Incidental Mutation 'IGL02271:Kdm6b'
ID 287142
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Kdm6b
Ensembl Gene ENSMUSG00000018476
Gene Name KDM1 lysine (K)-specific demethylase 6B
Synonyms Jmjd3
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL02271
Quality Score
Status
Chromosome 11
Chromosomal Location 69289334-69304501 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 69296893 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Valine at position 458 (A458V)
Ref Sequence ENSEMBL: ENSMUSP00000091620 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000094077]
AlphaFold Q5NCY0
PDB Structure The free structure of the mouse C-terminal domain of KDM6B [X-RAY DIFFRACTION]
free KDM6B structure [X-RAY DIFFRACTION]
the crystal structure of KDM6B bound with H3K27me3 peptide [X-RAY DIFFRACTION]
Predicted Effect possibly damaging
Transcript: ENSMUST00000094077
AA Change: A458V

PolyPhen 2 Score 0.654 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000091620
Gene: ENSMUSG00000018476
AA Change: A458V

DomainStartEndE-ValueType
low complexity region 29 43 N/A INTRINSIC
low complexity region 54 71 N/A INTRINSIC
SCOP:d1elwa_ 91 152 9e-5 SMART
low complexity region 214 227 N/A INTRINSIC
low complexity region 239 270 N/A INTRINSIC
low complexity region 312 329 N/A INTRINSIC
low complexity region 333 345 N/A INTRINSIC
low complexity region 389 415 N/A INTRINSIC
low complexity region 461 487 N/A INTRINSIC
low complexity region 515 524 N/A INTRINSIC
low complexity region 544 577 N/A INTRINSIC
low complexity region 585 615 N/A INTRINSIC
low complexity region 643 650 N/A INTRINSIC
low complexity region 711 719 N/A INTRINSIC
low complexity region 743 766 N/A INTRINSIC
low complexity region 771 811 N/A INTRINSIC
low complexity region 840 879 N/A INTRINSIC
low complexity region 890 909 N/A INTRINSIC
low complexity region 950 989 N/A INTRINSIC
low complexity region 993 1011 N/A INTRINSIC
low complexity region 1044 1068 N/A INTRINSIC
low complexity region 1284 1317 N/A INTRINSIC
JmjC 1337 1500 1.61e-47 SMART
Blast:JmjC 1536 1600 1e-18 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129924
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156562
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a lysine-specific demethylase that specifically demethylates di- or tri-methylated lysine 27 of histone H3 (H3K27me2 or H3K27me3). H3K27 trimethylation is a repressive epigenetic mark controlling chromatin organization and gene silencing. This protein can also demethylate non-histone proteins such as retinoblastoma protein. Through its demethylation actvity this gene influences cellular differentiation and development, tumorigenesis, inflammatory diseases, and neurodegenerative diseases. This protein has two classical nuclear localization signals at its N-terminus. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]
PHENOTYPE: Mice homozygous for a null allele show perinatal death, thick alveolar septum, and absence of air space in the lungs. Mice homozygous for a different null allele die neonatally displaying abnormal lung development, dwarfism, kyphosis, short limbs, and a severe delay in endochondral ossification. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Astn1 C T 1: 158,338,520 (GRCm39) probably benign Het
Bms1 C A 6: 118,366,290 (GRCm39) V1068F probably benign Het
Cand1 A T 10: 119,047,626 (GRCm39) N621K probably damaging Het
Cd44 C T 2: 102,661,732 (GRCm39) E418K possibly damaging Het
Clip2 A T 5: 134,531,425 (GRCm39) N758K probably benign Het
Cst11 A T 2: 148,613,161 (GRCm39) Y55N probably damaging Het
Cytip A T 2: 58,023,872 (GRCm39) L316* probably null Het
Ddx52 T C 11: 83,843,057 (GRCm39) M352T probably damaging Het
Fancd2 G A 6: 113,512,720 (GRCm39) probably benign Het
Fat4 A T 3: 39,034,068 (GRCm39) E2573D probably benign Het
Fbxl13 T G 5: 21,695,454 (GRCm39) D646A probably damaging Het
Fhdc1 G A 3: 84,352,042 (GRCm39) A1061V possibly damaging Het
Grid2ip A G 5: 143,374,664 (GRCm39) D928G probably benign Het
Hmgxb3 A G 18: 61,265,285 (GRCm39) L1231P probably damaging Het
Ifitm7 A G 16: 13,801,541 (GRCm39) F73L probably damaging Het
Ikbkb T A 8: 23,155,919 (GRCm39) T583S probably benign Het
Klra2 T C 6: 131,207,180 (GRCm39) K143R probably benign Het
Kmt2d A G 15: 98,764,309 (GRCm39) S42P possibly damaging Het
Krt78 T A 15: 101,857,028 (GRCm39) M360L probably benign Het
Lamb1 A G 12: 31,350,250 (GRCm39) N677S probably damaging Het
Lrrc9 G A 12: 72,557,155 (GRCm39) V1407I probably benign Het
Myo6 A G 9: 80,168,113 (GRCm39) T426A probably benign Het
Net1 T C 13: 3,937,663 (GRCm39) Y146C probably damaging Het
Nlrp4d T A 7: 10,122,625 (GRCm39) noncoding transcript Het
Notch4 A T 17: 34,787,445 (GRCm39) N335I probably damaging Het
Or14j6 A T 17: 38,215,134 (GRCm39) E232D probably benign Het
Or5ac20 A T 16: 59,104,584 (GRCm39) I92K probably damaging Het
Or8b53 A T 9: 38,667,784 (GRCm39) T267S probably benign Het
Pax3 A T 1: 78,171,969 (GRCm39) H80Q probably damaging Het
Pclo A T 5: 14,729,508 (GRCm39) probably benign Het
Pdgfra A G 5: 75,348,567 (GRCm39) D869G probably damaging Het
Per2 T C 1: 91,373,332 (GRCm39) Y152C probably damaging Het
Pilrb2 T C 5: 137,865,125 (GRCm39) D223G probably benign Het
Rag1 T A 2: 101,473,733 (GRCm39) I470F probably damaging Het
Rap1gap T C 4: 137,445,317 (GRCm39) S333P probably damaging Het
Rundc3b A G 5: 8,542,530 (GRCm39) Y430H probably damaging Het
Ryr1 T C 7: 28,793,472 (GRCm39) D1332G probably benign Het
Sgo1 G A 17: 53,986,567 (GRCm39) A208V possibly damaging Het
Skint5 C T 4: 113,794,778 (GRCm39) probably null Het
Slc26a4 C T 12: 31,578,853 (GRCm39) probably benign Het
Slc28a3 A T 13: 58,706,451 (GRCm39) S597T probably benign Het
Slc4a5 T A 6: 83,248,085 (GRCm39) probably benign Het
Slc52a3 A G 2: 151,847,448 (GRCm39) probably benign Het
Stac3 A G 10: 127,339,768 (GRCm39) D158G probably benign Het
Tdo2 T C 3: 81,871,224 (GRCm39) probably benign Het
Usp25 A T 16: 76,912,335 (GRCm39) E1018V probably damaging Het
Vmn1r46 T A 6: 89,953,886 (GRCm39) F245Y probably damaging Het
Other mutations in Kdm6b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00484:Kdm6b APN 11 69,297,132 (GRCm39) missense possibly damaging 0.85
beine UTSW 11 69,294,418 (GRCm39) missense unknown
Gaudy UTSW 11 69,291,032 (GRCm39) missense unknown
Hypocrisy UTSW 11 69,292,977 (GRCm39) nonsense probably null
Knochen UTSW 11 69,290,881 (GRCm39) unclassified probably benign
Ostentatious UTSW 11 69,294,424 (GRCm39) missense unknown
Piquant UTSW 11 69,294,620 (GRCm39) missense unknown
preen UTSW 11 69,292,919 (GRCm39) missense unknown
Tart UTSW 11 69,297,192 (GRCm39) missense probably damaging 1.00
BB007:Kdm6b UTSW 11 69,290,778 (GRCm39) missense unknown
BB017:Kdm6b UTSW 11 69,290,778 (GRCm39) missense unknown
PIT4458001:Kdm6b UTSW 11 69,290,778 (GRCm39) missense unknown
R0455:Kdm6b UTSW 11 69,297,822 (GRCm39) nonsense probably null
R0645:Kdm6b UTSW 11 69,295,844 (GRCm39) missense unknown
R1659:Kdm6b UTSW 11 69,298,414 (GRCm39) missense possibly damaging 0.88
R1855:Kdm6b UTSW 11 69,298,112 (GRCm39) missense probably damaging 0.99
R1962:Kdm6b UTSW 11 69,292,191 (GRCm39) unclassified probably benign
R1993:Kdm6b UTSW 11 69,297,129 (GRCm39) missense probably null 0.85
R2029:Kdm6b UTSW 11 69,294,418 (GRCm39) missense unknown
R2181:Kdm6b UTSW 11 69,291,952 (GRCm39) nonsense probably null
R2215:Kdm6b UTSW 11 69,295,870 (GRCm39) missense unknown
R2904:Kdm6b UTSW 11 69,296,611 (GRCm39) missense possibly damaging 0.63
R2992:Kdm6b UTSW 11 69,297,133 (GRCm39) small deletion probably benign
R3236:Kdm6b UTSW 11 69,297,192 (GRCm39) missense probably damaging 1.00
R3950:Kdm6b UTSW 11 69,296,441 (GRCm39) missense probably damaging 1.00
R4027:Kdm6b UTSW 11 69,297,094 (GRCm39) missense possibly damaging 0.92
R4830:Kdm6b UTSW 11 69,294,620 (GRCm39) missense unknown
R4996:Kdm6b UTSW 11 69,296,557 (GRCm39) missense probably damaging 1.00
R5034:Kdm6b UTSW 11 69,292,736 (GRCm39) splice site probably benign
R5140:Kdm6b UTSW 11 69,290,881 (GRCm39) unclassified probably benign
R5160:Kdm6b UTSW 11 69,291,594 (GRCm39) unclassified probably benign
R5240:Kdm6b UTSW 11 69,292,730 (GRCm39) splice site probably benign
R5273:Kdm6b UTSW 11 69,295,027 (GRCm39) missense unknown
R5386:Kdm6b UTSW 11 69,291,636 (GRCm39) unclassified probably benign
R5597:Kdm6b UTSW 11 69,296,900 (GRCm39) missense probably damaging 0.96
R5598:Kdm6b UTSW 11 69,296,900 (GRCm39) missense probably damaging 0.96
R5812:Kdm6b UTSW 11 69,296,755 (GRCm39) missense probably damaging 0.98
R5976:Kdm6b UTSW 11 69,294,614 (GRCm39) critical splice donor site probably null
R6000:Kdm6b UTSW 11 69,294,424 (GRCm39) missense unknown
R6145:Kdm6b UTSW 11 69,295,852 (GRCm39) missense unknown
R6191:Kdm6b UTSW 11 69,297,584 (GRCm39) missense probably benign 0.01
R6256:Kdm6b UTSW 11 69,297,555 (GRCm39) missense probably damaging 0.96
R6304:Kdm6b UTSW 11 69,295,084 (GRCm39) missense unknown
R6917:Kdm6b UTSW 11 69,297,419 (GRCm39) missense probably benign 0.04
R6939:Kdm6b UTSW 11 69,297,588 (GRCm39) missense probably damaging 0.99
R7356:Kdm6b UTSW 11 69,292,991 (GRCm39) nonsense probably null
R7644:Kdm6b UTSW 11 69,291,032 (GRCm39) missense unknown
R7673:Kdm6b UTSW 11 69,296,568 (GRCm39) missense probably damaging 0.98
R7698:Kdm6b UTSW 11 69,296,807 (GRCm39) missense probably benign 0.14
R7776:Kdm6b UTSW 11 69,296,960 (GRCm39) missense possibly damaging 0.84
R7930:Kdm6b UTSW 11 69,290,778 (GRCm39) missense unknown
R8383:Kdm6b UTSW 11 69,296,876 (GRCm39) missense probably benign
R8725:Kdm6b UTSW 11 69,292,919 (GRCm39) missense unknown
R8727:Kdm6b UTSW 11 69,292,919 (GRCm39) missense unknown
R8813:Kdm6b UTSW 11 69,297,658 (GRCm39) small insertion probably benign
R8813:Kdm6b UTSW 11 69,297,655 (GRCm39) small insertion probably benign
R8851:Kdm6b UTSW 11 69,291,993 (GRCm39) missense unknown
R9074:Kdm6b UTSW 11 69,292,977 (GRCm39) nonsense probably null
R9130:Kdm6b UTSW 11 69,295,424 (GRCm39) missense unknown
R9179:Kdm6b UTSW 11 69,297,521 (GRCm39) critical splice donor site probably null
R9535:Kdm6b UTSW 11 69,297,276 (GRCm39) nonsense probably null
Z1177:Kdm6b UTSW 11 69,294,692 (GRCm39) missense unknown
Posted On 2015-04-16