Incidental Mutation 'R2064:Phf21a'
ID 228928
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 040069-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2064 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 92014096-92195011 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 92157422 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 183 (N183K)
Ref Sequence ENSEMBL: ENSMUSP00000106925 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000044036] [ENSMUST00000068702] [ENSMUST00000090586] [ENSMUST00000111290] [ENSMUST00000111291] [ENSMUST00000111292] [ENSMUST00000111293] [ENSMUST00000111294] [ENSMUST00000111297] [ENSMUST00000159961]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000044036
SMART Domains Protein: ENSMUSP00000038497
Gene: ENSMUSG00000058318

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
SMART Domains Protein: ENSMUSP00000070649
Gene: ENSMUSG00000058318

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: N183K

PolyPhen 2 Score 0.158 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000088074
Gene: ENSMUSG00000058318
AA Change: N183K

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: N183K

PolyPhen 2 Score 0.144 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000106921
Gene: ENSMUSG00000058318
AA Change: N183K

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 probably benign
Transcript: ENSMUST00000111291
SMART Domains Protein: ENSMUSP00000106922
Gene: ENSMUSG00000058318

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
SMART Domains Protein: ENSMUSP00000106923
Gene: ENSMUSG00000058318

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: N183K

PolyPhen 2 Score 0.158 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000106924
Gene: ENSMUSG00000058318
AA Change: N183K

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: ENSMUST00000111294
AA Change: N183K

PolyPhen 2 Score 0.466 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000106925
Gene: ENSMUSG00000058318
AA Change: N183K

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 probably benign
Transcript: ENSMUST00000111297
AA Change: N182K

PolyPhen 2 Score 0.144 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000106928
Gene: ENSMUSG00000058318
AA Change: N182K

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: ENSMUST00000159366
AA Change: N179K
SMART Domains Protein: ENSMUSP00000124238
Gene: ENSMUSG00000058318
AA Change: N179K

DomainStartEndE-ValueType
coiled coil region 26 59 N/A INTRINSIC
low complexity region 83 127 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000159727
AA Change: N64K
SMART Domains Protein: ENSMUSP00000124845
Gene: ENSMUSG00000058318
AA Change: N64K

DomainStartEndE-ValueType
low complexity region 131 152 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000161067
SMART Domains Protein: ENSMUSP00000124255
Gene: ENSMUSG00000058318

DomainStartEndE-ValueType
PHD 140 183 3.12e-15 SMART
RING 141 182 1.85e-1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000159961
SMART Domains Protein: ENSMUSP00000123955
Gene: ENSMUSG00000058318

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
Meta Mutation Damage Score 0.0584 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.3%
Validation Efficiency 99% (114/115)
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: 112 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933436I01Rik T A X: 66,964,308 (GRCm39) I184L probably benign Het
9530002B09Rik T A 4: 122,583,115 (GRCm39) probably benign Het
Actr1b A G 1: 36,741,168 (GRCm39) F138L possibly damaging Het
Adamts14 G T 10: 61,041,301 (GRCm39) P803Q probably benign Het
Afap1l1 A T 18: 61,872,193 (GRCm39) probably null Het
Akt3 A G 1: 176,930,551 (GRCm39) S136P possibly damaging Het
Aldh16a1 C T 7: 44,796,585 (GRCm39) probably null Het
Alg12 A G 15: 88,696,318 (GRCm39) W238R probably damaging Het
Amy2a1 T C 3: 113,324,217 (GRCm39) I108V probably benign Het
Arhgap23 T A 11: 97,383,888 (GRCm39) C1144S probably benign Het
Arhgef40 G A 14: 52,233,640 (GRCm39) V829M probably damaging Het
Atg7 C A 6: 114,680,324 (GRCm39) N344K probably damaging Het
Aunip T A 4: 134,250,618 (GRCm39) S188T probably benign Het
Bmpr1b A T 3: 141,576,568 (GRCm39) H88Q probably benign Het
Brpf3 G A 17: 29,040,338 (GRCm39) G920S probably benign Het
Cdc123 C T 2: 5,800,354 (GRCm39) probably benign Het
Cdhr1 T C 14: 36,817,062 (GRCm39) R100G probably benign Het
Cdkn2d A G 9: 21,202,175 (GRCm39) V24A probably damaging Het
Cirbp T C 10: 80,006,166 (GRCm39) probably benign Het
Clptm1l C T 13: 73,755,842 (GRCm39) Q153* probably null Het
Col12a1 A G 9: 79,569,736 (GRCm39) probably benign Het
Cplane1 T A 15: 8,215,649 (GRCm39) S402T probably damaging Het
Cpox T A 16: 58,494,772 (GRCm39) C270S probably benign Het
Cspg4 A G 9: 56,803,940 (GRCm39) D1677G probably damaging Het
Cyp4a10 T A 4: 115,381,917 (GRCm39) probably benign Het
Dctn4 T C 18: 60,671,349 (GRCm39) F74L possibly damaging Het
Dennd5a G A 7: 109,497,900 (GRCm39) probably benign Het
Dnaaf3 T C 7: 4,526,798 (GRCm39) I426M possibly damaging Het
Dnah9 C T 11: 66,036,261 (GRCm39) S185N probably benign Het
Dqx1 T G 6: 83,035,524 (GRCm39) probably benign Het
Dtx2 C T 5: 136,059,431 (GRCm39) S493F probably damaging Het
Ehd1 T C 19: 6,348,108 (GRCm39) L362P probably benign Het
Endov T C 11: 119,390,408 (GRCm39) F12S probably damaging Het
Ep400 A C 5: 110,883,270 (GRCm39) probably benign Het
Epha1 G T 6: 42,342,987 (GRCm39) H187Q probably benign Het
Exoc2 T C 13: 31,119,544 (GRCm39) D119G probably benign Het
Fbn2 C T 18: 58,181,921 (GRCm39) E1827K probably damaging Het
Fbxo41 C T 6: 85,455,453 (GRCm39) W577* probably null Het
Fgd6 G A 10: 93,880,903 (GRCm39) A586T probably damaging Het
Gm12695 T C 4: 96,657,963 (GRCm39) T69A probably benign Het
Gm12888 A T 4: 121,182,069 (GRCm39) W8R unknown Het
Gm2959 A G 14: 42,235,658 (GRCm39) noncoding transcript Het
Gm6214 A G 3: 140,544,978 (GRCm39) noncoding transcript Het
Gm9912 T C 3: 148,890,795 (GRCm39) T113A unknown Het
Gmeb2 A G 2: 180,895,763 (GRCm39) L469P probably benign Het
Gosr1 T C 11: 76,628,224 (GRCm39) I177V probably benign Het
Gria1 T C 11: 57,208,534 (GRCm39) F810L probably damaging Het
Gtf2ird2 C T 5: 134,245,340 (GRCm39) Q533* probably null Het
Hadhb T A 5: 30,378,796 (GRCm39) probably null Het
Hat1 A T 2: 71,240,504 (GRCm39) Y66F possibly damaging Het
Hk1 T C 10: 62,122,315 (GRCm39) Y488C probably benign Het
Htt C T 5: 34,983,326 (GRCm39) T975I probably benign Het
Ifnb1 T A 4: 88,440,996 (GRCm39) I6F possibly damaging Het
Il19 T C 1: 130,866,854 (GRCm39) H42R probably benign Het
Il2rg A G X: 100,311,416 (GRCm39) L57P possibly damaging Het
Impg2 G A 16: 56,063,993 (GRCm39) probably null Het
Invs T A 4: 48,396,287 (GRCm39) L320Q probably damaging Het
Itga9 T C 9: 118,636,361 (GRCm39) F683S probably damaging Het
Itih2 A G 2: 10,135,385 (GRCm39) S2P possibly damaging Het
Itpr3 G A 17: 27,317,050 (GRCm39) M768I probably benign Het
Kcnab1 A G 3: 65,272,060 (GRCm39) E315G probably benign Het
Kcnmb2 A C 3: 32,252,437 (GRCm39) I213L probably damaging Het
Khdc1a T A 1: 21,421,196 (GRCm39) M127K probably benign Het
Klhl28 T C 12: 64,990,246 (GRCm39) N565S probably benign Het
Lcp1 A G 14: 75,435,515 (GRCm39) probably null Het
Mcm4 T C 16: 15,452,333 (GRCm39) T267A possibly damaging Het
Mlxipl A T 5: 135,161,631 (GRCm39) T517S possibly damaging Het
Mpp3 T A 11: 101,891,516 (GRCm39) I541L probably benign Het
Mpp4 G A 1: 59,182,941 (GRCm39) P322L possibly damaging Het
Myh15 G A 16: 48,975,984 (GRCm39) A1351T possibly damaging Het
Nacc1 A T 8: 85,399,747 (GRCm39) M490K probably benign Het
Nbeal1 C A 1: 60,309,515 (GRCm39) Q496K possibly damaging Het
Oas1g T C 5: 121,023,946 (GRCm39) E121G probably damaging Het
Or14j1 T A 17: 38,145,893 (GRCm39) M1K probably null Het
Pard3 T C 8: 128,337,092 (GRCm39) L1236P probably damaging Het
Phc2 T C 4: 128,640,929 (GRCm39) F672S probably damaging Het
Plxnb3 T A X: 72,815,357 (GRCm39) Y1845* probably null Het
Prl3c1 G A 13: 27,380,720 (GRCm39) probably null Het
Prl7a2 T A 13: 27,844,870 (GRCm39) Y172F probably damaging Het
Psg16 T G 7: 16,827,673 (GRCm39) S210A possibly damaging Het
Psg25 T A 7: 18,255,178 (GRCm39) K446M probably damaging Het
Ptprz1 A G 6: 23,050,388 (GRCm39) probably benign Het
Rgs7 A T 1: 174,949,508 (GRCm39) F160L probably damaging Het
Rpl22l1 A T 3: 28,860,957 (GRCm39) E57D possibly damaging Het
Rpl35 A G 2: 38,894,753 (GRCm39) L44P possibly damaging Het
Rtn4r T C 16: 17,969,121 (GRCm39) L183P probably damaging Het
Skint1 T A 4: 111,882,730 (GRCm39) V258D probably benign Het
Slc4a7 G A 14: 14,733,773 (GRCm38) R67H probably damaging Het
Smg1 C T 7: 117,756,090 (GRCm39) probably benign Het
Smurf2 T C 11: 106,762,374 (GRCm39) T39A probably damaging Het
Sspo A T 6: 48,450,596 (GRCm39) D2595V probably damaging Het
Tatdn2 A G 6: 113,681,103 (GRCm39) K379E probably benign Het
Tbc1d14 G A 5: 36,680,274 (GRCm39) R68* probably null Het
Tgm1 A G 14: 55,946,928 (GRCm39) I360T probably damaging Het
Thrap3 T C 4: 126,069,189 (GRCm39) Y654C possibly damaging Het
Traf1 A T 2: 34,838,202 (GRCm39) I212N probably benign Het
Ttc17 C A 2: 94,196,892 (GRCm39) W485L probably damaging Het
Ttn C A 2: 76,768,675 (GRCm39) V2920F probably damaging Het
Tyr T C 7: 87,142,051 (GRCm39) I93V probably benign Het
Ubap2 C T 4: 41,199,872 (GRCm39) A752T probably benign Het
Vmn1r212 A G 13: 23,068,285 (GRCm39) V16A probably benign Het
Vmn1r55 A G 7: 5,150,048 (GRCm39) V125A possibly damaging Het
Vmn2r120 T A 17: 57,831,553 (GRCm39) H412L possibly damaging Het
Xirp1 T C 9: 119,845,962 (GRCm39) I974V probably benign Het
Zap70 A G 1: 36,818,215 (GRCm39) T301A probably benign Het
Zfhx4 A G 3: 5,463,987 (GRCm39) K1382E probably damaging Het
Zfp280b T A 10: 75,875,017 (GRCm39) C299S probably damaging Het
Zfp352 C T 4: 90,113,357 (GRCm39) S499L probably benign Het
Zfp423 G A 8: 88,507,986 (GRCm39) A661V probably benign Het
Zfp57 T A 17: 37,320,568 (GRCm39) F141I possibly damaging Het
Zfp946 A T 17: 22,674,446 (GRCm39) H400L probably damaging Het
Zgrf1 T C 3: 127,406,999 (GRCm39) C1589R 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
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'- GTTCAGCAGCATATGGTTCAGTG -3'
(R):5'- GGAGCCCAAAATGGATACCC -3'

Sequencing Primer
(F):5'- CAGCATATGGTTCAGTGGGATCAC -3'
(R):5'- ATGGATACCCTCTTCAATGCAC -3'
Posted On 2014-09-17