Incidental Mutation 'IGL00484:Kdm6b'
ID4568
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Kdm6b
Ensembl Gene ENSMUSG00000018476
Gene NameKDM1 lysine (K)-specific demethylase 6B
SynonymsJmjd3
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #IGL00484
Quality Score
Status
Chromosome11
Chromosomal Location69398508-69413675 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 69406306 bp
ZygosityHeterozygous
Amino Acid Change Serine to Glycine at position 407 (S407G)
Ref Sequence ENSEMBL: ENSMUSP00000091620 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000094077]
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: S407G

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000091620
Gene: ENSMUSG00000018476
AA Change: S407G

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: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1810013L24Rik T C 16: 8,831,311 probably benign Het
Adgra1 A G 7: 139,875,944 Q496R probably benign Het
Ankrd17 A T 5: 90,268,361 S1151T probably damaging Het
Ankrd55 A G 13: 112,367,794 K330R probably benign Het
Anln A T 9: 22,360,824 Y666* probably null Het
Atp1a2 A G 1: 172,276,002 W984R probably damaging Het
Atp8b3 G T 10: 80,526,164 probably benign Het
Casc3 A G 11: 98,823,202 E420G possibly damaging Het
Cep250 G A 2: 155,991,329 D1724N probably benign Het
Dhx15 T G 5: 52,166,812 E379D probably benign Het
Dock1 T A 7: 135,146,531 probably benign Het
Exph5 C T 9: 53,376,706 Q1696* probably null Het
Fkbp6 C A 5: 135,339,948 A213S possibly damaging Het
Fndc4 A G 5: 31,293,496 probably benign Het
Gli3 A T 13: 15,644,392 T260S possibly damaging Het
Glmp T A 3: 88,325,862 probably null Het
Gm12794 T C 4: 101,941,701 F290L probably benign Het
Gm13101 G A 4: 143,966,614 probably benign Het
Hist1h2an G T 13: 21,786,921 R100S probably benign Het
Ighv1-19 G A 12: 114,708,709 T97I probably benign Het
Lrp1b T C 2: 41,110,861 Y2231C probably damaging Het
Lyst T A 13: 13,709,603 S2999T probably benign Het
Lztr1 T C 16: 17,517,450 probably benign Het
N4bp2 T C 5: 65,807,524 V972A probably damaging Het
Ncoa6 A T 2: 155,406,208 S1725R probably damaging Het
Nfkbiz A G 16: 55,817,909 V396A probably benign Het
Nup205 A G 6: 35,214,802 Q1074R probably damaging Het
Pard3 T C 8: 127,371,846 V456A probably benign Het
Peli1 T A 11: 21,146,952 V114E probably damaging Het
Phf20l1 T G 15: 66,615,633 probably benign Het
Pik3r1 A C 13: 101,701,747 I267S probably benign Het
Polh C T 17: 46,172,243 probably benign Het
Ppl A G 16: 5,087,952 I1493T probably benign Het
Prg3 A G 2: 84,988,747 I6V probably benign Het
Ptprg T C 14: 12,215,220 V1069A probably damaging Het
Rasal2 A T 1: 157,174,175 probably null Het
Slc36a2 A T 11: 55,162,788 Y341* probably null Het
Smim4 T A 14: 31,088,922 probably benign Het
Snapc3 A G 4: 83,436,396 I215V probably damaging Het
Srrm2 T A 17: 23,818,518 S1475T probably benign Het
Sycp2 A T 2: 178,382,348 D414E probably damaging Het
Tanc1 A G 2: 59,793,176 T468A probably benign Het
Tfap2d A G 1: 19,142,881 T310A probably benign Het
Tgfbr2 T A 9: 116,158,289 I51F probably benign Het
Trip11 A T 12: 101,885,311 C546* probably null Het
Ttbk2 C T 2: 120,773,886 W210* probably null Het
Upk1b T G 16: 38,780,016 N201H possibly damaging Het
Ush2a A T 1: 188,782,513 T3180S probably benign Het
Vps13d T G 4: 145,126,575 Q2323P probably benign Het
Zfp810 A T 9: 22,278,309 Y434* probably null Het
Other mutations in Kdm6b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02271:Kdm6b APN 11 69406067 missense possibly damaging 0.65
beine UTSW 11 69403592 missense unknown
Knochen UTSW 11 69400055 unclassified probably benign
Ostentatious UTSW 11 69403598 missense unknown
Piquant UTSW 11 69403794 missense unknown
Tart UTSW 11 69406366 missense probably damaging 1.00
PIT4458001:Kdm6b UTSW 11 69399952 missense unknown
R0455:Kdm6b UTSW 11 69406996 nonsense probably null
R0645:Kdm6b UTSW 11 69405018 missense unknown
R1659:Kdm6b UTSW 11 69407588 missense possibly damaging 0.88
R1855:Kdm6b UTSW 11 69407286 missense probably damaging 0.99
R1962:Kdm6b UTSW 11 69401365 unclassified probably benign
R1993:Kdm6b UTSW 11 69406303 missense probably null 0.85
R2029:Kdm6b UTSW 11 69403592 missense unknown
R2181:Kdm6b UTSW 11 69401126 nonsense probably null
R2215:Kdm6b UTSW 11 69405044 missense unknown
R2904:Kdm6b UTSW 11 69405785 missense possibly damaging 0.63
R2992:Kdm6b UTSW 11 69406307 small deletion probably benign
R3236:Kdm6b UTSW 11 69406366 missense probably damaging 1.00
R3950:Kdm6b UTSW 11 69405615 missense probably damaging 1.00
R4027:Kdm6b UTSW 11 69406268 missense possibly damaging 0.92
R4830:Kdm6b UTSW 11 69403794 missense unknown
R4996:Kdm6b UTSW 11 69405731 missense probably damaging 1.00
R5034:Kdm6b UTSW 11 69401910 splice site probably benign
R5140:Kdm6b UTSW 11 69400055 unclassified probably benign
R5160:Kdm6b UTSW 11 69400768 unclassified probably benign
R5240:Kdm6b UTSW 11 69401904 splice site probably benign
R5273:Kdm6b UTSW 11 69404201 missense unknown
R5386:Kdm6b UTSW 11 69400810 unclassified probably benign
R5597:Kdm6b UTSW 11 69406074 missense probably damaging 0.96
R5598:Kdm6b UTSW 11 69406074 missense probably damaging 0.96
R5812:Kdm6b UTSW 11 69405929 missense probably damaging 0.98
R5976:Kdm6b UTSW 11 69403788 critical splice donor site probably null
R6000:Kdm6b UTSW 11 69403598 missense unknown
R6145:Kdm6b UTSW 11 69405026 missense unknown
R6191:Kdm6b UTSW 11 69406758 missense probably benign 0.01
R6256:Kdm6b UTSW 11 69406729 missense probably damaging 0.96
R6304:Kdm6b UTSW 11 69404258 missense unknown
R6917:Kdm6b UTSW 11 69406593 missense probably benign 0.04
R6939:Kdm6b UTSW 11 69406762 missense probably damaging 0.99
R7356:Kdm6b UTSW 11 69402165 nonsense probably null
R7644:Kdm6b UTSW 11 69400206 missense unknown
R7673:Kdm6b UTSW 11 69405742 missense probably damaging 0.98
R7698:Kdm6b UTSW 11 69405981 missense probably benign 0.14
R7776:Kdm6b UTSW 11 69406134 missense possibly damaging 0.84
Z1177:Kdm6b UTSW 11 69403866 missense not run
Posted On2012-04-20