Incidental Mutation 'R5034:Kdm6b'
ID 389455
Institutional Source Beutler Lab
Gene Symbol Kdm6b
Ensembl Gene ENSMUSG00000018476
Gene Name KDM1 lysine (K)-specific demethylase 6B
Synonyms Jmjd3
MMRRC Submission 042625-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5034 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 69289334-69304501 bp(-) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) A to G at 69292736 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000091620 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000050140] [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 probably benign
Transcript: ENSMUST00000050140
SMART Domains Protein: ENSMUSP00000055528
Gene: ENSMUSG00000045377

DomainStartEndE-ValueType
transmembrane domain 44 66 N/A INTRINSIC
transmembrane domain 86 108 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000094077
SMART Domains Protein: ENSMUSP00000091620
Gene: ENSMUSG00000018476

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: 99.2%
  • 3x: 98.5%
  • 10x: 96.7%
  • 20x: 93.6%
Validation Efficiency 97% (67/69)
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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acaca T A 11: 84,136,090 (GRCm39) S482T probably benign Het
Adam6b G T 12: 113,454,547 (GRCm39) G455C probably damaging Het
Ahsg C A 16: 22,717,650 (GRCm39) P237Q probably damaging Het
Asxl2 A G 12: 3,552,193 (GRCm39) S1312G probably damaging Het
Brinp3 C T 1: 146,603,458 (GRCm39) probably benign Het
Col12a1 T C 9: 79,564,649 (GRCm39) H1677R probably damaging Het
Cops7a A G 6: 124,939,583 (GRCm39) probably null Het
Csmd2 G A 4: 127,952,901 (GRCm39) A117T probably damaging Het
Csmd3 T C 15: 47,492,683 (GRCm39) R3153G possibly damaging Het
Dctn4 A G 18: 60,685,956 (GRCm39) N342D probably benign Het
Dennd5a A T 7: 109,499,004 (GRCm39) I953N probably damaging Het
Dmwd T C 7: 18,814,219 (GRCm39) S290P probably damaging Het
Dsc1 T A 18: 20,228,084 (GRCm39) Y424F possibly damaging Het
Far2 C A 6: 148,074,939 (GRCm39) L391M probably benign Het
Foxd3 G A 4: 99,545,327 (GRCm39) G156S probably damaging Het
Galk2 A T 2: 125,771,495 (GRCm39) E173D probably benign Het
Hcar1 T C 5: 124,017,732 (GRCm39) probably benign Het
Hsd17b11 C T 5: 104,166,087 (GRCm39) V91M possibly damaging Het
Ighv1-77 C T 12: 115,825,494 (GRCm39) C115Y probably damaging Het
Ighv9-2 A G 12: 114,073,025 (GRCm39) F9S probably damaging Het
Kif21a T A 15: 90,852,561 (GRCm39) R890W probably null Het
Lin9 T A 1: 180,496,763 (GRCm39) L351I probably benign Het
Magel2 A T 7: 62,029,616 (GRCm39) H840L unknown Het
Mrgpra4 A G 7: 47,631,317 (GRCm39) F95L probably benign Het
Myo7b A G 18: 32,104,440 (GRCm39) L1436P probably damaging Het
Nf1 C T 11: 79,334,976 (GRCm39) P943S probably damaging Het
Obscn T A 11: 58,952,502 (GRCm39) R4153* probably null Het
Oosp2 T C 19: 11,628,899 (GRCm39) I67M probably damaging Het
Or5m13b C A 2: 85,753,891 (GRCm39) S93Y probably damaging Het
Pcdh9 T A 14: 93,564,285 (GRCm39) D1023V probably benign Het
Pcdhb14 T C 18: 37,581,859 (GRCm39) S322P probably damaging Het
Pde2a A G 7: 101,151,231 (GRCm39) D285G probably benign Het
Pde5a G C 3: 122,646,235 (GRCm39) G809R probably damaging Het
Pde5a G T 3: 122,646,236 (GRCm39) G809V probably damaging Het
Pphln1 T C 15: 93,350,010 (GRCm39) V120A probably benign Het
Rictor T C 15: 6,797,576 (GRCm39) S311P probably damaging Het
Rilpl1 T C 5: 124,631,887 (GRCm39) D153G probably damaging Het
Rmdn3 G T 2: 118,978,058 (GRCm39) A181E probably damaging Het
Rnf213 G A 11: 119,301,633 (GRCm39) V369M probably damaging Het
Scyl1 T A 19: 5,810,022 (GRCm39) R601S probably benign Het
Sdcbp G A 4: 6,393,118 (GRCm39) probably null Het
Septin8 A G 11: 53,425,265 (GRCm39) T53A probably damaging Het
Sfpq A G 4: 126,917,462 (GRCm39) probably benign Het
Slc35b3 A G 13: 39,127,134 (GRCm39) Y163H probably damaging Het
Sra1 A G 18: 36,812,048 (GRCm39) probably null Het
Sspo A T 6: 48,457,757 (GRCm39) N3231Y possibly damaging Het
Tcf3 A G 10: 80,253,377 (GRCm39) V218A possibly damaging Het
Tgm3 T C 2: 129,879,404 (GRCm39) V332A possibly damaging Het
Tmprss11f C T 5: 86,739,243 (GRCm39) probably benign Het
Trbv4 A G 6: 41,036,624 (GRCm39) T50A probably benign Het
Trdv2-2 C A 14: 54,198,882 (GRCm39) Y57* probably null Het
Trim50 T C 5: 135,396,147 (GRCm39) V365A possibly damaging Het
Ubash3b T C 9: 40,941,036 (GRCm39) Q245R probably benign Het
Ulk3 T A 9: 57,501,047 (GRCm39) V338E possibly damaging Het
Usf3 A C 16: 44,036,762 (GRCm39) K414T probably damaging Het
Usp48 C T 4: 137,334,068 (GRCm39) R161* probably null Het
Vps18 A T 2: 119,123,787 (GRCm39) D238V probably benign Het
Vps35l T C 7: 118,390,611 (GRCm39) V368A probably damaging Het
Zfp354c T C 11: 50,705,866 (GRCm39) E403G probably benign Het
Zscan18 A G 7: 12,508,072 (GRCm39) V476A 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
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
Predicted Primers PCR Primer
(F):5'- ACTGGTCTAGCCTCACTGAC -3'
(R):5'- ACAAATCTGGCCCTGTGAG -3'

Sequencing Primer
(F):5'- TGACCTCTTGGCATCAGACAG -3'
(R):5'- AAATCTGGCCCTGTGAGAGCTC -3'
Posted On 2016-06-06