Incidental Mutation 'R3804:Phf8'
ID274533
Institutional Source Beutler Lab
Gene Symbol Phf8
Ensembl Gene ENSMUSG00000041229
Gene NamePHD finger protein 8
Synonyms
MMRRC Submission 040879-MU
Accession Numbers
Is this an essential gene? Possibly essential (E-score: 0.529) question?
Stock #R3804 (G1)
Quality Score222
Status Validated
ChromosomeX
Chromosomal Location151520672-151633859 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 151572576 bp
ZygosityHeterozygous
Amino Acid Change Serine to Proline at position 512 (S512P)
Ref Sequence ENSEMBL: ENSMUSP00000127653 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046950] [ENSMUST00000046962] [ENSMUST00000112662] [ENSMUST00000112666] [ENSMUST00000112668] [ENSMUST00000112670] [ENSMUST00000168501]
Predicted Effect possibly damaging
Transcript: ENSMUST00000046950
AA Change: S512P

PolyPhen 2 Score 0.891 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000040765
Gene: ENSMUSG00000041229
AA Change: S512P

DomainStartEndE-ValueType
PHD 7 54 1.16e-9 SMART
JmjC 195 351 2.69e-49 SMART
low complexity region 480 498 N/A INTRINSIC
low complexity region 549 565 N/A INTRINSIC
low complexity region 733 742 N/A INTRINSIC
low complexity region 749 771 N/A INTRINSIC
low complexity region 789 794 N/A INTRINSIC
low complexity region 872 900 N/A INTRINSIC
low complexity region 912 941 N/A INTRINSIC
low complexity region 986 995 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000046962
SMART Domains Protein: ENSMUSP00000041312
Gene: ENSMUSG00000041229

DomainStartEndE-ValueType
PHD 7 54 1.16e-9 SMART
JmjC 195 351 2.69e-49 SMART
low complexity region 448 464 N/A INTRINSIC
low complexity region 632 641 N/A INTRINSIC
low complexity region 648 670 N/A INTRINSIC
low complexity region 688 693 N/A INTRINSIC
low complexity region 771 779 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000112662
SMART Domains Protein: ENSMUSP00000108281
Gene: ENSMUSG00000041229

DomainStartEndE-ValueType
PHD 7 54 1.16e-9 SMART
JmjC 195 351 2.69e-49 SMART
low complexity region 448 464 N/A INTRINSIC
low complexity region 632 641 N/A INTRINSIC
low complexity region 648 670 N/A INTRINSIC
low complexity region 688 693 N/A INTRINSIC
low complexity region 771 779 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000112666
SMART Domains Protein: ENSMUSP00000108285
Gene: ENSMUSG00000041229

DomainStartEndE-ValueType
PHD 7 54 1.16e-9 SMART
JmjC 195 351 2.69e-49 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112668
AA Change: S512P

PolyPhen 2 Score 0.174 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000108287
Gene: ENSMUSG00000041229
AA Change: S512P

DomainStartEndE-ValueType
PHD 7 54 1.16e-9 SMART
JmjC 195 351 2.69e-49 SMART
low complexity region 480 498 N/A INTRINSIC
low complexity region 549 565 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000112670
AA Change: S512P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000108289
Gene: ENSMUSG00000041229
AA Change: S512P

DomainStartEndE-ValueType
PHD 7 54 1.16e-9 SMART
JmjC 195 351 2.69e-49 SMART
low complexity region 480 498 N/A INTRINSIC
low complexity region 549 565 N/A INTRINSIC
low complexity region 733 742 N/A INTRINSIC
low complexity region 749 771 N/A INTRINSIC
low complexity region 789 794 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000151941
SMART Domains Protein: ENSMUSP00000116792
Gene: ENSMUSG00000041229

DomainStartEndE-ValueType
PDB:4DO0|A 2 71 2e-44 PDB
low complexity region 78 94 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000168501
AA Change: S512P

PolyPhen 2 Score 0.891 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000127653
Gene: ENSMUSG00000041229
AA Change: S512P

DomainStartEndE-ValueType
PHD 7 54 1.16e-9 SMART
JmjC 195 351 2.69e-49 SMART
low complexity region 480 498 N/A INTRINSIC
low complexity region 549 565 N/A INTRINSIC
low complexity region 733 742 N/A INTRINSIC
low complexity region 749 771 N/A INTRINSIC
low complexity region 789 794 N/A INTRINSIC
low complexity region 872 900 N/A INTRINSIC
low complexity region 912 941 N/A INTRINSIC
low complexity region 986 995 N/A INTRINSIC
Meta Mutation Damage Score 0.0717 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
Validation Efficiency 100% (67/67)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a histone lysine demethylase that preferentially acts on histones in the monomethyl or dimethyl states. The encoded protein requires Fe(2+) ion, 2-oxoglutarate, and oxygen for its catalytic activity. Defects in this gene are a cause of mental retardation syndromic X-linked Siderius type (MRXSSD). Four transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
Allele List at MGI
Other mutations in this stock
Total: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700011L22Rik C T 8: 79,248,293 E54K probably benign Het
2610301B20Rik A G 4: 10,898,014 T199A probably benign Het
Adgra1 A G 7: 139,845,594 T8A probably benign Het
Alms1 A G 6: 85,619,647 Y954C probably damaging Het
AU021092 A C 16: 5,216,762 F199V possibly damaging Het
Bahcc1 C T 11: 120,283,358 P1648L probably benign Het
Cacna1s T A 1: 136,107,018 C1319S possibly damaging Het
Capn13 G A 17: 73,339,401 P339L probably benign Het
Ccdc39 A T 3: 33,819,895 M596K probably damaging Het
Cntn5 A G 9: 9,781,663 probably benign Het
Cyth4 A G 15: 78,609,802 K159E probably damaging Het
Dgkz C A 2: 91,939,630 R563L probably benign Het
Dnah8 A G 17: 30,670,647 E718G probably benign Het
Dopey1 T C 9: 86,520,995 L1416P probably damaging Het
Dstyk G A 1: 132,449,726 A110T probably damaging Het
Eif1 A G 11: 100,320,824 K95E probably damaging Het
Espnl A G 1: 91,322,221 D30G probably benign Het
Gast T C 11: 100,336,810 S73P probably damaging Het
Gmppb T C 9: 108,050,574 Y176H probably damaging Het
Grap2 A G 15: 80,623,746 T4A possibly damaging Het
Grm8 T G 6: 28,125,636 N164H possibly damaging Het
Gstm3 G A 3: 107,964,235 T210I probably benign Het
Gtf3c3 A G 1: 54,424,007 probably null Het
Hmcn2 A G 2: 31,352,885 probably null Het
Icam2 A G 11: 106,380,822 L94P probably damaging Het
Iqcm C A 8: 75,669,393 T188K possibly damaging Het
Jarid2 T A 13: 44,902,831 N365K probably benign Het
Kank4 A G 4: 98,780,133 S26P probably damaging Het
Lgr4 A G 2: 110,008,197 K498E probably benign Het
Meltf A G 16: 31,884,998 H181R probably benign Het
Mslnl G A 17: 25,742,934 V128M probably damaging Het
Nf1 A G 11: 79,559,521 D511G probably null Het
Nhlrc3 A G 3: 53,458,631 V147A possibly damaging Het
Nrap C T 19: 56,321,779 D1595N probably damaging Het
Olfr1 T C 11: 73,395,950 Q24R probably benign Het
Olfr430 T A 1: 174,069,908 N203K probably damaging Het
Olfr481 A T 7: 108,081,171 I126F probably damaging Het
Olfr805 T A 10: 129,723,049 D165V possibly damaging Het
Pak3 G A X: 143,709,731 V87I probably damaging Het
Pgm2l1 T C 7: 100,252,267 V121A probably benign Het
Phf19 A G 2: 34,899,658 L350P probably damaging Het
Phkb G T 8: 85,922,229 E225* probably null Het
Pif1 T A 9: 65,588,306 V166E probably damaging Het
Plaa T C 4: 94,569,888 D615G probably damaging Het
Prpf4b T C 13: 34,883,682 probably benign Het
Rxra T C 2: 27,756,260 C374R probably damaging Het
Sept3 T C 15: 82,286,429 probably benign Het
Skint4 G T 4: 112,118,181 V113L probably damaging Het
Slc16a10 G C 10: 40,056,624 H314D possibly damaging Het
Slc22a15 C T 3: 101,897,274 G145D probably damaging Het
Slc28a1 A T 7: 81,126,221 I222F probably damaging Het
Slc43a2 T C 11: 75,563,598 L323P probably benign Het
Sorbs3 A G 14: 70,199,351 probably benign Het
Spink10 C T 18: 62,653,414 probably benign Het
Suclg2 A T 6: 95,497,668 I372N probably damaging Het
Sun1 C A 5: 139,225,362 C164* probably null Het
Tax1bp1 T C 6: 52,742,785 F453L probably benign Het
Tmem54 A G 4: 129,108,220 N9S probably benign Het
Tmx4 A G 2: 134,620,577 W145R probably damaging Het
Top1 A G 2: 160,702,768 H268R probably damaging Het
Ttn A G 2: 76,810,731 L13598P probably damaging Het
Vmn1r40 A G 6: 89,715,009 I269M probably benign Het
Wdr7 G T 18: 63,720,836 R80L probably benign Het
Zap70 A T 1: 36,771,142 Q111L possibly damaging Het
Zfp808 T A 13: 62,172,083 H375Q probably damaging Het
Zkscan2 A T 7: 123,495,142 probably benign Het
Other mutations in Phf8
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01288:Phf8 APN X 151547925 critical splice donor site probably null
IGL01693:Phf8 APN X 151550875 missense probably damaging 1.00
IGL02437:Phf8 APN X 151631360 missense possibly damaging 0.96
IGL02494:Phf8 APN X 151625231 missense probably benign 0.08
R0389:Phf8 UTSW X 151552622 missense probably benign 0.05
R2265:Phf8 UTSW X 151572601 missense possibly damaging 0.95
R2268:Phf8 UTSW X 151572601 missense possibly damaging 0.95
R3801:Phf8 UTSW X 151572576 missense possibly damaging 0.89
R3802:Phf8 UTSW X 151572576 missense possibly damaging 0.89
R3803:Phf8 UTSW X 151572576 missense possibly damaging 0.89
Predicted Primers PCR Primer
(F):5'- TGGGAAGACGAGCAATATCTTTGG -3'
(R):5'- ACTGGTAGCCAAACACCAGG -3'

Sequencing Primer
(F):5'- ACGAGCAATATCTTTGGGCTGC -3'
(R):5'- CACCAGGGGCCCTAAGAGATG -3'
Posted On2015-04-02