Incidental Mutation 'R2217:Phf6'
ID 241242
Institutional Source Beutler Lab
Gene Symbol Phf6
Ensembl Gene ENSMUSG00000025626
Gene Name PHD finger protein 6
Synonyms 4931428F02Rik, 2700007B13Rik
MMRRC Submission 040219-MU
Accession Numbers
Essential gene? Not available question?
Stock # R2217 (G1)
Quality Score 222
Status Not validated
Chromosome X
Chromosomal Location 52001143-52045820 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 52031525 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 272 (I272F)
Ref Sequence ENSEMBL: ENSMUSP00000110497 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000078944] [ENSMUST00000101587] [ENSMUST00000154864]
AlphaFold Q9D4J7
Predicted Effect probably damaging
Transcript: ENSMUST00000078944
AA Change: I272F

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000077971
Gene: ENSMUSG00000025626
AA Change: I272F

DomainStartEndE-ValueType
PHD 81 132 2.9e-1 SMART
low complexity region 153 170 N/A INTRINSIC
PHD 279 330 2.39e-2 SMART
low complexity region 333 343 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000101587
AA Change: I272F

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000110497
Gene: ENSMUSG00000025626
AA Change: I272F

DomainStartEndE-ValueType
PHD 81 132 2.9e-1 SMART
low complexity region 153 170 N/A INTRINSIC
PHD 279 314 1.49e1 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000154864
AA Change: I192F

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000130358
Gene: ENSMUSG00000025626
AA Change: I192F

DomainStartEndE-ValueType
PHD 1 52 2.9e-1 SMART
low complexity region 73 90 N/A INTRINSIC
PHD 199 250 2.39e-2 SMART
low complexity region 253 263 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000177780
Predicted Effect noncoding transcript
Transcript: ENSMUST00000179014
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.1%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the plant homeodomain (PHD)-like finger (PHF) family. It encodes a protein with two PHD-type zinc finger domains, indicating a potential role in transcriptional regulation, that localizes to the nucleolus. Mutations affecting the coding region of this gene or the splicing of the transcript have been associated with Borjeson-Forssman-Lehmann syndrome (BFLS), a disorder characterized by mental retardation, epilepsy, hypogonadism, hypometabolism, obesity, swelling of subcutaneous tissue of the face, narrow palpebral fissures, and large ears. Alternate splicing results in multiple transcript variants, encoding different isoforms. [provided by RefSeq, Jun 2010]
Allele List at MGI
Other mutations in this stock
Total: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adat1 T C 8: 112,709,128 (GRCm39) K232E probably benign Het
Apba1 T C 19: 23,871,326 (GRCm39) M386T probably damaging Het
Appl2 G T 10: 83,444,601 (GRCm39) F472L possibly damaging Het
Atxn2 T C 5: 121,941,140 (GRCm39) Y56H probably damaging Het
Cacna1c T C 6: 118,647,368 (GRCm39) Y809C probably damaging Het
Canx C T 11: 50,201,694 (GRCm39) V59I probably benign Het
Catsperb T C 12: 101,560,478 (GRCm39) L823P probably damaging Het
Crb3 T C 17: 57,372,090 (GRCm39) S46P probably benign Het
Daam1 G A 12: 72,036,601 (GRCm39) R1058H probably damaging Het
Ehd1 T A 19: 6,348,502 (GRCm39) D493E probably damaging Het
Eml6 T A 11: 29,768,907 (GRCm39) Q746L probably damaging Het
Epg5 T A 18: 77,992,287 (GRCm39) M328K probably benign Het
Flt4 T A 11: 49,515,555 (GRCm39) S48T probably benign Het
Gm10608 CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 9: 118,989,784 (GRCm39) probably null Het
Gm7535 A G 17: 18,131,936 (GRCm39) probably benign Het
Gpat4 G A 8: 23,670,171 (GRCm39) P286L probably damaging Het
Hmcn2 A T 2: 31,240,586 (GRCm39) T494S probably benign Het
Hydin G A 8: 111,145,138 (GRCm39) V830I probably benign Het
Map3k6 T A 4: 132,973,983 (GRCm39) H487Q possibly damaging Het
Myh14 G A 7: 44,283,800 (GRCm39) P735S probably damaging Het
Nfkb2 T C 19: 46,296,163 (GRCm39) probably null Het
Nlrp4c T C 7: 6,076,113 (GRCm39) V671A probably benign Het
Nsrp1 A T 11: 76,936,587 (GRCm39) Y536* probably null Het
Or4c112 G T 2: 88,853,770 (GRCm39) H192Q probably benign Het
Pak5 A G 2: 135,958,123 (GRCm39) S322P probably damaging Het
Pank2 A G 2: 131,124,601 (GRCm39) probably null Het
Plxna2 T C 1: 194,480,056 (GRCm39) L1409P probably damaging Het
Polr2a A G 11: 69,633,511 (GRCm39) probably null Het
Pp2d1 C A 17: 53,822,482 (GRCm39) V195L probably benign Het
Psma1 C T 7: 113,864,173 (GRCm39) E227K unknown Het
Ptger1 C T 8: 84,395,357 (GRCm39) T278I probably benign Het
Slc20a2 C A 8: 23,050,532 (GRCm39) S250R probably benign Het
Slc27a2 A G 2: 126,409,672 (GRCm39) T285A probably damaging Het
Slc47a2 T C 11: 61,204,497 (GRCm39) T285A probably benign Het
Slf1 T A 13: 77,194,825 (GRCm39) probably null Het
Tiam2 A G 17: 3,465,389 (GRCm39) T373A probably benign Het
Timd2 T A 11: 46,577,844 (GRCm39) I96L probably damaging Het
Tmem59l A G 8: 70,939,951 (GRCm39) L6S unknown Het
Tmem64 T C 4: 15,266,658 (GRCm39) I236T possibly damaging Het
Trpm2 T A 10: 77,777,016 (GRCm39) D427V probably damaging Het
Vax2 A T 6: 83,714,871 (GRCm39) Y262F probably damaging Het
Virma T C 4: 11,544,924 (GRCm39) S1628P probably damaging Het
Zan C A 5: 137,408,568 (GRCm39) probably benign Het
Zbtb22 T G 17: 34,136,939 (GRCm39) D361E probably damaging Het
Zfp27 A G 7: 29,595,536 (GRCm39) L143P possibly damaging Het
Other mutations in Phf6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00467:Phf6 APN X 52,020,523 (GRCm39) missense probably damaging 1.00
IGL00565:Phf6 APN X 52,020,516 (GRCm39) missense probably damaging 1.00
R2447:Phf6 UTSW X 52,042,435 (GRCm39) missense probably benign 0.07
Predicted Primers PCR Primer
(F):5'- GGCAAAGTCTCTGGAAGATTTCG -3'
(R):5'- TCTCTGCAGTCAAGTTGTAGTTC -3'

Sequencing Primer
(F):5'- CAAAGTCTCTGGAAGATTTCGAAATG -3'
(R):5'- GTTCTTAAAGCTAGTGACCAATGACC -3'
Posted On 2014-10-15