717G probably damaging Het
Mndal G T 1: 173,699,032 (GRCm39) P155H possibly damaging Het
Mycbpap A G 11: 94,402,449 (GRCm39) probably null Het
Nedd1 T C 10: 92,555,476 (GRCm39) E3G probably damaging Het
Nlgn1 A T 3: 25,490,073 (GRCm39) N551K probably damaging Het
Nup210 G A 6: 91,046,148 (GRCm39) P595L possibly damaging Het
Or2ag15 A G 7: 106,340,212 (GRCm39) C310R probably benign Het
Or2g25 A T 17: 37,970,661 (GRCm39) C188S probably damaging Het
Or4k52 A T 2: 111,610,693 (GRCm39) probably null Het
Or5ac17 T G 16: 59,036,347 (GRCm39) T210P probably damaging Het
Or5p56 A G 7: 107,589,740 (GRCm39) H56R probably benign Het
Pank3 G A 11: 35,672,508 (GRCm39) V304M probably benign Het
Ppm1k A G 6: 57,502,142 (GRCm39) I7T possibly damaging Het
Ppp1r12c T C 7: 4,500,424 (GRCm39) D73G probably damaging Het
Prelid2 T G 18: 42,014,332 (GRCm39) M165L probably benign Het
Prkd3 A C 17: 79,260,125 (GRCm39) L826R probably damaging Het
Ptchd4 A T 17: 42,814,433 (GRCm39) N778I probably damaging Het
Ptprm T C 17: 67,000,866 (GRCm39) D1063G possibly damaging Het
Rab27a C A 9: 72,982,764 (GRCm39) T23N probably damaging Het
Rasgrf2 A T 13: 92,044,205 (GRCm39) F949L probably benign Het
Rbm33 A G 5: 28,542,002 (GRCm39) N68D probably damaging Het
Rgl1 A T 1: 152,462,284 (GRCm39) L109Q probably damaging Het
Rnf20 A G 4: 49,638,197 (GRCm39) N103S possibly damaging Het
Sbno1 G A 5: 124,530,675 (GRCm39) L875F probably damaging Het
Scube1 T A 15: 83,512,277 (GRCm39) probably null Het
Selenbp1 G A 3: 94,844,669 (GRCm39) V109M probably damaging Het
Serpina3c T A 12: 104,117,805 (GRCm39) I178F probably damaging Het
Shisa8 C T 15: 82,092,702 (GRCm39) G63D probably damaging Het
Snx14 T C 9: 88,284,277 (GRCm39) R464G possibly damaging Het
Snx25 A T 8: 46,577,119 (GRCm39) M1K probably null Het
Sorcs3 C A 19: 48,694,448 (GRCm39) T574K possibly damaging Het
Syne2 A G 12: 76,150,557 (GRCm39) E6528G probably damaging Het
Syt5 T C 7: 4,543,245 (GRCm39) E338G probably damaging Het
Tbk1 T C 10: 121,387,223 (GRCm39) K691E probably benign Het
Tenm3 G A 8: 48,848,611 (GRCm39) T11I probably damaging Het
Thrb A G 14: 18,002,597 (GRCm38) H87R probably damaging Het
Tlr4 T A 4: 66,757,933 (GRCm39) M242K possibly damaging Het
Tm4sf19 T C 16: 32,224,820 (GRCm39) M56T possibly damaging Het
Tmem212 T A 3: 27,940,620 (GRCm39) R66* probably null Het
Tmem39b G T 4: 129,578,275 (GRCm39) D315E probably benign Het
Tnxb T C 17: 34,937,612 (GRCm39) F3834L probably damaging Het
Trim36 A T 18: 46,319,250 (GRCm39) L225* probably null Het
Trim42 A T 9: 97,247,732 (GRCm39) H321Q probably damaging Het
Trio G T 15: 27,732,726 (GRCm39) Q3052K probably benign Het
Trpm3 T C 19: 22,955,698 (GRCm39) I1091T probably benign Het
Tst T C 15: 78,284,143 (GRCm39) E228G possibly damaging Het
Ttn T C 2: 76,702,060 (GRCm39) probably benign Het
Uap1 A C 1: 169,978,510 (GRCm39) probably null Het
Ush2a T C 1: 188,530,011 (GRCm39) S3267P possibly damaging Het
Usp5 T C 6: 124,802,129 (GRCm39) T38A probably benign Het
Uvssa A T 5: 33,545,152 (GRCm39) Q84L probably damaging Het
Vmn1r159 T G 7: 22,542,693 (GRCm39) H113P probably damaging Het
Vps13d A T 4: 144,824,742 (GRCm39) probably null Het
Zfp182 T A X: 20,897,799 (GRCm39) I166L probably benign Het
Zfp811 A T 17: 33,016,622 (GRCm39) Y472N probably damaging Het
Other mutations in Phf3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00234:Phf3 APN 1 30,850,928 (GRCm39) missense probably damaging 0.99
IGL00704:Phf3 APN 1 30,843,919 (GRCm39) missense probably benign
IGL01147:Phf3 APN 1 30,843,250 (GRCm39) missense probably damaging 1.00
IGL01360:Phf3 APN 1 30,847,809 (GRCm39) missense probably damaging 1.00
IGL01376:Phf3 APN 1 30,869,566 (GRCm39) missense possibly damaging 0.62
IGL01396:Phf3 APN 1 30,843,386 (GRCm39) nonsense probably null
IGL01830:Phf3 APN 1 30,853,148 (GRCm39) nonsense probably null
IGL02108:Phf3 APN 1 30,869,032 (GRCm39) missense probably damaging 1.00
IGL02156:Phf3 APN 1 30,847,859 (GRCm39) missense probably damaging 1.00
IGL02576:Phf3 APN 1 30,869,117 (GRCm39) missense probably benign 0.01
IGL03031:Phf3 APN 1 30,843,734 (GRCm39) missense probably benign 0.00
IGL03334:Phf3 APN 1 30,844,810 (GRCm39) missense probably damaging 0.99
IGL03411:Phf3 APN 1 30,843,482 (GRCm39) missense probably damaging 1.00
FR4976:Phf3 UTSW 1 30,844,104 (GRCm39) utr 3 prime probably benign
PIT4458001:Phf3 UTSW 1 30,855,622 (GRCm39) missense probably damaging 1.00
R0037:Phf3 UTSW 1 30,843,999 (GRCm39) missense probably benign 0.03
R0052:Phf3 UTSW 1 30,847,848 (GRCm39) missense probably damaging 1.00
R0114:Phf3 UTSW 1 30,844,524 (GRCm39) missense possibly damaging 0.87
R0123:Phf3 UTSW 1 30,844,146 (GRCm39) missense probably benign 0.01
R0225:Phf3 UTSW 1 30,844,146 (GRCm39) missense probably benign 0.01
R0715:Phf3 UTSW 1 30,850,919 (GRCm39) missense probably damaging 1.00
R0835:Phf3 UTSW 1 30,869,632 (GRCm39) missense probably benign 0.02
R0848:Phf3 UTSW 1 30,902,253 (GRCm39) missense probably damaging 1.00
R1473:Phf3 UTSW 1 30,845,021 (GRCm39) missense probably damaging 1.00
R1549:Phf3 UTSW 1 30,843,923 (GRCm39) missense probably benign 0.00
R1555:Phf3 UTSW 1 30,844,958 (GRCm39) missense possibly damaging 0.86
R1780:Phf3 UTSW 1 30,851,023 (GRCm39) missense probably damaging 1.00
R1789:Phf3 UTSW 1 30,845,287 (GRCm39) missense probably damaging 1.00
R1875:Phf3 UTSW 1 30,869,704 (GRCm39) missense possibly damaging 0.81
R1912:Phf3 UTSW 1 30,843,426 (GRCm39) missense probably damaging 1.00
R1957:Phf3 UTSW 1 30,870,601 (GRCm39) missense probably damaging 1.00
R2019:Phf3 UTSW 1 30,850,928 (GRCm39) missense probably damaging 0.99
R2259:Phf3 UTSW 1 30,843,424 (GRCm39) missense probably benign 0.20
R2305:Phf3 UTSW 1 30,844,556 (GRCm39) nonsense probably null
R2345:Phf3 UTSW 1 30,844,432 (GRCm39) nonsense probably null
R2424:Phf3 UTSW 1 30,845,430 (GRCm39) missense probably damaging 1.00
R2497:Phf3 UTSW 1 30,869,095 (GRCm39) missense probably damaging 1.00
R2504:Phf3 UTSW 1 30,849,870 (GRCm39) missense probably damaging 1.00
R3522:Phf3 UTSW 1 30,844,684 (GRCm39) missense probably damaging 1.00
R3816:Phf3 UTSW 1 30,844,834 (GRCm39) missense probably damaging 1.00
R4152:Phf3 UTSW 1 30,870,539 (GRCm39) missense probably benign 0.13
R4403:Phf3 UTSW 1 30,843,490 (GRCm39) missense probably damaging 1.00
R4658:Phf3 UTSW 1 30,902,169 (GRCm39) missense probably damaging 1.00
R4663:Phf3 UTSW 1 30,860,296 (GRCm39) missense probably damaging 1.00
R4669:Phf3 UTSW 1 30,869,027 (GRCm39) missense probably damaging 1.00
R4706:Phf3 UTSW 1 30,844,687 (GRCm39) missense probably damaging 1.00
R4757:Phf3 UTSW 1 30,859,908 (GRCm39) missense probably damaging 1.00
R4766:Phf3 UTSW 1 30,853,020 (GRCm39) unclassified probably benign
R4786:Phf3 UTSW 1 30,855,638 (GRCm39) nonsense probably null
R5107:Phf3 UTSW 1 30,870,566 (GRCm39) missense probably benign 0.03
R5155:Phf3 UTSW 1 30,863,457 (GRCm39) missense possibly damaging 0.87
R5310:Phf3 UTSW 1 30,842,887 (GRCm39) missense probably damaging 1.00
R5823:Phf3 UTSW 1 30,843,764 (GRCm39) missense probably damaging 1.00
R5944:Phf3 UTSW 1 30,859,785 (GRCm39) missense probably damaging 1.00
R5979:Phf3 UTSW 1 30,844,827 (GRCm39) missense probably damaging 1.00
R6007:Phf3 UTSW 1 30,843,426 (GRCm39) missense probably damaging 1.00
R6024:Phf3 UTSW 1 30,902,307 (GRCm39) missense probably damaging 1.00
R6072:Phf3 UTSW 1 30,869,769 (GRCm39) missense probably benign 0.08
R6533:Phf3 UTSW 1 30,845,399 (GRCm39) missense probably damaging 1.00
R6649:Phf3 UTSW 1 30,844,104 (GRCm39) missense possibly damaging 0.75
R6653:Phf3 UTSW 1 30,844,104 (GRCm39) missense possibly damaging 0.75
R6852:Phf3 UTSW 1 30,843,711 (GRCm39) missense probably damaging 0.97
R6855:Phf3 UTSW 1 30,859,204 (GRCm39) missense probably damaging 1.00
R6862:Phf3 UTSW 1 30,853,063 (GRCm39) missense probably damaging 1.00
R6930:Phf3 UTSW 1 30,850,958 (GRCm39) missense probably damaging 1.00
R7135:Phf3 UTSW 1 30,870,190 (GRCm39) missense possibly damaging 0.61
R7323:Phf3 UTSW 1 30,852,211 (GRCm39) missense probably benign 0.01
R7352:Phf3 UTSW 1 30,843,407 (GRCm39) missense possibly damaging 0.87
R7455:Phf3 UTSW 1 30,876,239 (GRCm39) missense probably damaging 0.96
R7549:Phf3 UTSW 1 30,870,556 (GRCm39) missense probably benign 0.01
R7609:Phf3 UTSW 1 30,844,582 (GRCm39) missense probably benign 0.05
R7720:Phf3 UTSW 1 30,868,938 (GRCm39) missense probably damaging 1.00
R7745:Phf3 UTSW 1 30,843,305 (GRCm39) missense probably damaging 1.00
R8134:Phf3 UTSW 1 30,863,552 (GRCm39) missense unknown
R8264:Phf3 UTSW 1 30,870,138 (GRCm39) missense possibly damaging 0.48
R8545:Phf3 UTSW 1 30,863,391 (GRCm39) missense possibly damaging 0.48
R8821:Phf3 UTSW 1 30,860,347 (GRCm39) nonsense probably null
R8831:Phf3 UTSW 1 30,860,347 (GRCm39) nonsense probably null
R8873:Phf3 UTSW 1 30,843,773 (GRCm39) missense possibly damaging 0.74
R9101:Phf3 UTSW 1 30,843,026 (GRCm39) missense possibly damaging 0.56
R9402:Phf3 UTSW 1 30,850,928 (GRCm39) missense probably damaging 0.99
R9426:Phf3 UTSW 1 30,870,625 (GRCm39) nonsense probably null
R9594:Phf3 UTSW 1 30,869,003 (GRCm39) missense probably benign 0.07
R9707:Phf3 UTSW 1 30,868,923 (GRCm39) critical splice donor site probably null
R9803:Phf3 UTSW 1 30,869,872 (GRCm39) missense probably benign 0.16
Z1177:Phf3 UTSW 1 30,851,049 (GRCm39) critical splice acceptor site probably null
Z1177:Phf3 UTSW 1 30,844,132 (GRCm39) missense unknown
Z1177:Phf3 UTSW 1 30,843,376 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GCTGAGCCTGCTCATATACTTGACC -3'
(R):5'- GGCCTGATTATCCGTCAGAAGCTG -3'

Sequencing Primer
(F):5'- TGCTCATATACTTGACCAGTGG -3'
(R):5'- TTATCCGTCAGAAGCTGAAGCG -3'
Posted On 2014-04-13