Incidental Mutation 'R5273:Kdm6b'
ID 403773
Institutional Source Beutler Lab
Gene Symbol Kdm6b
Ensembl Gene ENSMUSG00000018476
Gene Name KDM1 lysine (K)-specific demethylase 6B
Synonyms Jmjd3
MMRRC Submission 042862-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5273 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 69289334-69304501 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 69295027 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Glutamine at position 1080 (P1080Q)
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 unknown
Transcript: ENSMUST00000094077
AA Change: P1080Q
SMART Domains Protein: ENSMUSP00000091620
Gene: ENSMUSG00000018476
AA Change: P1080Q

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
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
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: 39 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc4 T C 14: 118,832,233 (GRCm39) N799S possibly damaging Het
Arhgap20 A G 9: 51,759,916 (GRCm39) N589S probably damaging Het
Armc10 C T 5: 21,858,426 (GRCm39) A157V possibly damaging Het
Atp2b2 A G 6: 113,736,193 (GRCm39) L958P probably damaging Het
Bhmt2 G A 13: 93,803,086 (GRCm39) A149V possibly damaging Het
Ccdc7a CATCAGCTGATAT CAT 8: 129,788,090 (GRCm39) probably null Het
Cntnap4 A G 8: 113,460,070 (GRCm39) D141G probably damaging Het
Cplane1 T C 15: 8,273,825 (GRCm39) S2603P probably damaging Het
Cplane1 T C 15: 8,292,422 (GRCm39) S3012P unknown Het
Dis3 A G 14: 99,336,242 (GRCm39) V88A probably benign Het
Dnajc21 A T 15: 10,454,893 (GRCm39) C316S probably damaging Het
Dnhd1 A G 7: 105,363,689 (GRCm39) T4084A probably damaging Het
Dock3 A C 9: 106,777,904 (GRCm39) probably null Het
Eml5 T C 12: 98,756,947 (GRCm39) H1894R probably damaging Het
Galc T C 12: 98,218,330 (GRCm39) Y174C probably damaging Het
Gm4841 C T 18: 60,403,815 (GRCm39) V93I probably benign Het
Gm7995 T C 14: 42,133,413 (GRCm39) Y98H probably damaging Het
Gnrhr T A 5: 86,330,105 (GRCm39) H305L possibly damaging Het
Gpr179 A T 11: 97,238,256 (GRCm39) F323I probably damaging Het
Man2a1 C T 17: 65,040,780 (GRCm39) T126I probably damaging Het
Mdm4 G A 1: 132,922,320 (GRCm39) T274M probably benign Het
Mug1 T A 6: 121,850,748 (GRCm39) V748E probably damaging Het
Nav3 A T 10: 109,528,899 (GRCm39) probably null Het
Nhsl3 T C 4: 129,118,005 (GRCm39) T208A possibly damaging Het
Or8d6 T C 9: 39,853,853 (GRCm39) V99A probably benign Het
Or8g36 A G 9: 39,422,795 (GRCm39) S74P possibly damaging Het
Pcdhb1 T C 18: 37,398,766 (GRCm39) V239A probably benign Het
Ppic T A 18: 53,542,330 (GRCm39) H126L probably damaging Het
Sdk1 T C 5: 141,984,583 (GRCm39) F463L probably damaging Het
Shroom1 A G 11: 53,354,671 (GRCm39) E197G possibly damaging Het
Slc22a14 A G 9: 118,999,704 (GRCm39) S496P probably benign Het
Slc27a1 G A 8: 72,036,900 (GRCm39) G379S probably benign Het
Slco1a5 T C 6: 142,187,824 (GRCm39) E505G probably benign Het
Snrpe A C 1: 133,537,518 (GRCm39) probably benign Het
Sp100 G T 1: 85,636,825 (GRCm39) V299F possibly damaging Het
Stard9 A G 2: 120,535,568 (GRCm39) S3942G possibly damaging Het
Ttn A G 2: 76,644,948 (GRCm39) V12969A probably damaging Het
Txndc11 T C 16: 10,946,487 (GRCm39) Q108R probably benign Het
Wnk4 A T 11: 101,154,695 (GRCm39) I295F probably damaging Het
Other mutations in Kdm6b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00484:Kdm6b APN 11 69,297,132 (GRCm39) missense possibly damaging 0.85
IGL02271:Kdm6b APN 11 69,296,893 (GRCm39) missense possibly damaging 0.65
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
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
Predicted Primers PCR Primer
(F):5'- GGTAACGAGCACAAGCCTAG -3'
(R):5'- CTTGCAGAGTGAGGAGATCCAG -3'

Sequencing Primer
(F):5'- TTGCTGGCACGCATGACATC -3'
(R):5'- TGAGGAGATCCAGGGCCG -3'
Posted On 2016-07-22