Incidental Mutation 'R1962:Kdm6b'
ID 217010
Institutional Source Beutler Lab
Gene Symbol Kdm6b
Ensembl Gene ENSMUSG00000018476
Gene Name KDM1 lysine (K)-specific demethylase 6B
Synonyms Jmjd3
MMRRC Submission 039976-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1962 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 69289334-69304501 bp(-) (GRCm39)
Type of Mutation unclassified
DNA Base Change (assembly) T to C at 69292191 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000123155 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000050140] [ENSMUST00000094077] [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 noncoding transcript
Transcript: ENSMUST00000082283
Predicted Effect unknown
Transcript: ENSMUST00000094077
AA Change: N1391S
SMART Domains Protein: ENSMUSP00000091620
Gene: ENSMUSG00000018476
AA Change: N1391S

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: ENSMUST00000124932
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129924
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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156562
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.4%
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: 108 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca15 A G 7: 119,940,468 (GRCm39) I354M probably damaging Het
Abca8a T C 11: 109,917,731 (GRCm39) probably null Het
Abca8b T C 11: 109,870,724 (GRCm39) R143G probably benign Het
Actn4 T C 7: 28,594,047 (GRCm39) D840G probably damaging Het
Agpat5 T C 8: 18,928,026 (GRCm39) L197P probably damaging Het
Akr1d1 T C 6: 37,512,983 (GRCm39) V93A probably benign Het
Arap2 T C 5: 62,834,007 (GRCm39) K820R possibly damaging Het
Armc9 T A 1: 86,135,696 (GRCm39) C551S probably damaging Het
Atg7 T C 6: 114,683,191 (GRCm39) L418P probably damaging Het
Awat2 G A X: 99,448,165 (GRCm39) P148S probably damaging Het
Brms1 C T 19: 5,096,027 (GRCm39) R34W probably damaging Het
Cbx2 A G 11: 118,919,395 (GRCm39) Q320R possibly damaging Het
Ccdc106 G A 7: 5,062,539 (GRCm39) D11N possibly damaging Het
Ccdc30 C T 4: 119,196,988 (GRCm39) R426Q probably benign Het
Cdc42bpg T A 19: 6,356,885 (GRCm39) V47E probably damaging Het
Cep170b C T 12: 112,704,495 (GRCm39) S751L probably damaging Het
Cfap46 A T 7: 139,246,957 (GRCm39) L328Q probably damaging Het
Crtc3 A G 7: 80,239,679 (GRCm39) F558L probably damaging Het
Cyp2d34 A G 15: 82,502,809 (GRCm39) V139A probably benign Het
Dchs1 A G 7: 105,413,408 (GRCm39) Y1136H probably damaging Het
Dhrs4 T C 14: 55,725,060 (GRCm39) V185A probably damaging Het
Dnah7b A G 1: 46,281,263 (GRCm39) K2775E possibly damaging Het
Dst C A 1: 34,230,097 (GRCm39) S2238R possibly damaging Het
Duox2 T C 2: 122,127,853 (GRCm39) probably null Het
Dusp16 G T 6: 134,695,099 (GRCm39) Y577* probably null Het
Dync1h1 G A 12: 110,602,943 (GRCm39) E2195K probably benign Het
Eml5 A G 12: 98,842,570 (GRCm39) F176S probably damaging Het
Esco2 C A 14: 66,068,982 (GRCm39) R109S probably damaging Het
Galnt7 C T 8: 57,985,748 (GRCm39) E541K probably benign Het
Gbf1 C T 19: 46,255,658 (GRCm39) T707I probably damaging Het
Gdf5 A G 2: 155,783,672 (GRCm39) C427R probably damaging Het
Glyctk T C 9: 106,035,064 (GRCm39) M1V probably null Het
Gm5478 T C 15: 101,552,830 (GRCm39) E367G probably damaging Het
Golga7b G A 19: 42,251,768 (GRCm39) V5I probably benign Het
Gpt2 T C 8: 86,219,764 (GRCm39) L70P probably damaging Het
Gsdmc3 C A 15: 63,730,315 (GRCm39) Q416H probably damaging Het
Hoxb5 A G 11: 96,194,918 (GRCm39) E160G probably benign Het
Ift81 A T 5: 122,698,772 (GRCm39) Y532N probably benign Het
Igf1 G A 10: 87,700,726 (GRCm39) C66Y probably damaging Het
Igf1r T C 7: 67,857,023 (GRCm39) V995A probably damaging Het
Ip6k1 T C 9: 107,918,287 (GRCm39) probably null Het
Jaml T C 9: 45,015,495 (GRCm39) I333T possibly damaging Het
Kdm4c T C 4: 74,225,253 (GRCm39) probably benign Het
Krt6a C T 15: 101,599,900 (GRCm39) R404H probably damaging Het
Larp4b C A 13: 9,186,878 (GRCm39) H69N probably benign Het
Lcat A T 8: 106,668,355 (GRCm39) W222R probably damaging Het
Lrrc40 T A 3: 157,746,086 (GRCm39) C54S probably benign Het
Mcpt9 T A 14: 56,265,024 (GRCm39) H159L probably benign Het
Megf8 T C 7: 25,062,976 (GRCm39) V2444A probably damaging Het
Memo1 T C 17: 74,552,003 (GRCm39) T98A possibly damaging Het
Mical2 A T 7: 112,012,051 (GRCm39) I634L probably benign Het
Mov10 C T 3: 104,704,293 (GRCm39) R835Q probably damaging Het
Mybpc1 A T 10: 88,384,688 (GRCm39) L546Q probably damaging Het
Myo6 T C 9: 80,168,117 (GRCm39) V427A probably damaging Het
Myom2 T A 8: 15,182,599 (GRCm39) probably null Het
Mzt2 G A 16: 15,666,543 (GRCm39) R125C probably damaging Het
Neb T A 2: 52,162,949 (GRCm39) R2031* probably null Het
Nphp3 T C 9: 103,898,537 (GRCm39) S447P probably benign Het
Nrp2 T A 1: 62,758,090 (GRCm39) D25E probably benign Het
Nts A G 10: 102,320,918 (GRCm39) L57S probably damaging Het
Nudt9 G A 5: 104,212,971 (GRCm39) R348H probably benign Het
Or10d5j T C 9: 39,867,979 (GRCm39) Y84C probably benign Het
Or13a1 C T 6: 116,470,725 (GRCm39) P52S probably benign Het
Or3a1b C A 11: 74,012,650 (GRCm39) D178E probably benign Het
Or4k49 T C 2: 111,495,234 (GRCm39) I221T probably damaging Het
Or5ac16 T A 16: 59,022,271 (GRCm39) I173F possibly damaging Het
Pafah1b1 T C 11: 74,590,177 (GRCm39) probably benign Het
Piezo2 C A 18: 63,211,911 (GRCm39) M1291I probably damaging Het
Pik3ca T C 3: 32,498,016 (GRCm39) F486S probably benign Het
Podnl1 C T 8: 84,853,926 (GRCm39) H99Y probably benign Het
Prdm6 A T 18: 53,701,233 (GRCm39) Y341F probably damaging Het
Prr5l C T 2: 101,588,854 (GRCm39) probably null Het
Psmd4 G T 3: 94,944,012 (GRCm39) T24N possibly damaging Het
Rbbp8nl G A 2: 179,922,667 (GRCm39) T242M probably benign Het
Rsf1 GCG GCGACG 7: 97,229,114 (GRCm39) probably benign Het
Rsf1 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGC GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC 7: 97,229,113 (GRCm39) probably benign Het
Scfd1 T C 12: 51,469,769 (GRCm39) V438A probably benign Het
Scn9a A G 2: 66,314,655 (GRCm39) C1677R probably damaging Het
Sgsm2 T A 11: 74,782,854 (GRCm39) H34L probably damaging Het
Shank1 T A 7: 43,993,747 (GRCm39) probably null Het
Smarca2 G T 19: 26,650,124 (GRCm39) E24* probably null Het
Sncaip C T 18: 53,004,434 (GRCm39) H354Y probably damaging Het
St8sia2 T A 7: 73,593,057 (GRCm39) D333V probably damaging Het
Stxbp2 C A 8: 3,692,672 (GRCm39) R575S probably benign Het
Syt9 T A 7: 107,024,314 (GRCm39) V69D probably damaging Het
Tanc2 A G 11: 105,689,558 (GRCm39) N240S probably benign Het
Tcl1b1 T C 12: 105,130,727 (GRCm39) L70S probably benign Het
Tmem44 C T 16: 30,362,219 (GRCm39) probably null Het
Tor1b A G 2: 30,846,931 (GRCm39) R293G probably benign Het
Trim29 T C 9: 43,222,615 (GRCm39) V148A probably benign Het
Trmt10b C A 4: 45,314,378 (GRCm39) Y271* probably null Het
Ubqln5 A T 7: 103,778,095 (GRCm39) V243E possibly damaging Het
Ubqln5 T C 7: 103,778,134 (GRCm39) D230G probably damaging Het
Ugt2b37 A G 5: 87,402,193 (GRCm39) F146S probably damaging Het
Vmn1r160 T A 7: 22,570,827 (GRCm39) V60E probably damaging Het
Vmn2r109 T A 17: 20,774,185 (GRCm39) D390V probably damaging Het
Vmn2r27 C T 6: 124,200,793 (GRCm39) R388Q possibly damaging Het
Vmn2r72 A T 7: 85,398,369 (GRCm39) V537D probably benign Het
Vmn2r84 A G 10: 130,226,591 (GRCm39) S416P probably damaging Het
Vmn2r98 C A 17: 19,285,595 (GRCm39) Y138* probably null Het
Vmn2r-ps158 T C 7: 42,696,824 (GRCm39) V620A probably benign Het
Xrra1 A C 7: 99,560,227 (GRCm39) E401A probably damaging Het
Zfp280d T A 9: 72,242,362 (GRCm39) C688* probably null Het
Zfp3 T A 11: 70,662,954 (GRCm39) Y304* probably null Het
Zfp407 A T 18: 84,577,461 (GRCm39) D1217E probably benign Het
Zfp658 T C 7: 43,223,245 (GRCm39) Y507H possibly damaging Het
Zfyve16 T C 13: 92,659,252 (GRCm39) T220A possibly damaging Het
Zmym4 C G 4: 126,796,463 (GRCm39) K820N 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
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'- GGAACCAGTCAAGTAGTCCAC -3'
(R):5'- GCAGCTATACATGAAGGTCCC -3'

Sequencing Primer
(F):5'- AGTAGTCCACACCATGCCTGTG -3'
(R):5'- CTATACATGAAGGTCCCTGGCAG -3'
Posted On 2014-08-01