Incidental Mutation 'R0539:Phf1'
ID 49747
Institutional Source Beutler Lab
Gene Symbol Phf1
Ensembl Gene ENSMUSG00000024193
Gene Name PHD finger protein 1
Synonyms PHF2, Tctex3, Tctex-3, D17Ertd455e, mPcl1
MMRRC Submission 038731-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0539 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 27152101-27156882 bp(+) (GRCm39)
Type of Mutation splice site (1879 bp from exon)
DNA Base Change (assembly) A to G at 27153432 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000077984 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025027] [ENSMUST00000073724] [ENSMUST00000078961] [ENSMUST00000114935]
AlphaFold Q9Z1B8
Predicted Effect probably benign
Transcript: ENSMUST00000025027
SMART Domains Protein: ENSMUSP00000025027
Gene: ENSMUSG00000024194

DomainStartEndE-ValueType
transmembrane domain 7 29 N/A INTRINSIC
low complexity region 45 60 N/A INTRINSIC
Pfam:CutA1 67 165 6.9e-44 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000073724
AA Change: D55G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000073402
Gene: ENSMUSG00000024193
AA Change: D55G

DomainStartEndE-ValueType
TUDOR 29 86 5.61e-11 SMART
PHD 89 140 2.81e-8 SMART
PHD 188 238 2.42e0 SMART
low complexity region 410 416 N/A INTRINSIC
low complexity region 481 495 N/A INTRINSIC
Pfam:Mtf2_C 523 557 7.7e-11 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000078961
SMART Domains Protein: ENSMUSP00000077984
Gene: ENSMUSG00000024301

DomainStartEndE-ValueType
low complexity region 25 36 N/A INTRINSIC
low complexity region 108 117 N/A INTRINSIC
low complexity region 222 240 N/A INTRINSIC
KISc 307 670 1.34e-143 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000114935
SMART Domains Protein: ENSMUSP00000110585
Gene: ENSMUSG00000024194

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Pfam:CutA1 43 144 1.7e-44 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184739
Meta Mutation Damage Score 0.2177 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 94.3%
Validation Efficiency 100% (107/107)
MGI Phenotype FUNCTION: The protein encoded by this gene belongs to the polycomb-like protein family, which is a component of polycomb repressive complex-2. This complex represses gene expression by catalyzing the trimethylation of histone H3 lysine 27 and is required for the regulation of developmental genes including homeotic genes. The gene is expressed primarily in testis tissue. Small interfering RNA-mediated knockdown in cultured cell lines results in changes in homeotic gene expression coincident with alterations in promoter methylation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
Allele List at MGI
Other mutations in this stock
Total: 108 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5730480H06Rik T A 5: 48,536,692 (GRCm39) H129Q probably damaging Het
Abca14 G A 7: 119,807,020 (GRCm39) R22Q probably damaging Het
Abcg5 T A 17: 84,976,503 (GRCm39) M445L probably benign Het
Abhd3 T A 18: 10,645,208 (GRCm39) N357I possibly damaging Het
Adamts5 C T 16: 85,665,580 (GRCm39) G574S probably damaging Het
Adgrg5 T A 8: 95,665,260 (GRCm39) N389K probably damaging Het
Ankk1 A G 9: 49,329,330 (GRCm39) V80A probably benign Het
Arhgap20 A G 9: 51,761,455 (GRCm39) Q1066R probably benign Het
Arhgap21 T A 2: 20,919,610 (GRCm39) K32* probably null Het
AW209491 T C 13: 14,812,317 (GRCm39) F390S probably damaging Het
Axl A T 7: 25,478,142 (GRCm39) probably benign Het
Bri3bp A G 5: 125,531,603 (GRCm39) Y183C probably damaging Het
Cad T C 5: 31,232,801 (GRCm39) probably benign Het
Capns2 A G 8: 93,628,360 (GRCm39) Q83R possibly damaging Het
Ccdc180 G T 4: 45,922,010 (GRCm39) R1028L probably damaging Het
Cdh19 C A 1: 110,852,892 (GRCm39) V348F possibly damaging Het
Chrm2 T C 6: 36,500,641 (GRCm39) V166A possibly damaging Het
Clmp A G 9: 40,693,782 (GRCm39) Y333C probably benign Het
Cntn3 A G 6: 102,254,178 (GRCm39) probably null Het
Copz1 A G 15: 103,199,792 (GRCm39) Y69C probably damaging Het
Crybg1 T C 10: 43,874,894 (GRCm39) D738G probably benign Het
Ctnna2 T A 6: 76,950,882 (GRCm39) I165F probably damaging Het
Dcaf7 T G 11: 105,942,652 (GRCm39) S200A probably damaging Het
Deup1 T A 9: 15,493,893 (GRCm39) R416S possibly damaging Het
Dmxl1 T A 18: 49,990,497 (GRCm39) probably benign Het
Dnaaf11 A T 15: 66,319,455 (GRCm39) V305D probably damaging Het
Dnase2b A T 3: 146,294,910 (GRCm39) probably benign Het
Dst C T 1: 34,228,200 (GRCm39) P1606L probably damaging Het
Eef2 C CN 10: 81,014,602 (GRCm39) probably null Het
Ephb2 T C 4: 136,383,287 (GRCm39) Y931C probably damaging Het
Fam83h T C 15: 75,875,076 (GRCm39) S754G possibly damaging Het
Fibp T A 19: 5,513,216 (GRCm39) V177D probably damaging Het
Gfpt2 T C 11: 49,723,725 (GRCm39) I571T probably damaging Het
Grm7 T G 6: 111,336,055 (GRCm39) probably benign Het
Gsdma3 A G 11: 98,526,745 (GRCm39) Y335C probably damaging Het
H2-T23 A T 17: 36,343,033 (GRCm39) probably benign Het
H4c3 A G 13: 23,882,131 (GRCm39) F101S probably damaging Het
Hydin A G 8: 111,249,704 (GRCm39) I2216V probably benign Het
Ipo8 A G 6: 148,719,606 (GRCm39) M113T probably benign Het
Kdm6a A G X: 18,128,664 (GRCm39) E1045G probably damaging Het
Kyat1 C T 2: 30,078,229 (GRCm39) E117K probably damaging Het
Lin7b A G 7: 45,019,326 (GRCm39) probably benign Het
Lipn G A 19: 34,062,003 (GRCm39) probably benign Het
Lrfn2 C A 17: 49,378,072 (GRCm39) N384K probably damaging Het
Map1b T C 13: 99,570,526 (GRCm39) K732E unknown Het
Mpl A G 4: 118,300,705 (GRCm39) M541T possibly damaging Het
Mprip T C 11: 59,631,943 (GRCm39) probably benign Het
Mrc1 T C 2: 14,274,937 (GRCm39) probably benign Het
Ms4a13 T C 19: 11,149,235 (GRCm39) probably benign Het
Myo18b G T 5: 112,871,734 (GRCm39) R2116S probably damaging Het
Nav2 A G 7: 49,111,686 (GRCm39) T731A probably damaging Het
Ncoa6 G T 2: 155,257,617 (GRCm39) A642D probably benign Het
Ndufs7 T A 10: 80,090,665 (GRCm39) probably benign Het
Nfkbiz G A 16: 55,638,242 (GRCm39) T406M probably benign Het
Nr4a1 A G 15: 101,168,765 (GRCm39) E267G probably damaging Het
Nrxn2 T G 19: 6,543,434 (GRCm39) F1103V probably damaging Het
Or10ab4 C T 7: 107,655,029 (GRCm39) T280I probably damaging Het
Or10d3 A T 9: 39,461,593 (GRCm39) D191E probably damaging Het
Or1e22 T C 11: 73,376,889 (GRCm39) T254A probably benign Het
Or5a3 C T 19: 12,400,173 (GRCm39) L167F probably damaging Het
Or5g27 T A 2: 85,410,119 (GRCm39) C179S probably damaging Het
Or5m11 G T 2: 85,782,353 (GRCm39) M315I probably benign Het
Or8u9 A T 2: 86,001,387 (GRCm39) M258K probably damaging Het
Pip C T 6: 41,826,819 (GRCm39) Q53* probably null Het
Ppp2ca T C 11: 52,008,989 (GRCm39) probably null Het
Prl2c5 A G 13: 13,363,906 (GRCm39) probably null Het
Psph T A 5: 129,843,641 (GRCm39) probably benign Het
Ptch1 C T 13: 63,691,294 (GRCm39) probably benign Het
Ptprs C T 17: 56,765,255 (GRCm39) V10M probably damaging Het
Rarg T C 15: 102,147,312 (GRCm39) R358G probably damaging Het
Rbl2 T C 8: 91,839,133 (GRCm39) probably benign Het
Robo2 A T 16: 73,782,462 (GRCm39) probably benign Het
Scin A T 12: 40,131,765 (GRCm39) D256E possibly damaging Het
Scn8a T C 15: 100,914,449 (GRCm39) Y1152H probably damaging Het
Sh2b2 T G 5: 136,254,155 (GRCm39) probably benign Het
Slc13a2 G A 11: 78,289,964 (GRCm39) P450L probably damaging Het
Slc2a12 A G 10: 22,568,129 (GRCm39) I519V probably benign Het
Slc30a9 C T 5: 67,491,953 (GRCm39) T260M probably damaging Het
Slc9a7 A T X: 20,069,001 (GRCm39) F184Y probably damaging Het
Smc2 G T 4: 52,458,558 (GRCm39) K466N probably benign Het
Snx16 T C 3: 10,491,278 (GRCm39) E209G probably damaging Het
Sp3 A T 2: 72,800,876 (GRCm39) I423N possibly damaging Het
Ssh2 G T 11: 77,345,620 (GRCm39) V1202F probably benign Het
Stam2 A T 2: 52,593,268 (GRCm39) probably benign Het
Stox2 T C 8: 47,647,070 (GRCm39) Y194C probably damaging Het
Sult3a1 A G 10: 33,742,519 (GRCm39) T49A probably damaging Het
Supt3 A T 17: 45,314,018 (GRCm39) I136F possibly damaging Het
Syne2 A T 12: 76,070,895 (GRCm39) R103S possibly damaging Het
Synj2 T A 17: 6,047,163 (GRCm39) M1K probably null Het
Tas2r110 T C 6: 132,845,334 (GRCm39) S122P possibly damaging Het
Tln1 A G 4: 43,543,434 (GRCm39) probably null Het
Tmem117 A G 15: 94,612,793 (GRCm39) T110A possibly damaging Het
Tmem247 A G 17: 87,224,906 (GRCm39) D5G probably benign Het
Tmem39a T A 16: 38,411,337 (GRCm39) F363I probably benign Het
Tmem80 G A 7: 140,915,808 (GRCm39) A73T possibly damaging Het
Trpm4 C T 7: 44,954,896 (GRCm39) G901S probably damaging Het
Upk3bl T C 5: 136,092,840 (GRCm39) probably benign Het
Vmn1r120 A T 7: 20,787,397 (GRCm39) C105S probably damaging Het
Vmn1r69 A T 7: 10,314,874 (GRCm39) probably benign Het
Vmn2r95 T C 17: 18,672,362 (GRCm39) F700L probably damaging Het
Wdr70 G A 15: 7,915,118 (GRCm39) T550M possibly damaging Het
Zbtb22 A G 17: 34,137,118 (GRCm39) D421G possibly damaging Het
Zbtb45 G A 7: 12,740,260 (GRCm39) R452C probably damaging Het
Zfhx3 T C 8: 109,527,141 (GRCm39) Y1013H probably damaging Het
Zfp329 C T 7: 12,540,520 (GRCm39) probably null Het
Zfp532 T A 18: 65,756,837 (GRCm39) S257T probably benign Het
Zfp933 G A 4: 147,911,005 (GRCm39) T197I probably benign Het
Zgrf1 T A 3: 127,408,841 (GRCm39) N1649K probably damaging Het
Other mutations in Phf1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00905:Phf1 APN 17 27,155,568 (GRCm39) missense possibly damaging 0.90
IGL01629:Phf1 APN 17 27,153,247 (GRCm39) missense probably benign 0.07
IGL01931:Phf1 APN 17 27,154,509 (GRCm39) unclassified probably benign
IGL02008:Phf1 APN 17 27,154,260 (GRCm39) missense possibly damaging 0.95
IGL02048:Phf1 APN 17 27,153,515 (GRCm39) unclassified probably benign
IGL02206:Phf1 APN 17 27,155,843 (GRCm39) unclassified probably benign
IGL02252:Phf1 APN 17 27,154,109 (GRCm39) missense possibly damaging 0.65
IGL02548:Phf1 APN 17 27,154,600 (GRCm39) missense probably damaging 1.00
IGL03145:Phf1 APN 17 27,153,344 (GRCm39) critical splice donor site probably null
R0815:Phf1 UTSW 17 27,156,114 (GRCm39) unclassified probably benign
R0863:Phf1 UTSW 17 27,156,114 (GRCm39) unclassified probably benign
R1028:Phf1 UTSW 17 27,153,307 (GRCm39) missense possibly damaging 0.90
R1083:Phf1 UTSW 17 27,156,244 (GRCm39) unclassified probably benign
R1537:Phf1 UTSW 17 27,154,372 (GRCm39) critical splice donor site probably null
R1587:Phf1 UTSW 17 27,156,466 (GRCm39) missense probably damaging 0.99
R1656:Phf1 UTSW 17 27,156,333 (GRCm39) missense possibly damaging 0.93
R1956:Phf1 UTSW 17 27,154,719 (GRCm39) splice site probably null
R2566:Phf1 UTSW 17 27,156,062 (GRCm39) missense probably damaging 1.00
R3196:Phf1 UTSW 17 27,153,429 (GRCm39) missense probably damaging 1.00
R4223:Phf1 UTSW 17 27,156,474 (GRCm39) nonsense probably null
R4835:Phf1 UTSW 17 27,153,652 (GRCm39) missense probably benign
R6439:Phf1 UTSW 17 27,155,586 (GRCm39) missense probably benign
R7070:Phf1 UTSW 17 27,153,307 (GRCm39) missense possibly damaging 0.90
R7289:Phf1 UTSW 17 27,154,289 (GRCm39) missense probably damaging 1.00
R7846:Phf1 UTSW 17 27,154,291 (GRCm39) nonsense probably null
R8165:Phf1 UTSW 17 27,156,044 (GRCm39) missense possibly damaging 0.95
R9645:Phf1 UTSW 17 27,154,130 (GRCm39) critical splice donor site probably null
X0028:Phf1 UTSW 17 27,155,162 (GRCm39) missense possibly damaging 0.95
Predicted Primers PCR Primer
(F):5'- ACCATCCTATCTTGGAATAGGCCCC -3'
(R):5'- GGCAGACTGCACCACCTAAGTATC -3'

Sequencing Primer
(F):5'- ATGCAATGGCGCAGCTC -3'
(R):5'- TGGCGACACTTCTCACAG -3'
Posted On 2013-06-12