Incidental Mutation 'R3500:Hdac9'
ID 273774
Institutional Source Beutler Lab
Gene Symbol Hdac9
Ensembl Gene ENSMUSG00000004698
Gene Name histone deacetylase 9
Synonyms HDRP, Mitr, Hdac7b, D030072B18Rik
MMRRC Submission 040663-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R3500 (G1)
Quality Score 225
Status Validated
Chromosome 12
Chromosomal Location 34097579-34967094 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 34487352 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Isoleucine at position 16 (M16I)
Ref Sequence ENSEMBL: ENSMUSP00000147903 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000110819] [ENSMUST00000209463] [ENSMUST00000209667] [ENSMUST00000209750] [ENSMUST00000209902] [ENSMUST00000209990] [ENSMUST00000211752] [ENSMUST00000210724] [ENSMUST00000211107]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000110819
AA Change: M16I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000106443
Gene: ENSMUSG00000004698
AA Change: M16I

DomainStartEndE-ValueType
Pfam:HDAC4_Gln 37 124 5.4e-36 PFAM
low complexity region 260 284 N/A INTRINSIC
low complexity region 370 382 N/A INTRINSIC
low complexity region 389 400 N/A INTRINSIC
low complexity region 464 480 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000209463
AA Change: M16I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
Predicted Effect probably benign
Transcript: ENSMUST00000209667
AA Change: M16I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
Predicted Effect probably benign
Transcript: ENSMUST00000209750
AA Change: M16I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Predicted Effect probably benign
Transcript: ENSMUST00000209902
AA Change: M16I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Predicted Effect probably benign
Transcript: ENSMUST00000209990
AA Change: M16I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
Predicted Effect probably benign
Transcript: ENSMUST00000211752
AA Change: M37I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Predicted Effect probably benign
Transcript: ENSMUST00000210724
AA Change: M16I

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
Predicted Effect probably benign
Transcript: ENSMUST00000211107
Predicted Effect noncoding transcript
Transcript: ENSMUST00000211632
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.7%
  • 20x: 96.2%
Validation Efficiency 98% (53/54)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene has sequence homology to members of the histone deacetylase family. This gene is orthologous to the Xenopus and mouse MITR genes. The MITR protein lacks the histone deacetylase catalytic domain. It represses MEF2 activity through recruitment of multicomponent corepressor complexes that include CtBP and HDACs. This encoded protein may play a role in hematopoiesis. Multiple alternatively spliced transcripts have been described for this gene but the full-length nature of some of them has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for disruptions in this gene display age dependent cardiac hypertrophy. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Amhr2 A G 15: 102,355,501 (GRCm39) D188G probably benign Het
Arl15 G A 13: 114,104,228 (GRCm39) E102K probably damaging Het
Atp10d C T 5: 72,403,066 (GRCm39) R319C probably damaging Het
Cetn4 A T 3: 37,364,109 (GRCm39) F34I probably benign Het
Chd8 G T 14: 52,443,110 (GRCm39) H510N probably benign Het
Chil5 T C 3: 105,925,536 (GRCm39) D157G probably damaging Het
Clcn1 T C 6: 42,269,929 (GRCm39) S251P probably damaging Het
Clstn3 A T 6: 124,408,670 (GRCm39) C881S probably benign Het
Cnot4 G A 6: 35,057,076 (GRCm39) probably benign Het
Copg1 G A 6: 87,872,905 (GRCm39) probably benign Het
Czib C T 4: 107,748,710 (GRCm39) R83W probably damaging Het
Eftud2 A G 11: 102,735,006 (GRCm39) M631T probably damaging Het
Elavl3 A G 9: 21,930,040 (GRCm39) V288A probably damaging Het
Fancb A G X: 163,779,104 (GRCm39) T721A probably damaging Het
Fat2 A G 11: 55,151,342 (GRCm39) F3800S probably damaging Het
Fgd2 T C 17: 29,584,575 (GRCm39) V173A possibly damaging Het
Gabrr1 T C 4: 33,158,184 (GRCm39) probably benign Het
Gata4 C T 14: 63,437,982 (GRCm39) G390S possibly damaging Het
Gm9396 C A 3: 129,862,144 (GRCm39) noncoding transcript Het
Grid2 T C 6: 63,480,383 (GRCm39) S66P probably damaging Het
Kmt2c A T 5: 25,504,477 (GRCm39) D3610E probably benign Het
Lactb2 A T 1: 13,730,673 (GRCm39) M1K probably null Het
Ldhb T C 6: 142,447,173 (GRCm39) D47G probably damaging Het
Map3k11 A T 19: 5,740,275 (GRCm39) M1L probably benign Het
Mecom C T 3: 30,035,061 (GRCm39) R205H probably damaging Het
Mob1b A G 5: 88,897,479 (GRCm39) D129G probably benign Het
Nbea A G 3: 55,588,431 (GRCm39) V2436A possibly damaging Het
Neb T C 2: 52,215,797 (GRCm39) N170S probably damaging Het
Nedd4l G A 18: 65,345,931 (GRCm39) A848T probably damaging Het
Nr5a1 G A 2: 38,597,952 (GRCm39) R282* probably null Het
Or4c102 A G 2: 88,422,285 (GRCm39) T46A probably damaging Het
Or4c119 C T 2: 88,987,403 (GRCm39) G39R probably damaging Het
Or4d10c A G 19: 12,065,421 (GRCm39) V245A possibly damaging Het
Or4f47 T C 2: 111,972,472 (GRCm39) F61L possibly damaging Het
Or52e2 T C 7: 102,804,297 (GRCm39) Y219C probably damaging Het
Pcdhb19 T A 18: 37,630,532 (GRCm39) L109* probably null Het
Plcg2 A G 8: 118,339,717 (GRCm39) M1043V probably benign Het
Podxl2 T C 6: 88,819,900 (GRCm39) D554G probably damaging Het
Ppp3ca A G 3: 136,587,273 (GRCm39) T252A probably benign Het
Pramel6 A G 2: 87,339,569 (GRCm39) H111R probably damaging Het
Prr19 A G 7: 25,002,692 (GRCm39) E130G probably damaging Het
Rab44 C T 17: 29,357,041 (GRCm39) A57V probably benign Het
Rhbdl3 T C 11: 80,210,531 (GRCm39) F95L probably damaging Het
Sdk1 G T 5: 141,992,371 (GRCm39) probably benign Het
Tas2r122 T A 6: 132,688,523 (GRCm39) K123N probably damaging Het
Tbpl2 C T 2: 23,977,151 (GRCm39) R289Q probably benign Het
Trpm2 A G 10: 77,768,136 (GRCm39) F788L probably benign Het
Ttn G A 2: 76,560,628 (GRCm39) L29258F probably damaging Het
Ttn G T 2: 76,591,509 (GRCm39) F19307L possibly damaging Het
Vmn2r23 T C 6: 123,690,129 (GRCm39) I335T possibly damaging Het
Other mutations in Hdac9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01317:Hdac9 APN 12 34,479,488 (GRCm39) splice site probably benign
IGL01484:Hdac9 APN 12 34,487,164 (GRCm39) missense probably damaging 1.00
IGL02010:Hdac9 APN 12 34,481,944 (GRCm39) missense probably damaging 1.00
IGL02059:Hdac9 APN 12 34,481,967 (GRCm39) missense probably damaging 0.97
IGL02276:Hdac9 APN 12 34,481,925 (GRCm39) missense probably damaging 1.00
IGL02797:Hdac9 APN 12 34,443,273 (GRCm39) splice site probably benign
IGL03202:Hdac9 APN 12 34,423,950 (GRCm39) missense probably damaging 1.00
PIT4468001:Hdac9 UTSW 12 34,145,933 (GRCm39) missense unknown
R0304:Hdac9 UTSW 12 34,424,110 (GRCm39) missense probably damaging 1.00
R0432:Hdac9 UTSW 12 34,487,221 (GRCm39) missense probably damaging 1.00
R0659:Hdac9 UTSW 12 34,487,221 (GRCm39) missense probably damaging 1.00
R1826:Hdac9 UTSW 12 34,479,491 (GRCm39) splice site probably benign
R1879:Hdac9 UTSW 12 34,440,332 (GRCm39) missense probably damaging 0.98
R1942:Hdac9 UTSW 12 34,479,544 (GRCm39) missense probably damaging 1.00
R2113:Hdac9 UTSW 12 34,439,331 (GRCm39) missense probably damaging 1.00
R2151:Hdac9 UTSW 12 34,440,255 (GRCm39) missense probably damaging 1.00
R2216:Hdac9 UTSW 12 34,479,516 (GRCm39) missense probably damaging 1.00
R2224:Hdac9 UTSW 12 34,457,801 (GRCm39) missense probably benign 0.09
R2225:Hdac9 UTSW 12 34,457,801 (GRCm39) missense probably benign 0.09
R2227:Hdac9 UTSW 12 34,457,801 (GRCm39) missense probably benign 0.09
R4441:Hdac9 UTSW 12 34,439,375 (GRCm39) missense probably damaging 1.00
R4674:Hdac9 UTSW 12 34,423,959 (GRCm39) missense possibly damaging 0.96
R4694:Hdac9 UTSW 12 34,487,246 (GRCm39) missense probably damaging 1.00
R5033:Hdac9 UTSW 12 34,423,906 (GRCm39) missense probably benign
R5229:Hdac9 UTSW 12 34,487,163 (GRCm39) missense probably damaging 1.00
R5353:Hdac9 UTSW 12 34,443,392 (GRCm39) nonsense probably null
R5384:Hdac9 UTSW 12 34,479,557 (GRCm39) missense probably damaging 1.00
R5958:Hdac9 UTSW 12 34,423,882 (GRCm39) missense probably damaging 0.97
R6129:Hdac9 UTSW 12 34,337,474 (GRCm39) missense probably damaging 1.00
R6157:Hdac9 UTSW 12 34,439,428 (GRCm39) missense probably damaging 1.00
R6248:Hdac9 UTSW 12 34,578,293 (GRCm39) missense possibly damaging 0.79
R6333:Hdac9 UTSW 12 34,102,323 (GRCm39) missense probably damaging 0.98
R6474:Hdac9 UTSW 12 34,481,990 (GRCm39) critical splice acceptor site probably null
R6589:Hdac9 UTSW 12 34,265,028 (GRCm39) missense probably damaging 1.00
R6737:Hdac9 UTSW 12 34,265,451 (GRCm39) missense probably damaging 1.00
R6767:Hdac9 UTSW 12 34,337,528 (GRCm39) missense probably damaging 1.00
R6837:Hdac9 UTSW 12 34,337,463 (GRCm39) missense probably benign 0.12
R6857:Hdac9 UTSW 12 34,443,362 (GRCm39) missense probably benign 0.37
R7069:Hdac9 UTSW 12 34,479,548 (GRCm39) missense possibly damaging 0.92
R7237:Hdac9 UTSW 12 34,424,139 (GRCm39) critical splice acceptor site probably null
R7768:Hdac9 UTSW 12 34,440,239 (GRCm39) missense possibly damaging 0.81
R7917:Hdac9 UTSW 12 34,483,209 (GRCm39) missense probably benign 0.31
R7974:Hdac9 UTSW 12 34,353,219 (GRCm39) missense possibly damaging 0.87
R7990:Hdac9 UTSW 12 34,265,452 (GRCm39) missense probably benign 0.05
R8489:Hdac9 UTSW 12 34,487,180 (GRCm39) missense probably damaging 1.00
R8683:Hdac9 UTSW 12 34,440,220 (GRCm39) missense probably damaging 1.00
R9208:Hdac9 UTSW 12 34,220,101 (GRCm39) missense probably benign 0.01
R9397:Hdac9 UTSW 12 34,353,275 (GRCm39) missense probably damaging 0.99
R9431:Hdac9 UTSW 12 34,440,327 (GRCm39) nonsense probably null
R9629:Hdac9 UTSW 12 34,439,389 (GRCm39) missense probably damaging 0.99
R9646:Hdac9 UTSW 12 34,487,167 (GRCm39) missense probably damaging 1.00
R9709:Hdac9 UTSW 12 34,362,602 (GRCm39) missense probably benign 0.21
Z1088:Hdac9 UTSW 12 34,457,788 (GRCm39) missense probably damaging 1.00
Z1176:Hdac9 UTSW 12 34,423,986 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- GCTGCCTTGTCAAATTCTCG -3'
(R):5'- GATGGGCAGAACACAATTCACC -3'

Sequencing Primer
(F):5'- AAATTCTCGTGCTGCTTCTGAAAC -3'
(R):5'- ATGAAGCAGAGATTATACCCATTTC -3'
Posted On 2015-04-02