Incidental Mutation 'R0645:Kdm6b'
ID 57088
Institutional Source Beutler Lab
Gene Symbol Kdm6b
Ensembl Gene ENSMUSG00000018476
Gene Name KDM1 lysine (K)-specific demethylase 6B
Synonyms Jmjd3
MMRRC Submission 038830-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0645 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 69289334-69304501 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 69295844 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 808 (S808T)
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: S808T
SMART Domains Protein: ENSMUSP00000091620
Gene: ENSMUSG00000018476
AA Change: S808T

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
Meta Mutation Damage Score 0.0715 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.5%
Validation Efficiency 99% (94/95)
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: 92 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam18 G T 8: 25,162,136 (GRCm39) Y46* probably null Het
Adam26b A C 8: 43,973,524 (GRCm39) C493G probably damaging Het
Ak5 A T 3: 152,359,252 (GRCm39) L182Q probably damaging Het
Akt1s1 T C 7: 44,498,645 (GRCm39) probably benign Het
Amhr2 G T 15: 102,354,863 (GRCm39) G133C probably damaging Het
Btbd9 A T 17: 30,743,941 (GRCm39) L187Q probably damaging Het
Ccdc117 A T 11: 5,484,385 (GRCm39) probably benign Het
Ccdc138 A T 10: 58,411,542 (GRCm39) I637F probably damaging Het
Ccdc162 A G 10: 41,462,407 (GRCm39) probably benign Het
Cdc25b C A 2: 131,033,533 (GRCm39) H157Q probably benign Het
Cdon A G 9: 35,388,379 (GRCm39) probably null Het
Cdt1 G A 8: 123,298,884 (GRCm39) probably benign Het
Cep350 C T 1: 155,816,458 (GRCm39) probably null Het
Cfb T C 17: 35,078,992 (GRCm39) K831R probably benign Het
Cldn4 C A 5: 134,975,645 (GRCm39) probably benign Het
Cntnap5b T C 1: 99,999,767 (GRCm39) probably benign Het
Cyp27b1 T G 10: 126,884,967 (GRCm39) S77A probably benign Het
Dlc1 T C 8: 37,041,203 (GRCm39) D1342G possibly damaging Het
Dlgap4 A G 2: 156,603,799 (GRCm39) H887R probably damaging Het
Duox2 A G 2: 122,123,139 (GRCm39) I503T probably damaging Het
Eml4 T C 17: 83,770,922 (GRCm39) probably benign Het
Ermap A G 4: 119,042,888 (GRCm39) S212P probably benign Het
Esrrg T A 1: 187,775,538 (GRCm39) C22S probably benign Het
Evx2 T A 2: 74,488,238 (GRCm39) Y194F possibly damaging Het
Fbn2 T G 18: 58,191,461 (GRCm39) D1554A probably damaging Het
Flrt1 G A 19: 7,074,508 (GRCm39) probably benign Het
Fndc5 A G 4: 129,033,630 (GRCm39) probably benign Het
Frem1 A T 4: 82,907,403 (GRCm39) I837N probably damaging Het
Fzd10 G T 5: 128,679,662 (GRCm39) A461S possibly damaging Het
Ganab T A 19: 8,888,477 (GRCm39) Y511N probably damaging Het
Gbp7 A G 3: 142,243,926 (GRCm39) probably null Het
Gm5919 T A 9: 83,765,436 (GRCm39) C91S unknown Het
Gpr31b A T 17: 13,271,093 (GRCm39) C25* probably null Het
Grb10 A G 11: 11,886,755 (GRCm39) S505P probably damaging Het
Grm4 A T 17: 27,654,183 (GRCm39) V542E probably damaging Het
Gsta5 T C 9: 78,206,303 (GRCm39) I75T possibly damaging Het
Hivep3 G A 4: 119,954,531 (GRCm39) R949H possibly damaging Het
Hycc1 C T 5: 24,184,506 (GRCm39) G242D probably damaging Het
Invs A T 4: 48,407,653 (GRCm39) M543L probably benign Het
Kcnk2 T C 1: 188,988,927 (GRCm39) probably null Het
Klhl30 C T 1: 91,283,228 (GRCm39) R277W probably damaging Het
Lama1 A G 17: 68,080,707 (GRCm39) Q1245R probably benign Het
Lingo3 G T 10: 80,671,169 (GRCm39) H254N probably benign Het
Lzts1 A T 8: 69,588,392 (GRCm39) H521Q possibly damaging Het
Map3k19 A C 1: 127,749,919 (GRCm39) I1144S possibly damaging Het
Mast2 T C 4: 116,170,043 (GRCm39) probably benign Het
Mast2 A G 4: 116,165,184 (GRCm39) S1411P probably damaging Het
Mesp1 G T 7: 79,442,328 (GRCm39) S225R possibly damaging Het
Micu1 A G 10: 59,675,503 (GRCm39) T366A possibly damaging Het
Mideas G T 12: 84,205,077 (GRCm39) N834K possibly damaging Het
Mknk2 T C 10: 80,507,742 (GRCm39) probably null Het
Msh5 A G 17: 35,258,199 (GRCm39) L309P probably damaging Het
Myo7b T C 18: 32,127,962 (GRCm39) I577V probably benign Het
Myom2 T A 8: 15,167,698 (GRCm39) D1094E probably damaging Het
Nedd1 T C 10: 92,527,693 (GRCm39) probably null Het
Neu4 T C 1: 93,950,191 (GRCm39) L50S probably damaging Het
Noa1 T C 5: 77,457,722 (GRCm39) Y61C probably benign Het
Nr1h4 A T 10: 89,342,390 (GRCm39) M30K probably benign Het
Nsd3 A G 8: 26,199,096 (GRCm39) I1219V probably benign Het
Nup188 T A 2: 30,233,478 (GRCm39) probably null Het
Or10ag2 T A 2: 87,248,612 (GRCm39) Y71* probably null Het
Or5al5 A G 2: 85,961,378 (GRCm39) S210P probably damaging Het
Or6c208 T A 10: 129,224,162 (GRCm39) I220N possibly damaging Het
Or6k2 A T 1: 173,986,920 (GRCm39) T194S probably benign Het
Pbk G A 14: 66,051,245 (GRCm39) probably benign Het
Pcnx2 G A 8: 126,487,459 (GRCm39) T1848M possibly damaging Het
Pdzd7 C T 19: 45,033,914 (GRCm39) G57R possibly damaging Het
Pik3r4 C A 9: 105,546,386 (GRCm39) probably benign Het
Plce1 A G 19: 38,766,433 (GRCm39) S2153G probably damaging Het
Potefam1 C T 2: 111,044,928 (GRCm39) probably null Het
Pphln1 G A 15: 93,318,192 (GRCm39) V34M possibly damaging Het
Prrc2a T C 17: 35,375,308 (GRCm39) D1114G probably damaging Het
Prss16 T C 13: 22,193,546 (GRCm39) probably benign Het
Rtp3 T C 9: 110,816,168 (GRCm39) K128E probably damaging Het
Scn3a T A 2: 65,355,194 (GRCm39) I241F possibly damaging Het
Setd1a G A 7: 127,386,382 (GRCm39) V336I probably damaging Het
Sfpq A G 4: 126,916,762 (GRCm39) I320V possibly damaging Het
Skint5 A T 4: 113,620,679 (GRCm39) D678E unknown Het
Slc12a9 G A 5: 137,313,638 (GRCm39) P774S probably benign Het
Slc25a54 C G 3: 109,019,481 (GRCm39) L362V possibly damaging Het
Smarcd1 A G 15: 99,605,267 (GRCm39) probably null Het
Spata31e5 T A 1: 28,816,011 (GRCm39) N674Y probably damaging Het
Suco A T 1: 161,661,683 (GRCm39) M916K probably damaging Het
Tiam2 T C 17: 3,564,973 (GRCm39) S1404P possibly damaging Het
Topors T C 4: 40,260,333 (GRCm39) T984A unknown Het
Trabd2b A T 4: 114,443,767 (GRCm39) K308M probably damaging Het
Trmo A T 4: 46,377,083 (GRCm39) probably benign Het
Trpc3 A T 3: 36,725,654 (GRCm39) D107E probably benign Het
Ugcg C T 4: 59,207,798 (GRCm39) P46S probably benign Het
Uggt2 A C 14: 119,295,010 (GRCm39) Y539D probably benign Het
Wwc2 T G 8: 48,353,674 (GRCm39) probably benign Het
Zdbf2 T A 1: 63,344,109 (GRCm39) D829E possibly 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
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
Predicted Primers PCR Primer
(F):5'- AAGCCCGACTGATTTCTTCTAGCAC -3'
(R):5'- AGAGCCCTTTGCATCTCTACAGCC -3'

Sequencing Primer
(F):5'- CCGCCTGAGGTAGAGAACTG -3'
(R):5'- ccaccaccactgctgcc -3'
Posted On 2013-07-11