Incidental Mutation 'R4901:Phf21a'
ID 376139
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 # R4901 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 92014096-92195011 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) T to A at 92187346 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Stop codon at position 178 (C178*)
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 probably null
Transcript: ENSMUST00000044036
AA Change: C454*
SMART Domains Protein: ENSMUSP00000038497
Gene: ENSMUSG00000058318
AA Change: C454*

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 null
Transcript: ENSMUST00000068702
AA Change: C406*
SMART Domains Protein: ENSMUSP00000070649
Gene: ENSMUSG00000058318
AA Change: C406*

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 null
Transcript: ENSMUST00000090586
AA Change: C538*
SMART Domains Protein: ENSMUSP00000088074
Gene: ENSMUSG00000058318
AA Change: C538*

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 null
Transcript: ENSMUST00000111290
AA Change: C509*
SMART Domains Protein: ENSMUSP00000106921
Gene: ENSMUSG00000058318
AA Change: C509*

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 null
Transcript: ENSMUST00000111291
AA Change: C454*
SMART Domains Protein: ENSMUSP00000106922
Gene: ENSMUSG00000058318
AA Change: C454*

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 null
Transcript: ENSMUST00000111292
AA Change: C406*
SMART Domains Protein: ENSMUSP00000106923
Gene: ENSMUSG00000058318
AA Change: C406*

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 null
Transcript: ENSMUST00000161067
AA Change: C178*
SMART Domains Protein: ENSMUSP00000124255
Gene: ENSMUSG00000058318
AA Change: C178*

DomainStartEndE-ValueType
PHD 140 183 3.12e-15 SMART
RING 141 182 1.85e-1 SMART
Predicted Effect probably null
Transcript: ENSMUST00000111293
AA Change: C538*
SMART Domains Protein: ENSMUSP00000106924
Gene: ENSMUSG00000058318
AA Change: C538*

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 null
Transcript: ENSMUST00000159961
AA Change: C425*
SMART Domains Protein: ENSMUSP00000123955
Gene: ENSMUSG00000058318
AA Change: C425*

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 null
Transcript: ENSMUST00000111297
AA Change: C461*
SMART Domains Protein: ENSMUSP00000106928
Gene: ENSMUSG00000058318
AA Change: C461*

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 null
Transcript: ENSMUST00000111294
AA Change: C491*
SMART Domains Protein: ENSMUSP00000106925
Gene: ENSMUSG00000058318
AA Change: C491*

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 noncoding transcript
Transcript: ENSMUST00000161044
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.4%
  • 20x: 92.6%
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
Abcg4 C T 9: 44,188,954 (GRCm39) probably null Het
Arg2 T C 12: 79,194,485 (GRCm39) V103A probably damaging Het
Bicra T A 7: 15,721,526 (GRCm39) T664S possibly damaging Het
Bptf A T 11: 107,001,686 (GRCm39) Y475* probably null Het
Calcrl T C 2: 84,163,857 (GRCm39) I445V probably benign Het
Ccdc110 G A 8: 46,396,437 (GRCm39) R776Q probably benign Het
Ccnc A G 4: 21,727,894 (GRCm39) N4S probably damaging Het
Ccni G A 5: 93,331,003 (GRCm39) R323W probably damaging Het
Celsr2 T A 3: 108,314,303 (GRCm39) M1241L possibly damaging Het
Cpd T C 11: 76,681,707 (GRCm39) I1145M probably damaging Het
Cybb C G X: 9,316,989 (GRCm39) D246H probably benign Het
Cyp2j8 T A 4: 96,367,323 (GRCm39) D265V probably benign Het
Dennd2a T C 6: 39,499,621 (GRCm39) T315A probably benign Het
Dgkz T A 2: 91,767,076 (GRCm39) Q905L probably benign Het
Dnah8 G A 17: 31,059,688 (GRCm39) probably null Het
Elp2 A G 18: 24,752,542 (GRCm39) H365R probably damaging Het
Gm136 G A 4: 34,746,580 (GRCm39) Q144* probably null Het
Gon4l T C 3: 88,815,458 (GRCm39) V2008A possibly damaging Het
Hjurp GT GTT 1: 88,194,246 (GRCm39) probably null Het
Isyna1 A T 8: 71,049,246 (GRCm39) H414L probably damaging Het
Kif20b A G 19: 34,911,836 (GRCm39) Y233C probably benign Het
Klk1 A T 7: 43,878,139 (GRCm39) I132F probably damaging Het
Klre1 A T 6: 129,561,188 (GRCm39) H183L probably benign Het
Lrp1b T C 2: 40,711,657 (GRCm39) T3188A probably damaging Het
Mapk12 A T 15: 89,018,841 (GRCm39) L198* probably null Het
Mt4 A C 8: 94,864,912 (GRCm39) T29P possibly damaging Het
Myh14 C T 7: 44,310,464 (GRCm39) V140I probably damaging Het
Nr1h4 T C 10: 89,314,659 (GRCm39) Q269R possibly damaging Het
Or4p23 C G 2: 88,577,231 (GRCm39) probably null Het
Or51e1 A G 7: 102,359,405 (GRCm39) H313R probably benign Het
Pde1b A G 15: 103,435,112 (GRCm39) I421V probably null Het
Pde3b A T 7: 114,107,425 (GRCm39) T519S probably damaging Het
Phtf2 A G 5: 21,010,722 (GRCm39) S88P possibly damaging Het
Pik3c3 A G 18: 30,435,982 (GRCm39) M394V possibly damaging Het
Plxnb1 C T 9: 108,934,027 (GRCm39) P752S probably benign Het
Pp2d1 C A 17: 53,822,037 (GRCm39) G343V probably benign Het
Ppp6r2 A G 15: 89,143,272 (GRCm39) I140V possibly damaging Het
Ppp6r3 C A 19: 3,517,229 (GRCm39) V75L probably damaging Het
Ptprq T A 10: 107,524,275 (GRCm39) H486L probably benign Het
Rasgrf1 C T 9: 89,877,056 (GRCm39) T807M probably benign Het
Rasgrp3 C A 17: 75,821,111 (GRCm39) Y439* probably null Het
Rbm44 A G 1: 91,081,050 (GRCm39) T413A probably benign Het
Rnf135 T C 11: 80,089,662 (GRCm39) C333R probably damaging Het
Scfd2 A G 5: 74,680,226 (GRCm39) V309A probably damaging Het
Semp2l1 T C 1: 32,585,701 (GRCm39) S70G probably benign Het
Serpina3m A T 12: 104,355,908 (GRCm39) K192* probably null Het
Sft2d1rt A G 11: 45,942,656 (GRCm39) S156P probably damaging Het
Sh3tc2 A G 18: 62,123,506 (GRCm39) I756V probably benign Het
Slc27a4 T C 2: 29,702,648 (GRCm39) V516A probably damaging Het
Sult2a5 T A 7: 13,359,188 (GRCm39) C55S probably benign Het
Tars3 C T 7: 65,341,042 (GRCm39) T783M probably benign Het
Tet2 A T 3: 133,172,805 (GRCm39) I1819N possibly damaging Het
Timeless T C 10: 128,086,631 (GRCm39) F1057L probably damaging Het
Ttn T A 2: 76,628,418 (GRCm39) I12835F probably damaging Het
Uhrf1 T A 17: 56,617,834 (GRCm39) D185E probably benign Het
Vmn2r74 G T 7: 85,605,199 (GRCm39) S483* probably null Het
Xpo1 A T 11: 23,231,327 (GRCm39) I304F possibly damaging Het
Zc3h11a A G 1: 133,552,449 (GRCm39) S553P probably benign Het
Zdhhc1 A G 8: 106,199,484 (GRCm39) S402P probably benign Het
Zwilch T C 9: 64,070,028 (GRCm39) Y101C 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
R4698:Phf21a UTSW 2 92,187,297 (GRCm39) missense probably damaging 1.00
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'- AATTGGAGGCCCATCTCTGAG -3'
(R):5'- AAAGGTTATGCTGTGTGCCTGC -3'

Sequencing Primer
(F):5'- ACTTATGTGCAGCCACGGTG -3'
(R):5'- CATGCTGTTTCATGAACCAGGAG -3'
Posted On 2016-03-17