Incidental Mutation 'R3950:Kdm6b'
ID 307884
Institutional Source Beutler Lab
Gene Symbol Kdm6b
Ensembl Gene ENSMUSG00000018476
Gene Name KDM1 lysine (K)-specific demethylase 6B
Synonyms Jmjd3
MMRRC Submission 040930-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3950 (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 69296441 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Threonine at position 609 (P609T)
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 probably damaging
Transcript: ENSMUST00000094077
AA Change: P609T

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000091620
Gene: ENSMUSG00000018476
AA Change: P609T

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: 98.6%
  • 10x: 97.3%
  • 20x: 95.1%
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: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4932414N04Rik T C 2: 68,494,747 (GRCm39) probably null Het
Ahnak2 A T 12: 112,749,409 (GRCm39) I186N probably damaging Het
Appbp2 A G 11: 85,085,532 (GRCm39) I458T probably damaging Het
Arhgef25 T C 10: 127,021,013 (GRCm39) Y291C probably damaging Het
Ate1 T C 7: 130,069,022 (GRCm39) Y415C probably damaging Het
B4galt4 G T 16: 38,588,384 (GRCm39) A72S probably benign Het
C3 T C 17: 57,532,286 (GRCm39) R178G probably benign Het
Cdh23 T C 10: 60,493,105 (GRCm39) Y3C probably benign Het
Col11a1 T C 3: 113,915,094 (GRCm39) probably null Het
Col22a1 A G 15: 71,849,207 (GRCm39) F294L possibly damaging Het
Dera A G 6: 137,814,118 (GRCm39) Y100C probably damaging Het
Dync2h1 A T 9: 7,112,061 (GRCm39) Y276* probably null Het
Eea1 A T 10: 95,877,996 (GRCm39) N1389I probably damaging Het
Epha4 A T 1: 77,376,353 (GRCm39) Y509N probably damaging Het
Fat3 G A 9: 15,909,567 (GRCm39) S2145F probably damaging Het
Fezf1 T A 6: 23,247,419 (GRCm39) K219* probably null Het
Fsd1 G A 17: 56,302,517 (GRCm39) probably null Het
Haspin A G 11: 73,027,221 (GRCm39) Y623H probably damaging Het
Hsd3b1 C T 3: 98,763,454 (GRCm39) V56M possibly damaging Het
Hyou1 C T 9: 44,296,524 (GRCm39) T483I probably damaging Het
Kdm2a A G 19: 4,393,260 (GRCm39) L365S possibly damaging Het
Klhl18 T A 9: 110,257,970 (GRCm39) Y490F probably damaging Het
Ky C T 9: 102,419,627 (GRCm39) Q545* probably null Het
L1td1 T C 4: 98,625,590 (GRCm39) L595P probably benign Het
Map3k20 T G 2: 72,268,644 (GRCm39) I550M probably damaging Het
Mug1 T A 6: 121,855,489 (GRCm39) V941E probably damaging Het
Ndst1 T C 18: 60,830,211 (GRCm39) N633S probably benign Het
Ninl A T 2: 150,794,408 (GRCm39) I740K possibly damaging Het
Npepl1 A G 2: 173,962,906 (GRCm39) N431D probably damaging Het
Or5w10 T C 2: 87,375,409 (GRCm39) T160A probably damaging Het
Pacs2 T C 12: 113,024,733 (GRCm39) S408P probably damaging Het
Pard6b C T 2: 167,941,114 (GRCm39) T367I probably damaging Het
Pcdhga7 A G 18: 37,849,568 (GRCm39) E525G probably damaging Het
Pctp A G 11: 89,878,144 (GRCm39) I130T probably benign Het
Pcx C T 19: 4,667,995 (GRCm39) H506Y probably benign Het
Pdhx A G 2: 102,865,586 (GRCm39) S199P probably damaging Het
Pdia2 C A 17: 26,416,590 (GRCm39) probably null Het
Pif1 C A 9: 65,499,116 (GRCm39) N445K probably damaging Het
Prickle4 T C 17: 47,999,507 (GRCm39) K349E probably benign Het
Ptch1 T G 13: 63,672,773 (GRCm39) E944A probably benign Het
Ptpdc1 A T 13: 48,742,670 (GRCm39) M173K probably damaging Het
Rb1 A G 14: 73,500,102 (GRCm39) L515P probably damaging Het
Rcvrn A G 11: 67,590,877 (GRCm39) K154E probably damaging Het
Ros1 C T 10: 51,942,484 (GRCm39) V2059I probably damaging Het
Rtn4ip1 T A 10: 43,785,893 (GRCm39) probably null Het
Sema5a T C 15: 32,689,484 (GRCm39) Y1050H probably damaging Het
Slc25a28 C T 19: 43,652,708 (GRCm39) V318I probably benign Het
Srek1 G A 13: 103,881,403 (GRCm39) R408W unknown Het
Synrg C T 11: 83,880,641 (GRCm39) T444I probably damaging Het
Ticrr T C 7: 79,331,817 (GRCm39) L776S probably damaging Het
Tmem127 T C 2: 127,090,577 (GRCm39) L31P probably damaging Het
Tmprss15 T A 16: 78,870,074 (GRCm39) T190S probably benign Het
Trip10 T A 17: 57,560,411 (GRCm39) probably null Het
Ttc6 A G 12: 57,696,292 (GRCm39) Y31C probably damaging Het
Unc80 A T 1: 66,661,729 (GRCm39) H1718L possibly damaging Het
Zbtb38 A G 9: 96,569,599 (GRCm39) F495S probably damaging Het
Zfp280d G T 9: 72,203,301 (GRCm39) Q16H possibly damaging Het
Zfp521 A G 18: 13,979,403 (GRCm39) S337P probably damaging Het
Zswim9 T A 7: 12,995,503 (GRCm39) T218S 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
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
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'- TGGGAAATCAAAGAGCCTCG -3'
(R):5'- TCAGGATTCGCATAACCCTC -3'

Sequencing Primer
(F):5'- CCTCGGGCAGGCAGCTC -3'
(R):5'- AGGATTCGCATAACCCTCCCATTC -3'
Posted On 2015-04-17