Incidental Mutation 'R4698:Phf21a'
ID 355812
Institutional Source Beutler Lab
Gene Symbol Phf21a
Ensembl Gene ENSMUSG00000058318
Gene Name PHD finger protein 21A
Synonyms Braf35/HDAC complex (Bhc), 80kDa, Bhc80, PFTF1, D030065N23Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4698 (G1)
Quality Score 189
Status Not validated
Chromosome 2
Chromosomal Location 92014096-92195011 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 92187297 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 445 (D445G)
Ref Sequence ENSEMBL: ENSMUSP00000106928 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000044036] [ENSMUST00000068702] [ENSMUST00000090586] [ENSMUST00000111290] [ENSMUST00000111291] [ENSMUST00000111292] [ENSMUST00000111293] [ENSMUST00000159961] [ENSMUST00000111297] [ENSMUST00000111294]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000044036
AA Change: D438G

PolyPhen 2 Score 0.952 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000038497
Gene: ENSMUSG00000058318
AA Change: D438G

DomainStartEndE-ValueType
coiled coil region 29 62 N/A INTRINSIC
low complexity region 85 129 N/A INTRINSIC
low complexity region 165 186 N/A INTRINSIC
AT_hook 350 362 4.28e-1 SMART
low complexity region 369 381 N/A INTRINSIC
PHD 415 458 3.12e-15 SMART
RING 416 457 1.85e-1 SMART
coiled coil region 482 527 N/A INTRINSIC
low complexity region 575 595 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000068702
AA Change: D390G

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000070649
Gene: ENSMUSG00000058318
AA Change: D390G

DomainStartEndE-ValueType
coiled coil region 29 62 N/A INTRINSIC
low complexity region 85 128 N/A INTRINSIC
low complexity region 164 185 N/A INTRINSIC
PHD 367 410 3.12e-15 SMART
RING 368 409 1.85e-1 SMART
coiled coil region 434 479 N/A INTRINSIC
low complexity region 527 547 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000090586
AA Change: D522G

PolyPhen 2 Score 0.442 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000088074
Gene: ENSMUSG00000058318
AA Change: D522G

DomainStartEndE-ValueType
coiled coil region 29 62 N/A INTRINSIC
low complexity region 85 128 N/A INTRINSIC
low complexity region 249 270 N/A INTRINSIC
AT_hook 434 446 4.28e-1 SMART
low complexity region 453 465 N/A INTRINSIC
PHD 499 542 3.12e-15 SMART
RING 500 541 1.85e-1 SMART
coiled coil region 566 611 N/A INTRINSIC
low complexity region 659 679 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000111290
AA Change: D493G

PolyPhen 2 Score 0.174 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000106921
Gene: ENSMUSG00000058318
AA Change: D493G

DomainStartEndE-ValueType
coiled coil region 29 62 N/A INTRINSIC
low complexity region 85 128 N/A INTRINSIC
low complexity region 249 270 N/A INTRINSIC
AT_hook 405 417 4.28e-1 SMART
low complexity region 424 436 N/A INTRINSIC
PHD 470 513 3.12e-15 SMART
RING 471 512 1.85e-1 SMART
coiled coil region 537 582 N/A INTRINSIC
low complexity region 630 650 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000111291
AA Change: D438G

PolyPhen 2 Score 0.952 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000106922
Gene: ENSMUSG00000058318
AA Change: D438G

DomainStartEndE-ValueType
coiled coil region 29 62 N/A INTRINSIC
low complexity region 85 129 N/A INTRINSIC
low complexity region 165 186 N/A INTRINSIC
AT_hook 350 362 4.28e-1 SMART
low complexity region 369 381 N/A INTRINSIC
PHD 415 458 3.12e-15 SMART
RING 416 457 1.85e-1 SMART
coiled coil region 482 527 N/A INTRINSIC
low complexity region 575 595 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000111292
AA Change: D390G

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000106923
Gene: ENSMUSG00000058318
AA Change: D390G

DomainStartEndE-ValueType
coiled coil region 29 62 N/A INTRINSIC
low complexity region 85 128 N/A INTRINSIC
low complexity region 164 185 N/A INTRINSIC
PHD 367 410 3.12e-15 SMART
RING 368 409 1.85e-1 SMART
coiled coil region 434 479 N/A INTRINSIC
low complexity region 527 547 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000111293
AA Change: D522G

PolyPhen 2 Score 0.442 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000106924
Gene: ENSMUSG00000058318
AA Change: D522G

DomainStartEndE-ValueType
coiled coil region 29 62 N/A INTRINSIC
low complexity region 85 128 N/A INTRINSIC
low complexity region 249 270 N/A INTRINSIC
AT_hook 434 446 4.28e-1 SMART
low complexity region 453 465 N/A INTRINSIC
PHD 499 542 3.12e-15 SMART
RING 500 541 1.85e-1 SMART
coiled coil region 566 611 N/A INTRINSIC
low complexity region 659 679 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161044
Predicted Effect probably benign
Transcript: ENSMUST00000159961
AA Change: D409G

PolyPhen 2 Score 0.151 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000123955
Gene: ENSMUSG00000058318
AA Change: D409G

DomainStartEndE-ValueType
coiled coil region 1 34 N/A INTRINSIC
low complexity region 57 100 N/A INTRINSIC
low complexity region 136 157 N/A INTRINSIC
AT_hook 321 333 4.28e-1 SMART
low complexity region 340 352 N/A INTRINSIC
PHD 386 429 3.12e-15 SMART
RING 387 428 1.85e-1 SMART
coiled coil region 453 498 N/A INTRINSIC
low complexity region 546 566 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000111297
AA Change: D445G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000106928
Gene: ENSMUSG00000058318
AA Change: D445G

DomainStartEndE-ValueType
coiled coil region 29 62 N/A INTRINSIC
low complexity region 85 129 N/A INTRINSIC
low complexity region 248 269 N/A INTRINSIC
PHD 422 465 3.12e-15 SMART
RING 423 464 1.85e-1 SMART
coiled coil region 489 534 N/A INTRINSIC
low complexity region 582 602 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000111294
AA Change: D475G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000106925
Gene: ENSMUSG00000058318
AA Change: D475G

DomainStartEndE-ValueType
coiled coil region 29 62 N/A INTRINSIC
low complexity region 85 128 N/A INTRINSIC
low complexity region 249 270 N/A INTRINSIC
PHD 452 495 3.12e-15 SMART
RING 453 494 1.85e-1 SMART
coiled coil region 519 564 N/A INTRINSIC
low complexity region 612 632 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000161067
AA Change: D162G
SMART Domains Protein: ENSMUSP00000124255
Gene: ENSMUSG00000058318
AA Change: D162G

DomainStartEndE-ValueType
PHD 140 183 3.12e-15 SMART
RING 141 182 1.85e-1 SMART
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.3%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The PHF21A gene encodes BHC80, a component of a BRAF35 (MIM 605535)/histone deacetylase (HDAC; see MIM 601241) complex (BHC) that mediates repression of neuron-specific genes through the cis-regulatory element known as repressor element-1 (RE1) or neural restrictive silencer (NRS) (Hakimi et al., 2002 [PubMed 12032298]).[supplied by OMIM, Nov 2010]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit neonatal lethality and insufficient milk-sucking behavior. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700122O11Rik A G 17: 48,349,049 (GRCm39) V11A possibly damaging Het
6030452D12Rik T C 8: 107,230,979 (GRCm39) I55T unknown Het
Aadacl2 A G 3: 59,932,460 (GRCm39) D325G probably benign Het
Adh1 A G 3: 137,988,274 (GRCm39) S113G probably benign Het
Agxt2 T C 15: 10,392,130 (GRCm39) probably null Het
Aicda C T 6: 122,530,847 (GRCm39) probably benign Het
Aifm2 T C 10: 61,563,535 (GRCm39) M135T probably benign Het
Asah2 T C 19: 32,031,871 (GRCm39) probably null Het
Btbd17 T C 11: 114,682,543 (GRCm39) R390G probably damaging Het
Cadps T C 14: 12,705,654 (GRCm38) E247G possibly damaging Het
Cds2 T C 2: 132,146,873 (GRCm39) I383T probably damaging Het
Celf3 T A 3: 94,392,174 (GRCm39) probably null Het
Crhr2 T C 6: 55,079,852 (GRCm39) S162G possibly damaging Het
Dapl1 A T 2: 59,335,118 (GRCm39) K91* probably null Het
Ddx60 A C 8: 62,465,458 (GRCm39) M1372L probably benign Het
Dnah2 A T 11: 69,389,358 (GRCm39) F845I probably damaging Het
Dscam T C 16: 96,411,524 (GRCm39) D1784G probably damaging Het
Ech1 T C 7: 28,531,478 (GRCm39) V310A probably benign Het
Eef1g A G 19: 8,955,330 (GRCm39) D393G possibly damaging Het
Eif3k T C 7: 28,671,969 (GRCm39) I172V possibly damaging Het
Foxd4 A G 19: 24,877,625 (GRCm39) F192L probably damaging Het
Gpr153 T A 4: 152,366,240 (GRCm39) S268R probably damaging Het
H3c13 C A 3: 96,176,394 (GRCm39) R129S probably damaging Het
Ivl T C 3: 92,478,698 (GRCm39) K456E unknown Het
Kif20b A T 19: 34,928,944 (GRCm39) D1190V probably damaging Het
Kif21a T A 15: 90,840,508 (GRCm39) I1223L possibly damaging Het
Lmf1 T C 17: 25,798,324 (GRCm39) V55A probably damaging Het
Loxhd1 A G 18: 77,459,987 (GRCm39) E659G possibly damaging Het
Lrrc37a T C 11: 103,394,930 (GRCm39) E165G possibly damaging Het
Mios T C 6: 8,228,113 (GRCm39) Y677H possibly damaging Het
Mnx1 T A 5: 29,679,057 (GRCm39) K342M unknown Het
Mtpap A T 18: 4,375,724 (GRCm39) T35S possibly damaging Het
Ndc1 C G 4: 107,268,334 (GRCm39) D623E probably benign Het
Nedd4l A G 18: 65,336,951 (GRCm39) Y666C probably damaging Het
Or52s6 T A 7: 103,091,842 (GRCm39) I163F possibly damaging Het
Or5ac22 T C 16: 59,135,720 (GRCm39) T17A probably damaging Het
Or5b12b T G 19: 12,861,985 (GRCm39) F247V probably benign Het
Or5m10b A G 2: 85,699,596 (GRCm39) Y220C possibly damaging Het
Papss1 G T 3: 131,313,092 (GRCm39) V369F probably damaging Het
Pcdhac2 T A 18: 37,278,822 (GRCm39) Y601N probably damaging Het
Pde7a C T 3: 19,365,095 (GRCm39) R24Q probably damaging Het
Plekho1 T A 3: 95,902,964 (GRCm39) N15I possibly damaging Het
Pprc1 T C 19: 46,057,634 (GRCm39) probably benign Het
Ralgapa1 A T 12: 55,724,061 (GRCm39) probably null Het
Rrp12 T C 19: 41,861,481 (GRCm39) E942G probably benign Het
Skor1 T C 9: 63,051,830 (GRCm39) D685G probably benign Het
Smim23 A T 11: 32,774,510 (GRCm39) I3N possibly damaging Het
Spata7 A T 12: 98,630,536 (GRCm39) I333F probably damaging Het
Sppl2c T C 11: 104,079,141 (GRCm39) I647T probably benign Het
Srgap1 C A 10: 121,628,392 (GRCm39) R837L probably benign Het
Stpg2 C A 3: 139,014,990 (GRCm39) P385H probably damaging Het
Tmem238 C A 7: 4,792,016 (GRCm39) E19* probably null Het
Top2b A T 14: 16,387,331 (GRCm38) K140* probably null Het
Trp53 T A 11: 69,479,248 (GRCm39) L142* probably null Het
Tyro3 A T 2: 119,633,751 (GRCm39) D133V probably damaging Het
Virma T A 4: 11,528,636 (GRCm39) I1291N probably damaging Het
Vmn1r213 A G 13: 23,195,507 (GRCm39) probably benign Het
Zbtb10 T C 3: 9,329,610 (GRCm39) S323P possibly damaging Het
Zfp521 A T 18: 13,978,660 (GRCm39) N584K probably damaging Het
Zfp944 A G 17: 22,558,180 (GRCm39) C356R probably damaging Het
Other mutations in Phf21a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00331:Phf21a APN 2 92,178,374 (GRCm39) missense probably damaging 1.00
IGL00826:Phf21a APN 2 92,174,881 (GRCm39) splice site probably benign
IGL01859:Phf21a APN 2 92,158,701 (GRCm39) missense probably damaging 1.00
IGL02124:Phf21a APN 2 92,179,767 (GRCm39) missense probably damaging 1.00
IGL02724:Phf21a APN 2 92,190,592 (GRCm39) missense probably damaging 1.00
IGL03155:Phf21a APN 2 92,150,611 (GRCm39) missense probably damaging 0.99
R0308:Phf21a UTSW 2 92,161,122 (GRCm39) missense possibly damaging 0.86
R1251:Phf21a UTSW 2 92,189,544 (GRCm39) missense probably benign 0.00
R1739:Phf21a UTSW 2 92,190,644 (GRCm39) missense possibly damaging 0.95
R1775:Phf21a UTSW 2 92,160,860 (GRCm39) missense probably damaging 1.00
R2013:Phf21a UTSW 2 92,058,828 (GRCm39) critical splice donor site probably null
R2064:Phf21a UTSW 2 92,157,422 (GRCm39) missense possibly damaging 0.47
R2073:Phf21a UTSW 2 92,178,381 (GRCm39) missense probably damaging 1.00
R4901:Phf21a UTSW 2 92,187,346 (GRCm39) nonsense probably null
R5055:Phf21a UTSW 2 92,182,201 (GRCm39) missense probably damaging 1.00
R5249:Phf21a UTSW 2 92,058,822 (GRCm39) missense probably damaging 1.00
R5401:Phf21a UTSW 2 92,182,097 (GRCm39) missense possibly damaging 0.71
R5770:Phf21a UTSW 2 92,182,199 (GRCm39) missense possibly damaging 0.52
R5969:Phf21a UTSW 2 92,051,956 (GRCm39) missense probably damaging 0.98
R6008:Phf21a UTSW 2 92,182,097 (GRCm39) missense possibly damaging 0.71
R6012:Phf21a UTSW 2 92,182,120 (GRCm39) missense probably damaging 1.00
R6128:Phf21a UTSW 2 92,181,953 (GRCm39) critical splice acceptor site probably null
R6354:Phf21a UTSW 2 92,179,282 (GRCm39) missense probably damaging 1.00
R7075:Phf21a UTSW 2 92,190,724 (GRCm39) nonsense probably null
R7117:Phf21a UTSW 2 92,189,502 (GRCm39) missense probably benign 0.25
R7270:Phf21a UTSW 2 92,157,484 (GRCm39) missense probably damaging 0.98
R7603:Phf21a UTSW 2 92,187,352 (GRCm39) missense probably benign 0.08
R7708:Phf21a UTSW 2 92,157,511 (GRCm39) critical splice donor site probably null
R7946:Phf21a UTSW 2 92,189,512 (GRCm39) missense probably damaging 0.99
R9788:Phf21a UTSW 2 92,181,978 (GRCm39) critical splice donor site probably null
Z1177:Phf21a UTSW 2 92,061,059 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AAAATTGGAGGCCCATCTCTGAG -3'
(R):5'- TTCATGAACCAGGAGGAGAACC -3'

Sequencing Primer
(F):5'- AGGCCCATCTCTGAGCCATC -3'
(R):5'- CATGAACCAGGAGGAGAACCAAGAG -3'
Posted On 2015-10-21