Incidental Mutation 'R1780:Phf3'
ID 197411
Institutional Source Beutler Lab
Gene Symbol Phf3
Ensembl Gene ENSMUSG00000048874
Gene Name PHD finger protein 3
Synonyms AU020177, 2310061N19Rik
MMRRC Submission 039811-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1780 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 30841417-30912989 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 30851023 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 1110 (D1110E)
Ref Sequence ENSEMBL: ENSMUSP00000139610 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000088310] [ENSMUST00000186733] [ENSMUST00000191329]
AlphaFold B2RQG2
Predicted Effect probably damaging
Transcript: ENSMUST00000088310
AA Change: D1110E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000085650
Gene: ENSMUSG00000048874
AA Change: D1110E

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: ENSMUST00000186105
Predicted Effect probably damaging
Transcript: ENSMUST00000186733
AA Change: D1110E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000139610
Gene: ENSMUSG00000048874
AA Change: D1110E

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: ENSMUST00000187316
Predicted Effect noncoding transcript
Transcript: ENSMUST00000190190
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191245
Predicted Effect probably benign
Transcript: ENSMUST00000191329
SMART Domains Protein: ENSMUSP00000139662
Gene: ENSMUSG00000048874

DomainStartEndE-ValueType
Pfam:SPOC 1 88 1.9e-17 PFAM
Meta Mutation Damage Score 0.1045 question?
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.8%
  • 10x: 95.2%
  • 20x: 92.3%
Validation Efficiency 98% (80/82)
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: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrl2 T C 3: 148,558,229 (GRCm39) E493G probably damaging Het
Aff3 A T 1: 38,574,783 (GRCm39) S66T probably damaging Het
Ankrd17 T A 5: 90,380,274 (GRCm39) K2470N probably damaging Het
Ap3m1 T C 14: 21,091,138 (GRCm39) T156A probably benign Het
Arhgef4 T A 1: 34,763,241 (GRCm39) S832R possibly damaging Het
Asb10 T C 5: 24,738,674 (GRCm39) D423G possibly damaging Het
Ash1l A G 3: 88,873,291 (GRCm39) T25A probably benign Het
Atp13a2 T A 4: 140,729,771 (GRCm39) L663I possibly damaging Het
Atp9b A T 18: 80,820,112 (GRCm39) Y174* probably null Het
Bche A G 3: 73,607,953 (GRCm39) I491T probably benign Het
Bckdhb T C 9: 83,835,836 (GRCm39) probably null Het
Cadps2 C T 6: 23,320,931 (GRCm39) probably null Het
Cdc42bpb A T 12: 111,289,341 (GRCm39) V468E probably damaging Het
Chrnd T C 1: 87,120,270 (GRCm39) V33A possibly damaging Het
Col6a5 A T 9: 105,814,077 (GRCm39) V645D unknown Het
Cpa1 C T 6: 30,643,007 (GRCm39) L312F probably damaging Het
Cyp2a5 A G 7: 26,541,301 (GRCm39) probably benign Het
Cyp2c39 C A 19: 39,527,295 (GRCm39) probably benign Het
Cyp2d26 T C 15: 82,678,208 (GRCm39) N56S probably damaging Het
Ddx21 A G 10: 62,429,926 (GRCm39) probably benign Het
Dnah11 A T 12: 117,991,293 (GRCm39) C2358S probably damaging Het
Entpd8 T C 2: 24,974,318 (GRCm39) S368P probably benign Het
Epg5 A T 18: 78,067,205 (GRCm39) Q2222L probably damaging Het
Ercc5 T A 1: 44,206,956 (GRCm39) V623E probably benign Het
Flg2 A G 3: 93,110,306 (GRCm39) E778G unknown Het
Gbe1 C T 16: 70,292,212 (GRCm39) R515* probably null Het
Hsd17b6 A G 10: 127,830,196 (GRCm39) probably null Het
Hyal6 C T 6: 24,734,031 (GRCm39) probably benign Het
Ifi27l2b A G 12: 103,417,578 (GRCm39) I203T probably damaging Het
Kcnk9 A C 15: 72,384,250 (GRCm39) D309E unknown Het
Lrp6 C T 6: 134,441,414 (GRCm39) R1184Q probably damaging Het
Mdn1 T C 4: 32,700,103 (GRCm39) F1399L probably damaging Het
Mroh2a C T 1: 88,158,402 (GRCm39) R150* probably null Het
Mx1 T C 16: 97,252,712 (GRCm39) *289W probably null Het
Myo7b T C 18: 32,094,238 (GRCm39) E1970G probably damaging Het
Mypn T C 10: 62,957,743 (GRCm39) Y24C probably damaging Het
Naxe G C 3: 87,964,440 (GRCm39) P167A probably benign Het
Nmnat2 A T 1: 152,988,186 (GRCm39) K272* probably null Het
Nmnat3 C T 9: 98,236,164 (GRCm39) T19M probably damaging Het
Or4f52 T C 2: 111,062,043 (GRCm39) I32V probably benign Het
Or51b17 A T 7: 103,542,762 (GRCm39) F60Y probably damaging Het
Or51b4 A G 7: 103,530,799 (GRCm39) V217A probably benign Het
Or5b118 A G 19: 13,448,726 (GRCm39) T131A probably benign Het
Or9s27 G A 1: 92,516,111 (GRCm39) V20M probably benign Het
Pgm3 T G 9: 86,438,257 (GRCm39) E509D probably damaging Het
Pkd1 T G 17: 24,800,543 (GRCm39) S3062A probably benign Het
Pogz A T 3: 94,777,437 (GRCm39) K372N possibly damaging Het
Pou1f1 A G 16: 65,320,356 (GRCm39) Y15C probably benign Het
Ppfia2 A G 10: 106,732,368 (GRCm39) T972A possibly damaging Het
Rasip1 A G 7: 45,284,742 (GRCm39) Y703C possibly damaging Het
Recql T A 6: 142,310,324 (GRCm39) Q502L probably benign Het
Rgs9 A T 11: 109,130,325 (GRCm39) Y383* probably null Het
Rimbp3 T C 16: 17,030,496 (GRCm39) S1307P probably benign Het
Rspo1 A G 4: 124,901,538 (GRCm39) T200A probably damaging Het
Ryr3 C T 2: 112,697,637 (GRCm39) M922I probably damaging Het
Samm50 C T 15: 84,095,328 (GRCm39) A438V probably damaging Het
Sec1 A C 7: 45,328,256 (GRCm39) S264A probably benign Het
Sec31a A T 5: 100,529,195 (GRCm39) probably null Het
Slc13a3 T C 2: 165,248,619 (GRCm39) N553S unknown Het
Smg6 T A 11: 74,836,942 (GRCm39) L852Q probably damaging Het
Spata13 A G 14: 60,929,174 (GRCm39) N244S probably damaging Het
Srbd1 T C 17: 86,365,113 (GRCm39) R648G probably damaging Het
Sugct T G 13: 17,627,039 (GRCm39) probably null Het
Tmed10 A G 12: 85,401,653 (GRCm39) Y85H probably damaging Het
Trim68 A G 7: 102,333,280 (GRCm39) I134T possibly damaging Het
Trio A G 15: 27,744,124 (GRCm39) C2603R possibly damaging Het
Tspyl3 G A 2: 153,067,176 (GRCm39) R21W probably damaging Het
Ttn T C 2: 76,641,043 (GRCm39) I11863V probably null Het
Ubp1 G A 9: 113,793,647 (GRCm39) A283T possibly damaging Het
Ubtf A T 11: 102,205,744 (GRCm39) F60L probably damaging Het
Vmn1r235 T C 17: 21,481,999 (GRCm39) I108T probably benign Het
Vmn2r125 T C 4: 156,703,668 (GRCm39) S349P probably damaging Het
Vmn2r25 A G 6: 123,805,424 (GRCm39) S478P probably damaging Het
Vmn2r88 T A 14: 51,656,029 (GRCm39) V746D probably damaging Het
Zcwpw1 A G 5: 137,794,914 (GRCm39) K37E probably damaging Het
Zdhhc24 T C 19: 4,933,794 (GRCm39) S284P probably damaging Het
Zswim8 C A 14: 20,766,395 (GRCm39) H841N 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
R1522:Phf3 UTSW 1 30,844,729 (GRCm39) missense probably benign 0.05
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
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'- AGCAAAGCTTATTCTAGACTATGCCCG -3'
(R):5'- TCACAGTGTGAGGAAACCACATTTCAG -3'

Sequencing Primer
(F):5'- TTATTCTAGACTATGCCCGAGAGAGG -3'
(R):5'- CTGGGTGCCATTGATAAATTATTTGC -3'
Posted On 2014-05-23