Incidental Mutation 'R7270:Phf21a'
ID 565208
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 045390-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7270 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 92014096-92195011 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 92157484 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 204 (I204T)
Ref Sequence ENSEMBL: ENSMUSP00000088074 (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 damaging
Transcript: ENSMUST00000090586
AA Change: I204T

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000088074
Gene: ENSMUSG00000058318
AA Change: I204T

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 damaging
Transcript: ENSMUST00000111290
AA Change: I204T

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000106921
Gene: ENSMUSG00000058318
AA Change: I204T

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 damaging
Transcript: ENSMUST00000111293
AA Change: I204T

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000106924
Gene: ENSMUSG00000058318
AA Change: I204T

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 damaging
Transcript: ENSMUST00000111294
AA Change: I204T

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000106925
Gene: ENSMUSG00000058318
AA Change: I204T

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 damaging
Transcript: ENSMUST00000111297
AA Change: I203T

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000106928
Gene: ENSMUSG00000058318
AA Change: I203T

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 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
SMART Domains Protein: ENSMUSP00000124845
Gene: ENSMUSG00000058318
AA Change: I85T

DomainStartEndE-ValueType
low complexity region 131 152 N/A INTRINSIC
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
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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Afg1l A T 10: 42,301,245 (GRCm39) Y193N probably damaging Het
Ahnak2 A T 12: 112,780,802 (GRCm38) V70E Het
Aimp1 T C 3: 132,382,772 (GRCm39) K44E probably damaging Het
Arid1b T A 17: 5,046,318 (GRCm39) Y369N unknown Het
Art5 A T 7: 101,747,080 (GRCm39) V233D probably damaging Het
Baz2b T A 2: 59,792,836 (GRCm39) N431Y possibly damaging Het
Bik T A 15: 83,428,364 (GRCm39) F131I possibly damaging Het
Bmpr1a A G 14: 34,163,082 (GRCm39) Y103H probably damaging Het
Cabp7 C T 11: 4,696,676 (GRCm39) V18M possibly damaging Het
Cacna1a C A 8: 85,297,866 (GRCm39) T1240N probably damaging Het
Cacna1h A G 17: 25,603,739 (GRCm39) V1311A probably damaging Het
Cbarp A C 10: 79,973,151 (GRCm39) S16A possibly damaging Het
Ccng2 C G 5: 93,421,202 (GRCm39) S237R probably benign Het
Ces2b A T 8: 105,564,472 (GRCm39) H494L possibly damaging Het
Cfap43 T A 19: 47,728,224 (GRCm39) H1511L possibly damaging Het
Cfap54 A G 10: 92,675,320 (GRCm39) V2867A probably benign Het
Col5a1 C T 2: 27,887,597 (GRCm39) P956L unknown Het
Dcakd T G 11: 102,891,032 (GRCm39) Q19P possibly damaging Het
Ddx47 T A 6: 135,000,301 (GRCm39) D432E probably benign Het
Dhrs7b T C 11: 60,735,055 (GRCm39) F29L probably benign Het
Dis3l2 A T 1: 86,918,025 (GRCm39) D558V possibly damaging Het
Dtx3l T A 16: 35,754,027 (GRCm39) D193V probably damaging Het
Eif1ad12 T C 12: 87,541,663 (GRCm39) L58P probably damaging Het
Epha4 G A 1: 77,376,422 (GRCm39) R486C probably damaging Het
Fam186a T C 15: 99,842,033 (GRCm39) T1404A possibly damaging Het
Fat1 A G 8: 45,490,475 (GRCm39) T3796A probably damaging Het
Ffar2 A T 7: 30,518,929 (GRCm39) W204R probably benign Het
Ftmt A G 18: 52,465,091 (GRCm39) I136V probably benign Het
Gm10300 T C 4: 131,802,167 (GRCm39) W54R unknown Het
Gm10518 C T 1: 179,630,949 (GRCm39) P3L unknown Het
Grm2 G A 9: 106,528,257 (GRCm39) T209M probably damaging Het
Gtdc1 C T 2: 44,525,322 (GRCm39) M176I probably benign Het
Insrr T C 3: 87,710,440 (GRCm39) L382P probably damaging Het
Jade2 A G 11: 51,708,011 (GRCm39) V734A possibly damaging Het
Kcnh4 C T 11: 100,638,472 (GRCm39) R586H probably benign Het
Kdm1a A T 4: 136,279,838 (GRCm39) D721E probably damaging Het
Knl1 G A 2: 118,933,003 (GRCm39) C2054Y possibly damaging Het
Lrrk2 C T 15: 91,584,644 (GRCm39) P354S probably benign Het
Luzp2 A G 7: 54,724,774 (GRCm39) I112V probably damaging Het
Mgl2 T C 11: 70,026,506 (GRCm39) S105P probably damaging Het
Mocs1 T A 17: 49,756,143 (GRCm39) M200K possibly damaging Het
Oat T A 7: 132,168,927 (GRCm39) I98L probably benign Het
Obscn T C 11: 58,920,312 (GRCm39) Y8C Het
Or5b108 G A 19: 13,168,768 (GRCm39) V246I possibly damaging Het
Or6c1b T G 10: 129,273,319 (GRCm39) F213V probably benign Het
Pde1b T A 15: 103,430,082 (GRCm39) M137K possibly damaging Het
Plcd4 A G 1: 74,593,838 (GRCm39) E321G possibly damaging Het
Plpp7 C T 2: 31,985,662 (GRCm39) probably benign Het
Prdm1 A G 10: 44,317,566 (GRCm39) I419T probably benign Het
Sec16b A T 1: 157,392,032 (GRCm39) R855W probably damaging Het
Sec16b G T 1: 157,392,033 (GRCm39) R855M probably damaging Het
Sec31b T C 19: 44,511,482 (GRCm39) T640A probably benign Het
Siglec1 T C 2: 130,923,471 (GRCm39) T425A possibly damaging Het
Sirpd A T 3: 15,385,704 (GRCm39) I66N probably benign Het
Skil T C 3: 31,151,324 (GRCm39) probably benign Het
Slc1a5 G A 7: 16,519,623 (GRCm39) V200M probably damaging Het
Slc25a12 T C 2: 71,154,369 (GRCm39) H139R probably benign Het
Slc25a32 A T 15: 38,961,630 (GRCm39) V187D probably damaging Het
Slc35a3 G A 3: 116,505,455 (GRCm39) probably benign Het
Smap2 C A 4: 120,829,264 (GRCm39) M328I probably benign Het
Spef2 C T 15: 9,600,066 (GRCm39) probably null Het
Srarp A G 4: 141,160,389 (GRCm39) V148A possibly damaging Het
Stard9 T A 2: 120,464,755 (GRCm39) Y73* probably null Het
Tars1 A G 15: 11,392,105 (GRCm39) C236R probably benign Het
Tchh G C 3: 93,351,837 (GRCm39) D426H unknown Het
Tnks2 T C 19: 36,836,545 (GRCm39) F17S Het
Ube2g1 T C 11: 72,553,939 (GRCm39) I30T possibly damaging Het
Ube2o C T 11: 116,434,761 (GRCm39) D567N possibly damaging Het
Unc5b A T 10: 60,608,002 (GRCm39) Y710* probably null Het
Vmn1r215 T C 13: 23,260,089 (GRCm39) V43A possibly damaging Het
Xkr8 A G 4: 132,455,648 (GRCm39) F242L probably benign Het
Zfp526 T A 7: 24,925,345 (GRCm39) C535S 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
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
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'- GACACTACCTCTCGTCTTGAAAG -3'
(R):5'- GGGTTTCAGCACTCAGATTTCG -3'

Sequencing Primer
(F):5'- TCTCGTCTTGAAAGCAGCAACTG -3'
(R):5'- CAGCACTCAGATTTCGATGTG -3'
Posted On 2019-06-26