Incidental Mutation 'R5140:Kdm6b'
ID 396410
Institutional Source Beutler Lab
Gene Symbol Kdm6b
Ensembl Gene ENSMUSG00000018476
Gene Name KDM1 lysine (K)-specific demethylase 6B
Synonyms Jmjd3
MMRRC Submission 042726-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5140 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 69289334-69304501 bp(-) (GRCm39)
Type of Mutation unclassified
DNA Base Change (assembly) T to C at 69290881 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000123155 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000050140] [ENSMUST00000051620] [ENSMUST00000094077] [ENSMUST00000108660] [ENSMUST00000144531]
AlphaFold Q5NCY0
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: ENSMUST00000051620
SMART Domains Protein: ENSMUSP00000059709
Gene: ENSMUSG00000044795

DomainStartEndE-ValueType
Cyt-b5 20 92 1.89e-6 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000082283
Predicted Effect unknown
Transcript: ENSMUST00000094077
AA Change: Y1596C
SMART Domains Protein: ENSMUSP00000091620
Gene: ENSMUSG00000018476
AA Change: Y1596C

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 probably benign
Transcript: ENSMUST00000108660
SMART Domains Protein: ENSMUSP00000104300
Gene: ENSMUSG00000044795

DomainStartEndE-ValueType
Cyt-b5 20 92 1.89e-6 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124932
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156562
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134903
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129924
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142126
Predicted Effect probably benign
Transcript: ENSMUST00000144531
SMART Domains Protein: ENSMUSP00000123155
Gene: ENSMUSG00000059278

DomainStartEndE-ValueType
low complexity region 18 36 N/A INTRINSIC
Sm 43 114 4.26e-15 SMART
Meta Mutation Damage Score 0.7430 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.6%
Validation Efficiency 98% (59/60)
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
Abcb1a T A 5: 8,752,154 (GRCm39) I405N probably damaging Het
Abhd17b T C 19: 21,661,545 (GRCm39) L244P probably damaging Het
Aebp2 T A 6: 140,579,532 (GRCm39) C34* probably null Het
Arhgap33 A G 7: 30,227,726 (GRCm39) V491A probably damaging Het
Cacul1 C T 19: 60,551,619 (GRCm39) R201Q probably benign Het
Cald1 T A 6: 34,730,515 (GRCm39) N77K probably damaging Het
Clcn6 A C 4: 148,122,774 (GRCm39) probably benign Het
Copb1 A T 7: 113,846,035 (GRCm39) H178Q probably benign Het
Dnah17 C T 11: 117,977,771 (GRCm39) V1854I probably damaging Het
Dnajc16 T G 4: 141,491,994 (GRCm39) T610P possibly damaging Het
Enpp1 T C 10: 24,528,750 (GRCm39) N624S possibly damaging Het
F2 CAGAAAG CAG 2: 91,465,302 (GRCm39) probably benign Het
Foxn1 T C 11: 78,252,459 (GRCm39) T310A probably benign Het
Galnt16 T A 12: 80,628,073 (GRCm39) D256E possibly damaging Het
Gbp11 T C 5: 105,478,919 (GRCm39) D173G probably damaging Het
Glmn A G 5: 107,718,066 (GRCm39) S284P probably damaging Het
Gm3985 A G 8: 33,380,693 (GRCm39) noncoding transcript Het
Hs3st6 A T 17: 24,977,521 (GRCm39) M334L probably benign Het
Idua T A 5: 108,828,180 (GRCm39) D155E probably damaging Het
Kiss1r T C 10: 79,757,461 (GRCm39) F272L probably damaging Het
Krt35 T C 11: 99,985,343 (GRCm39) K233E probably damaging Het
Krt36 C T 11: 99,994,328 (GRCm39) V250M probably damaging Het
Lhpp T C 7: 132,307,361 (GRCm39) Y253H probably damaging Het
Npas3 T A 12: 53,547,897 (GRCm39) L51* probably null Het
Or10ac1 T C 6: 42,515,449 (GRCm39) H169R probably benign Het
Or1j18 T A 2: 36,624,510 (GRCm39) M59K possibly damaging Het
Or4a74 T C 2: 89,439,627 (GRCm39) Y273C probably damaging Het
Or4c119 T C 2: 88,987,451 (GRCm39) K23E probably benign Het
Or56b2 T C 7: 104,338,107 (GRCm39) M295T probably benign Het
Pcdhb9 T G 18: 37,534,186 (GRCm39) V60G probably benign Het
Prkce T C 17: 86,789,570 (GRCm39) V239A probably benign Het
Ralgapa1 C T 12: 55,822,937 (GRCm39) C293Y probably damaging Het
Ralgapa1 C T 12: 55,712,459 (GRCm39) R1804Q probably damaging Het
Rnf26 C A 9: 44,024,071 (GRCm39) probably null Het
Safb2 T C 17: 56,884,901 (GRCm39) D178G probably benign Het
Scn9a C T 2: 66,395,511 (GRCm39) V178M possibly damaging Het
Sergef A G 7: 46,285,026 (GRCm39) probably benign Het
Serpinb9 G A 13: 33,190,544 (GRCm39) G7R probably benign Het
Setd2 C A 9: 110,380,197 (GRCm39) D1337E probably benign Het
Shprh T A 10: 11,030,449 (GRCm39) M222K probably benign Het
Slc25a40 T C 5: 8,480,486 (GRCm39) Y79H probably damaging Het
Slc41a2 A G 10: 83,133,155 (GRCm39) M297T probably damaging Het
Sparcl1 C T 5: 104,233,629 (GRCm39) M573I probably damaging Het
Spcs1 A G 14: 30,722,570 (GRCm39) L83S probably benign Het
Sult1c2 T C 17: 54,276,743 (GRCm39) N106S probably benign Het
Szt2 C T 4: 118,244,178 (GRCm39) R1309Q possibly damaging Het
Ube3c T A 5: 29,840,709 (GRCm39) F695I probably damaging Het
Uimc1 A G 13: 55,223,330 (GRCm39) L314P probably damaging Het
Usp17le C T 7: 104,418,645 (GRCm39) E166K probably damaging Het
Vmn2r92 G A 17: 18,372,312 (GRCm39) D41N probably benign 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
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'- GAAAGTGGGCAGCTTCAGTG -3'
(R):5'- GAAGAAGATCGCTTACCAAGGCC -3'

Sequencing Primer
(F):5'- CAGCTTCAGTGGTGGGC -3'
(R):5'- GCTTACCAAGGCCGTGTCAAAG -3'
Posted On 2016-06-21