Incidental Mutation 'R0308:Phf21a'
ID 24945
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
MMRRC Submission 038518-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0308 (G1)
Quality Score 217
Status Validated
Chromosome 2
Chromosomal Location 92014096-92195011 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 92161122 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 330 (V330A)
Ref Sequence ENSEMBL: ENSMUSP00000106924 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000044036] [ENSMUST00000068702] [ENSMUST00000090586] [ENSMUST00000111290] [ENSMUST00000111291] [ENSMUST00000111292] [ENSMUST00000111293] [ENSMUST00000159961] [ENSMUST00000111294] [ENSMUST00000111297]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000044036
AA Change: V246A

PolyPhen 2 Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000038497
Gene: ENSMUSG00000058318
AA Change: V246A

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 possibly damaging
Transcript: ENSMUST00000068702
AA Change: V245A

PolyPhen 2 Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000070649
Gene: ENSMUSG00000058318
AA Change: V245A

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 possibly damaging
Transcript: ENSMUST00000090586
AA Change: V330A

PolyPhen 2 Score 0.858 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000088074
Gene: ENSMUSG00000058318
AA Change: V330A

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: V330A

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000106921
Gene: ENSMUSG00000058318
AA Change: V330A

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: V246A

PolyPhen 2 Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000106922
Gene: ENSMUSG00000058318
AA Change: V246A

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 possibly damaging
Transcript: ENSMUST00000111292
AA Change: V245A

PolyPhen 2 Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000106923
Gene: ENSMUSG00000058318
AA Change: V245A

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 possibly damaging
Transcript: ENSMUST00000111293
AA Change: V330A

PolyPhen 2 Score 0.858 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000106924
Gene: ENSMUSG00000058318
AA Change: V330A

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 possibly damaging
Transcript: ENSMUST00000159961
AA Change: V217A

PolyPhen 2 Score 0.466 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000123955
Gene: ENSMUSG00000058318
AA Change: V217A

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 possibly damaging
Transcript: ENSMUST00000111294
AA Change: V330A

PolyPhen 2 Score 0.615 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000106925
Gene: ENSMUSG00000058318
AA Change: V330A

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 possibly damaging
Transcript: ENSMUST00000111297
AA Change: V329A

PolyPhen 2 Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000106928
Gene: ENSMUSG00000058318
AA Change: V329A

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 unknown
Transcript: ENSMUST00000161067
AA Change: V17A
SMART Domains Protein: ENSMUSP00000124255
Gene: ENSMUSG00000058318
AA Change: V17A

DomainStartEndE-ValueType
PHD 140 183 3.12e-15 SMART
RING 141 182 1.85e-1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000159366
SMART Domains Protein: ENSMUSP00000124238
Gene: ENSMUSG00000058318

DomainStartEndE-ValueType
coiled coil region 26 59 N/A INTRINSIC
low complexity region 83 127 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000159727
SMART Domains Protein: ENSMUSP00000124845
Gene: ENSMUSG00000058318

DomainStartEndE-ValueType
low complexity region 131 152 N/A INTRINSIC
Meta Mutation Damage Score 0.0839 question?
Coding Region Coverage
  • 1x: 98.8%
  • 3x: 97.7%
  • 10x: 95.1%
  • 20x: 89.5%
Validation Efficiency 100% (82/82)
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: 81 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700009N14Rik A T 4: 39,450,989 (GRCm39) D65V probably damaging Het
4933407L21Rik A T 1: 85,859,007 (GRCm39) probably benign Het
Abcc12 C T 8: 87,284,381 (GRCm39) probably benign Het
Adamts12 A G 15: 11,311,646 (GRCm39) E1301G probably damaging Het
Adh4 A T 3: 138,129,863 (GRCm39) N230Y probably damaging Het
Anapc15-ps T A 10: 95,508,954 (GRCm39) M109L probably benign Het
Angpt2 T C 8: 18,742,141 (GRCm39) I472V possibly damaging Het
Arhgef26 C A 3: 62,247,820 (GRCm39) D301E probably benign Het
Armc10 G A 5: 21,852,295 (GRCm39) probably benign Het
Atm T C 9: 53,365,773 (GRCm39) probably null Het
Atp5f1b T C 10: 127,921,908 (GRCm39) V265A probably benign Het
Atp8b1 G T 18: 64,678,315 (GRCm39) C860* probably null Het
Atrnl1 T G 19: 57,741,720 (GRCm39) S1160A probably benign Het
Bmal1 A T 7: 112,890,743 (GRCm39) I179F probably damaging Het
Cep55 A G 19: 38,048,659 (GRCm39) E105G possibly damaging Het
Cfap54 C A 10: 92,721,226 (GRCm39) D2502Y unknown Het
Cilp2 A G 8: 70,335,643 (GRCm39) S452P probably benign Het
Clptm1l A G 13: 73,759,786 (GRCm39) D282G possibly damaging Het
Csrp1 C A 1: 135,673,024 (GRCm39) T47N probably damaging Het
Cyp2c40 T A 19: 39,766,432 (GRCm39) I388F probably damaging Het
Dars1 C T 1: 128,291,996 (GRCm39) R494H probably damaging Het
Dna2 T C 10: 62,792,753 (GRCm39) V256A probably damaging Het
Dock7 T C 4: 98,873,051 (GRCm39) T1132A probably benign Het
Dpcd T G 19: 45,565,445 (GRCm39) F140V probably damaging Het
Elk3 A T 10: 93,101,067 (GRCm39) M228K probably benign Het
Erich6 A G 3: 58,543,525 (GRCm39) F182L probably damaging Het
Fhad1 A G 4: 141,712,904 (GRCm39) probably benign Het
Fryl A T 5: 73,198,947 (GRCm39) probably benign Het
Fzd9 A T 5: 135,278,260 (GRCm39) C542S probably damaging Het
Gba1 A G 3: 89,115,671 (GRCm39) T460A probably benign Het
Gli2 C T 1: 118,769,792 (GRCm39) A587T probably benign Het
Gm11011 C T 2: 169,424,614 (GRCm39) probably benign Het
Gmppb A G 9: 107,927,033 (GRCm39) E68G probably benign Het
Gpld1 A G 13: 25,146,818 (GRCm39) N260S possibly damaging Het
Hipk3 G A 2: 104,263,552 (GRCm39) S900L probably damaging Het
Idi2l T G 13: 8,990,877 (GRCm39) probably benign Het
Ints6l A T X: 55,526,715 (GRCm39) M215L possibly damaging Het
Irx6 T A 8: 93,403,659 (GRCm39) L128Q probably damaging Het
Itga10 T C 3: 96,558,780 (GRCm39) S373P probably damaging Het
Jak1 T C 4: 101,011,732 (GRCm39) probably null Het
Jak2 C T 19: 29,289,157 (GRCm39) T1103I probably benign Het
Katnal1 A T 5: 148,815,734 (GRCm39) V401D possibly damaging Het
Krbox5 A G 13: 67,991,232 (GRCm39) probably benign Het
Lrp2 T A 2: 69,313,326 (GRCm39) probably benign Het
Map3k13 A G 16: 21,710,738 (GRCm39) H7R probably benign Het
Mrgprx3-ps A G 7: 46,959,766 (GRCm39) V75A probably benign Het
Nol6 C T 4: 41,123,584 (GRCm39) A55T probably benign Het
Opa1 G A 16: 29,440,349 (GRCm39) R818Q probably damaging Het
Opn4 T C 14: 34,319,081 (GRCm39) Y168C possibly damaging Het
Or8b35 A G 9: 37,904,141 (GRCm39) I118V probably benign Het
Phykpl A G 11: 51,484,423 (GRCm39) probably benign Het
Plcb1 T G 2: 134,655,534 (GRCm39) V38G probably benign Het
Plxna4 T A 6: 32,214,703 (GRCm39) T593S probably benign Het
Poll A T 19: 45,544,404 (GRCm39) I339N probably damaging Het
Rev3l A G 10: 39,700,890 (GRCm39) I1796V probably benign Het
Rnf103 G A 6: 71,486,686 (GRCm39) R439H probably damaging Het
Rrn3 G A 16: 13,617,746 (GRCm39) probably benign Het
Sec14l4 G A 11: 3,991,726 (GRCm39) probably benign Het
Sec23a A C 12: 59,053,985 (GRCm39) Y4* probably null Het
Senp6 T C 9: 80,040,265 (GRCm39) probably null Het
Serpinb6b A T 13: 33,162,220 (GRCm39) N221Y probably benign Het
Slc6a2 A G 8: 93,687,988 (GRCm39) E38G possibly damaging Het
Smap1 A T 1: 23,888,423 (GRCm39) L196I probably damaging Het
Sorbs2 C T 8: 46,248,167 (GRCm39) Q473* probably null Het
Sphkap C A 1: 83,254,690 (GRCm39) V1020F probably damaging Het
Srfbp1 T C 18: 52,621,614 (GRCm39) V225A probably benign Het
Srprb G A 9: 103,079,204 (GRCm39) P728S possibly damaging Het
Tarm1 T C 7: 3,545,187 (GRCm39) probably benign Het
Tcp1 T A 17: 13,139,306 (GRCm39) I162N probably benign Het
Tmem237 C A 1: 59,146,676 (GRCm39) A292S probably damaging Het
Tnfrsf21 C T 17: 43,349,104 (GRCm39) H239Y probably benign Het
Tnpo1 A G 13: 98,983,011 (GRCm39) F884L probably damaging Het
Trim7 A G 11: 48,740,328 (GRCm39) T142A probably damaging Het
Ttn T A 2: 76,616,024 (GRCm39) I14894F probably damaging Het
Tubgcp6 T C 15: 89,006,639 (GRCm39) R128G possibly damaging Het
Ube2d2b A G 5: 107,978,774 (GRCm39) T142A possibly damaging Het
Unc13c G T 9: 73,388,400 (GRCm39) L2129I probably benign Het
Ushbp1 T C 8: 71,843,697 (GRCm39) D247G probably damaging Het
Usp43 G A 11: 67,770,966 (GRCm39) A556V probably damaging Het
Zfp438 T A 18: 5,213,638 (GRCm39) H440L probably benign Het
Zfp518b C T 5: 38,830,113 (GRCm39) E631K possibly 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
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
R4698:Phf21a UTSW 2 92,187,297 (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'- TGCTTGGAAACACTGGAAGACTTGC -3'
(R):5'- TGTGAATTTCTGCATCAAAGCCAGC -3'

Sequencing Primer
(F):5'- TGTGGCCCAGAATAACATTCCTATC -3'
(R):5'- ACATAAGACTCTGAAGCCTTGG -3'
Posted On 2013-04-16