Incidental Mutation 'R4791:Kdm5b'
ID 368532
Institutional Source Beutler Lab
Gene Symbol Kdm5b
Ensembl Gene ENSMUSG00000042207
Gene Name lysine (K)-specific demethylase 5B
Synonyms Jarid1b, Plu1, Rb-Bp2, 2210016I17Rik, 2010009J12Rik, PLU-1, D1Ertd202e
MMRRC Submission 041976-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.268) question?
Stock # R4791 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 134560171-134635285 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 134630800 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 1515 (E1515G)
Ref Sequence ENSEMBL: ENSMUSP00000107817 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047714] [ENSMUST00000112198]
AlphaFold Q80Y84
PDB Structure Solution structure of the ARID domain of Jarid1b protein [SOLUTION NMR]
Predicted Effect probably benign
Transcript: ENSMUST00000047714
SMART Domains Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207

DomainStartEndE-ValueType
low complexity region 7 30 N/A INTRINSIC
JmjN 31 72 2.87e-20 SMART
ARID 94 183 7.39e-32 SMART
BRIGHT 98 188 1.51e-35 SMART
low complexity region 228 239 N/A INTRINSIC
PHD 311 357 6.15e-14 SMART
JmjC 453 619 2.33e-67 SMART
Pfam:zf-C5HC2 692 744 2.2e-17 PFAM
Pfam:PLU-1 757 1088 5.6e-92 PFAM
low complexity region 1097 1109 N/A INTRINSIC
PHD 1178 1222 6.2e-10 SMART
low complexity region 1225 1236 N/A INTRINSIC
low complexity region 1406 1417 N/A INTRINSIC
low complexity region 1470 1484 N/A INTRINSIC
PHD 1486 1536 1.18e-6 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000112198
AA Change: E1515G

PolyPhen 2 Score 0.816 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: E1515G

DomainStartEndE-ValueType
low complexity region 7 30 N/A INTRINSIC
JmjN 31 72 2.87e-20 SMART
ARID 94 183 7.39e-32 SMART
BRIGHT 98 188 1.51e-35 SMART
low complexity region 228 239 N/A INTRINSIC
PHD 311 357 6.15e-14 SMART
JmjC 453 619 2.33e-67 SMART
Pfam:zf-C5HC2 692 745 6.7e-21 PFAM
Pfam:PLU-1 756 1088 6e-94 PFAM
low complexity region 1097 1109 N/A INTRINSIC
PHD 1178 1222 6.2e-10 SMART
low complexity region 1225 1236 N/A INTRINSIC
low complexity region 1406 1417 N/A INTRINSIC
low complexity region 1470 1484 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191572
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.3%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Homozygous mutant mice display decreased body weight, decreased female fertility, lower uterine weight, and a delay in mammary development. Knockout of this gene has also been associated with embryonic lethality. [provided by RefSeq, Dec 2016]
PHENOTYPE: Mice homozygous for a gene trapped allele exhibit decreased body weight, background-sensitive premature mortality, decreased female fertility, delayed mammary gland development, decreased serum estradiol levels, and reduced mammary epithelial cell proliferation in early puberty. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 97 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921507P07Rik G T 6: 50,595,837 (GRCm38) P32Q probably damaging Het
Abcc6 C T 7: 45,982,160 (GRCm38) V1231M probably benign Het
Agl A G 3: 116,786,528 (GRCm38) probably null Het
Ak7 T C 12: 105,710,145 (GRCm38) F35L probably benign Het
Aldh1a1 A G 19: 20,619,985 (GRCm38) N110S probably damaging Het
Arhgef5 C T 6: 43,283,183 (GRCm38) L1368F probably damaging Het
Atp5j2 T C 5: 145,184,555 (GRCm38) Y72C possibly damaging Het
Atp6v0a2 T G 5: 124,646,727 (GRCm38) F317V probably benign Het
Bank1 A T 3: 136,254,929 (GRCm38) S56T probably benign Het
BC080695 A G 4: 143,570,989 (GRCm38) probably benign Het
Cachd1 T A 4: 100,918,085 (GRCm38) C166S probably damaging Het
Cand1 A G 10: 119,210,702 (GRCm38) I961T probably benign Het
Ccdc73 G A 2: 104,981,105 (GRCm38) probably null Het
Cct6b A T 11: 82,742,004 (GRCm38) probably null Het
Chd2 A C 7: 73,468,577 (GRCm38) S1098A probably benign Het
Col6a4 A T 9: 106,080,202 (GRCm38) V141E possibly damaging Het
Col6a5 T C 9: 105,930,784 (GRCm38) T1022A unknown Het
Cr2 A T 1: 195,155,935 (GRCm38) C698S probably damaging Het
Diexf G A 1: 193,128,267 (GRCm38) H143Y probably benign Het
Dnaaf5 C A 5: 139,184,650 (GRCm38) Q786K possibly damaging Het
Dnah6 T C 6: 73,095,074 (GRCm38) D2423G probably benign Het
Dnhd1 T C 7: 105,721,117 (GRCm38) F4583S probably damaging Het
Duoxa2 A T 2: 122,301,198 (GRCm38) T123S probably damaging Het
Edem1 T G 6: 108,841,634 (GRCm38) V201G probably damaging Het
Eef1d C T 15: 75,903,682 (GRCm38) A43T possibly damaging Het
Elavl3 T C 9: 22,024,678 (GRCm38) K249E probably damaging Het
Epg5 G T 18: 77,948,996 (GRCm38) E303* probably null Het
Fam83h T C 15: 76,002,368 (GRCm38) D1040G probably damaging Het
Fndc7 A T 3: 108,876,659 (GRCm38) F211L probably benign Het
Fsip2 A G 2: 82,982,108 (GRCm38) T2924A possibly damaging Het
Gm5616 T C 9: 48,450,683 (GRCm38) noncoding transcript Het
Gpr135 T A 12: 72,069,868 (GRCm38) D375V probably benign Het
Hgd A G 16: 37,631,825 (GRCm38) *446W probably null Het
Hivep2 C A 10: 14,128,969 (GRCm38) T437K probably benign Het
Htra2 A G 6: 83,051,817 (GRCm38) L379P probably damaging Het
Hypk G T 2: 121,457,655 (GRCm38) probably null Het
Ica1l A G 1: 60,010,201 (GRCm38) F198L probably damaging Het
Igsf11 G A 16: 39,024,864 (GRCm38) S319N probably damaging Het
Il12rb1 T C 8: 70,813,368 (GRCm38) S213P possibly damaging Het
Katnal1 C T 5: 148,904,650 (GRCm38) V135M probably damaging Het
Kcnc4 G A 3: 107,447,543 (GRCm38) P530S probably benign Het
Kcnu1 T C 8: 25,913,752 (GRCm38) Y24H probably damaging Het
Kif18a A T 2: 109,287,875 (GRCm38) M12L probably benign Het
Klre1 T C 6: 129,584,155 (GRCm38) S160P probably damaging Het
Lama2 A T 10: 27,467,271 (GRCm38) H68Q probably damaging Het
Lgals8 T C 13: 12,453,322 (GRCm38) K49R possibly damaging Het
Lmf1 G A 17: 25,654,471 (GRCm38) V317M probably damaging Het
Lsr T C 7: 30,958,552 (GRCm38) T328A probably damaging Het
Mark4 C T 7: 19,451,657 (GRCm38) E51K probably benign Het
Mindy2 T C 9: 70,634,001 (GRCm38) probably null Het
Mkks G A 2: 136,876,162 (GRCm38) T400I probably benign Het
Mon2 T A 10: 123,006,057 (GRCm38) M1544L probably benign Het
Mrc2 G A 11: 105,348,431 (GRCm38) probably null Het
Myo5c T G 9: 75,290,916 (GRCm38) L1341R probably damaging Het
Nin T C 12: 70,043,807 (GRCm38) R945G possibly damaging Het
Nox4 T C 7: 87,304,847 (GRCm38) V120A probably benign Het
Olfr1196 C T 2: 88,700,898 (GRCm38) V144I probably benign Het
Olfr1496 T A 19: 13,781,342 (GRCm38) C243* probably null Het
Olfr169 G T 16: 19,566,663 (GRCm38) H73Q possibly damaging Het
Olfr30 A T 11: 58,455,544 (GRCm38) V135E possibly damaging Het
Olfr847 T C 9: 19,375,809 (GRCm38) E24G probably benign Het
Plekha2 T A 8: 25,042,762 (GRCm38) R398W probably damaging Het
Pradc1 A G 6: 85,447,191 (GRCm38) W58R probably damaging Het
Prrc2b A G 2: 32,217,339 (GRCm38) probably null Het
Psg19 T A 7: 18,794,146 (GRCm38) N224I probably damaging Het
Ranbp17 A C 11: 33,487,746 (GRCm38) V164G probably benign Het
Rasgrp3 A G 17: 75,500,173 (GRCm38) S211G probably benign Het
Rcc1l G A 5: 134,163,776 (GRCm38) P270S possibly damaging Het
Rfx6 T A 10: 51,719,944 (GRCm38) probably null Het
Rnf222 A T 11: 68,893,019 (GRCm38) E137D probably damaging Het
Selenof T G 3: 144,596,823 (GRCm38) Y120D probably damaging Het
Sema3b G T 9: 107,603,813 (GRCm38) D108E probably damaging Het
Shank3 T A 15: 89,500,354 (GRCm38) L143Q probably damaging Het
Shtn1 G C 19: 59,050,873 (GRCm38) R45G probably damaging Het
Sirt4 T C 5: 115,480,314 (GRCm38) T234A possibly damaging Het
Slc25a30 C A 14: 75,763,366 (GRCm38) W266L probably benign Het
Spata20 A T 11: 94,484,586 (GRCm38) N127K probably damaging Het
St14 C T 9: 31,095,622 (GRCm38) G636D probably benign Het
Stat5a G A 11: 100,865,463 (GRCm38) E170K probably damaging Het
Sugp2 C T 8: 70,242,790 (GRCm38) R138C probably damaging Het
Sult1e1 C A 5: 87,586,730 (GRCm38) W119L possibly damaging Het
Sv2a T C 3: 96,192,558 (GRCm38) V608A possibly damaging Het
Syne2 T C 12: 75,909,244 (GRCm38) Y575H possibly damaging Het
Taok2 G A 7: 126,868,132 (GRCm38) S167L possibly damaging Het
Thoc6 T C 17: 23,670,067 (GRCm38) H151R possibly damaging Het
Tm9sf2 T C 14: 122,139,650 (GRCm38) S197P probably benign Het
Tmem260 CAGGGACCGGCATAG CAG 14: 48,511,994 (GRCm38) probably benign Het
Tmx2 G A 2: 84,677,996 (GRCm38) P15L probably damaging Het
Top1mt C T 15: 75,668,625 (GRCm38) probably null Het
Trpm6 T A 19: 18,867,981 (GRCm38) S1682T probably benign Het
Trrap C T 5: 144,803,277 (GRCm38) R1171W probably damaging Het
Ugt3a2 A G 15: 9,361,579 (GRCm38) D147G probably damaging Het
Vnn3 A G 10: 23,864,621 (GRCm38) H274R probably benign Het
Vwf C A 6: 125,643,363 (GRCm38) T1668K Het
Zfp568 T C 7: 30,015,183 (GRCm38) S162P probably damaging Het
Zfp658 T A 7: 43,574,466 (GRCm38) C722S possibly damaging Het
Zfp808 T A 13: 62,171,231 (GRCm38) H91Q probably damaging Het
Other mutations in Kdm5b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00230:Kdm5b APN 1 134,620,955 (GRCm38) missense probably damaging 1.00
IGL01458:Kdm5b APN 1 134,621,986 (GRCm38) missense possibly damaging 0.53
IGL01567:Kdm5b APN 1 134,602,540 (GRCm38) missense probably damaging 1.00
IGL01625:Kdm5b APN 1 134,617,968 (GRCm38) missense possibly damaging 0.74
IGL01970:Kdm5b APN 1 134,600,727 (GRCm38) missense probably damaging 1.00
IGL02183:Kdm5b APN 1 134,624,931 (GRCm38) missense probably benign 0.09
IGL02592:Kdm5b APN 1 134,624,853 (GRCm38) missense probably damaging 0.99
IGL02695:Kdm5b APN 1 134,604,485 (GRCm38) missense possibly damaging 0.94
IGL02697:Kdm5b APN 1 134,588,773 (GRCm38) splice site probably benign
IGL03036:Kdm5b APN 1 134,608,937 (GRCm38) missense probably damaging 1.00
IGL03056:Kdm5b APN 1 134,587,979 (GRCm38) missense probably damaging 0.99
IGL03206:Kdm5b APN 1 134,627,317 (GRCm38) missense probably benign
IGL03342:Kdm5b APN 1 134,602,576 (GRCm38) missense probably benign 0.00
IGL03388:Kdm5b APN 1 134,627,322 (GRCm38) missense probably benign
amaryllis UTSW 1 134,609,061 (GRCm38) critical splice donor site probably null
PIT4486001:Kdm5b UTSW 1 134,628,685 (GRCm38) missense probably damaging 1.00
R0233:Kdm5b UTSW 1 134,604,634 (GRCm38) splice site probably benign
R0334:Kdm5b UTSW 1 134,604,522 (GRCm38) missense probably damaging 0.99
R0504:Kdm5b UTSW 1 134,621,023 (GRCm38) critical splice donor site probably null
R0505:Kdm5b UTSW 1 134,602,571 (GRCm38) missense probably damaging 0.96
R0521:Kdm5b UTSW 1 134,618,033 (GRCm38) missense possibly damaging 0.65
R1004:Kdm5b UTSW 1 134,588,904 (GRCm38) missense possibly damaging 0.71
R1087:Kdm5b UTSW 1 134,600,637 (GRCm38) missense probably damaging 1.00
R1126:Kdm5b UTSW 1 134,613,991 (GRCm38) missense possibly damaging 0.90
R1221:Kdm5b UTSW 1 134,599,091 (GRCm38) missense probably damaging 0.98
R1230:Kdm5b UTSW 1 134,613,254 (GRCm38) missense probably damaging 1.00
R1345:Kdm5b UTSW 1 134,630,550 (GRCm38) missense possibly damaging 0.94
R1482:Kdm5b UTSW 1 134,624,897 (GRCm38) missense probably damaging 1.00
R1582:Kdm5b UTSW 1 134,624,853 (GRCm38) missense probably damaging 0.99
R1653:Kdm5b UTSW 1 134,602,481 (GRCm38) missense probably damaging 1.00
R1693:Kdm5b UTSW 1 134,597,576 (GRCm38) splice site probably benign
R1721:Kdm5b UTSW 1 134,613,181 (GRCm38) splice site probably benign
R1741:Kdm5b UTSW 1 134,618,017 (GRCm38) missense possibly damaging 0.82
R1762:Kdm5b UTSW 1 134,604,467 (GRCm38) nonsense probably null
R1820:Kdm5b UTSW 1 134,597,670 (GRCm38) missense possibly damaging 0.87
R1872:Kdm5b UTSW 1 134,624,994 (GRCm38) missense probably damaging 1.00
R1966:Kdm5b UTSW 1 134,613,873 (GRCm38) splice site probably null
R2056:Kdm5b UTSW 1 134,613,214 (GRCm38) missense probably benign 0.05
R2059:Kdm5b UTSW 1 134,613,214 (GRCm38) missense probably benign 0.05
R2405:Kdm5b UTSW 1 134,609,016 (GRCm38) missense probably damaging 0.97
R3417:Kdm5b UTSW 1 134,587,977 (GRCm38) missense probably damaging 1.00
R3771:Kdm5b UTSW 1 134,613,345 (GRCm38) missense probably damaging 1.00
R3783:Kdm5b UTSW 1 134,630,542 (GRCm38) missense probably benign
R3803:Kdm5b UTSW 1 134,615,941 (GRCm38) missense probably benign 0.07
R3980:Kdm5b UTSW 1 134,619,670 (GRCm38) missense probably benign 0.11
R3983:Kdm5b UTSW 1 134,631,304 (GRCm38) missense possibly damaging 0.91
R4013:Kdm5b UTSW 1 134,627,329 (GRCm38) missense possibly damaging 0.86
R4162:Kdm5b UTSW 1 134,625,161 (GRCm38) missense probably benign 0.01
R4701:Kdm5b UTSW 1 134,606,012 (GRCm38) intron probably benign
R4836:Kdm5b UTSW 1 134,593,315 (GRCm38) splice site probably null
R4924:Kdm5b UTSW 1 134,631,351 (GRCm38) missense probably benign 0.00
R5135:Kdm5b UTSW 1 134,588,746 (GRCm38) intron probably benign
R5248:Kdm5b UTSW 1 134,620,997 (GRCm38) missense probably benign 0.11
R5290:Kdm5b UTSW 1 134,622,099 (GRCm38) splice site probably null
R5358:Kdm5b UTSW 1 134,607,694 (GRCm38) nonsense probably null
R5388:Kdm5b UTSW 1 134,608,897 (GRCm38) nonsense probably null
R5396:Kdm5b UTSW 1 134,622,098 (GRCm38) splice site probably null
R5397:Kdm5b UTSW 1 134,622,098 (GRCm38) splice site probably null
R5398:Kdm5b UTSW 1 134,622,098 (GRCm38) splice site probably null
R5399:Kdm5b UTSW 1 134,622,098 (GRCm38) splice site probably null
R5529:Kdm5b UTSW 1 134,588,003 (GRCm38) missense probably damaging 1.00
R5540:Kdm5b UTSW 1 134,631,241 (GRCm38) missense probably damaging 0.98
R5661:Kdm5b UTSW 1 134,599,073 (GRCm38) missense probably benign 0.01
R5663:Kdm5b UTSW 1 134,630,635 (GRCm38) missense probably benign
R5822:Kdm5b UTSW 1 134,588,773 (GRCm38) splice site probably benign
R6226:Kdm5b UTSW 1 134,608,878 (GRCm38) missense probably damaging 0.99
R6368:Kdm5b UTSW 1 134,599,207 (GRCm38) missense probably damaging 1.00
R6681:Kdm5b UTSW 1 134,613,269 (GRCm38) missense possibly damaging 0.90
R6715:Kdm5b UTSW 1 134,609,061 (GRCm38) critical splice donor site probably null
R7132:Kdm5b UTSW 1 134,599,106 (GRCm38) missense probably damaging 1.00
R7202:Kdm5b UTSW 1 134,624,759 (GRCm38) missense probably benign
R7258:Kdm5b UTSW 1 134,621,021 (GRCm38) missense probably damaging 1.00
R7335:Kdm5b UTSW 1 134,560,439 (GRCm38) missense probably damaging 1.00
R7420:Kdm5b UTSW 1 134,604,497 (GRCm38) missense probably benign 0.14
R7426:Kdm5b UTSW 1 134,595,833 (GRCm38) missense probably benign 0.02
R7452:Kdm5b UTSW 1 134,624,948 (GRCm38) missense probably damaging 1.00
R7595:Kdm5b UTSW 1 134,608,966 (GRCm38) missense probably benign 0.00
R7612:Kdm5b UTSW 1 134,624,918 (GRCm38) nonsense probably null
R7704:Kdm5b UTSW 1 134,587,931 (GRCm38) missense probably damaging 1.00
R7846:Kdm5b UTSW 1 134,617,840 (GRCm38) missense probably damaging 1.00
R8115:Kdm5b UTSW 1 134,619,673 (GRCm38) missense possibly damaging 0.83
R8146:Kdm5b UTSW 1 134,625,126 (GRCm38) missense probably benign 0.05
R8160:Kdm5b UTSW 1 134,613,919 (GRCm38) missense probably damaging 1.00
R8527:Kdm5b UTSW 1 134,605,774 (GRCm38) missense possibly damaging 0.78
R8542:Kdm5b UTSW 1 134,605,774 (GRCm38) missense possibly damaging 0.78
R8930:Kdm5b UTSW 1 134,616,272 (GRCm38) missense probably damaging 1.00
R8932:Kdm5b UTSW 1 134,616,272 (GRCm38) missense probably damaging 1.00
R8950:Kdm5b UTSW 1 134,613,926 (GRCm38) missense possibly damaging 0.84
R9089:Kdm5b UTSW 1 134,607,768 (GRCm38) missense probably damaging 0.98
R9109:Kdm5b UTSW 1 134,600,755 (GRCm38) critical splice donor site probably null
R9133:Kdm5b UTSW 1 134,602,585 (GRCm38) missense probably benign
R9298:Kdm5b UTSW 1 134,600,755 (GRCm38) critical splice donor site probably null
R9423:Kdm5b UTSW 1 134,587,967 (GRCm38) missense possibly damaging 0.85
R9630:Kdm5b UTSW 1 134,585,233 (GRCm38) critical splice donor site probably null
R9670:Kdm5b UTSW 1 134,630,502 (GRCm38) nonsense probably null
X0063:Kdm5b UTSW 1 134,588,876 (GRCm38) missense probably benign 0.07
Z1176:Kdm5b UTSW 1 134,625,035 (GRCm38) missense probably damaging 1.00
Z1177:Kdm5b UTSW 1 134,595,798 (GRCm38) frame shift probably null
Predicted Primers PCR Primer
(F):5'- CTATGACTTAGTGCGTAATGCTG -3'
(R):5'- AAGGGCACTCACTCCATCAG -3'

Sequencing Primer
(F):5'- GTGCGTAATGCTGAAACTCATTCC -3'
(R):5'- CCACCTTCTGAGCGCCG -3'
Posted On 2016-02-04