Incidental Mutation 'R5396:Kdm5b'
ID 429625
Institutional Source Beutler Lab
Gene Symbol Kdm5b
Ensembl Gene ENSMUSG00000042207
Gene Name lysine demethylase 5B
Synonyms 2010009J12Rik, PLU-1, Rb-Bp2, Jarid1b, D1Ertd202e, Plu1, 2210016I17Rik
MMRRC Submission 044394-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.451) question?
Stock # R5396 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 134487916-134560621 bp(+) (GRCm39)
Type of Mutation splice site (5 bp from exon)
DNA Base Change (assembly) G to A at 134549836 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
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 null
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 probably null
Transcript: ENSMUST00000112198
SMART Domains Protein: ENSMUSP00000107817
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 692 745 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: ENSMUST00000133725
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191572
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.5%
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: 88 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1810024B03Rik T C 2: 127,028,873 (GRCm39) T109A probably damaging Het
A430005L14Rik GCC G 4: 154,045,410 (GRCm39) probably null Het
Actr1a T C 19: 46,384,103 (GRCm39) D5G possibly damaging Het
Adra2c A G 5: 35,438,217 (GRCm39) T330A probably benign Het
Ahcyl2 C T 6: 29,859,697 (GRCm39) probably benign Het
Ahnak T C 19: 8,984,539 (GRCm39) V1941A probably damaging Het
Akr1b7 G A 6: 34,389,411 (GRCm39) probably null Het
Anapc15 C T 7: 101,547,810 (GRCm39) P68L probably damaging Het
Ank2 A G 3: 126,746,875 (GRCm39) V570A probably damaging Het
Ano4 T C 10: 88,948,702 (GRCm39) E302G probably damaging Het
Bop1 A T 15: 76,339,489 (GRCm39) H285Q probably damaging Het
Btbd19 G A 4: 116,980,957 (GRCm39) A104V probably damaging Het
Catsperb A T 12: 101,560,543 (GRCm39) I845L possibly damaging Het
Ccdc28b G T 4: 129,513,238 (GRCm39) Q184K probably damaging Het
Cd101 A G 3: 100,926,126 (GRCm39) S198P probably damaging Het
Cdc7 A T 5: 107,117,163 (GRCm39) probably null Het
Cdhr2 A G 13: 54,884,269 (GRCm39) D1268G probably benign Het
Celsr3 C T 9: 108,705,781 (GRCm39) R755W probably damaging Het
Chrnb1 T A 11: 69,684,979 (GRCm39) N117I probably damaging Het
Chst11 C A 10: 83,027,083 (GRCm39) P170Q probably damaging Het
Clca3b A G 3: 144,552,932 (GRCm39) Y98H probably damaging Het
Crnkl1 A G 2: 145,770,132 (GRCm39) V237A possibly damaging Het
Ctnnbl1 G A 2: 157,659,752 (GRCm39) probably null Het
Dbndd1 C A 8: 124,236,582 (GRCm39) R95S probably damaging Het
Ddx3y A G Y: 1,265,965 (GRCm39) V344A probably damaging Het
Defb30 A T 14: 63,273,559 (GRCm39) probably null Het
Dennd10 T C 19: 60,823,274 (GRCm39) L303P probably benign Het
Dnah17 C T 11: 118,018,108 (GRCm39) R129Q probably benign Het
Dnhd1 A T 7: 105,362,891 (GRCm39) M3818L probably benign Het
Dusp4 G T 8: 35,284,458 (GRCm39) D258Y probably damaging Het
E2f1 A T 2: 154,406,368 (GRCm39) F103I probably benign Het
Elavl2 T C 4: 91,149,055 (GRCm39) Y248C probably damaging Het
Ephb3 T C 16: 21,037,855 (GRCm39) V310A possibly damaging Het
Erbin A G 13: 103,993,917 (GRCm39) probably null Het
Etv4 A T 11: 101,666,167 (GRCm39) H120Q probably damaging Het
Fcgbpl1 T C 7: 27,839,608 (GRCm39) F474L probably benign Het
Flot2 T A 11: 77,940,314 (GRCm39) C20* probably null Het
Fsip2 G A 2: 82,821,262 (GRCm39) G5665D probably benign Het
Gad1-ps G A 10: 99,281,009 (GRCm39) noncoding transcript Het
Glrp1 TTGGTGCTGCTGGTGCTGCTGGTGCTGCTGGTGCTGCTGGTGCTGCTGGTGCTGTTGGTGCTGCTGGTGCTGCTGGTGCTGCTGGTGCTGCTGGTGCTGCTGGTGCTGTTGGTGCTGCTGGTGCTGCTG TTGGTGCTGCTGGTGCTGCTGGTGCTGCTGGTGCTGCTGGTGCTGTTGGTGCTGCTGGTGCTGCTGGTGCTGCTGGTGCTGCTGGTGCTGCTGGTGCTGTTGGTGCTGCTGGTGCTGCTG 1: 88,431,066 (GRCm39) probably benign Het
Gm43302 A T 5: 105,427,955 (GRCm39) L202* probably null Het
Gm4787 G C 12: 81,424,604 (GRCm39) T518S probably benign Het
Hnf1b A T 11: 83,746,863 (GRCm39) M160L probably damaging Het
Inhbe T C 10: 127,186,470 (GRCm39) T237A possibly damaging Het
Kmt2c A T 5: 25,499,732 (GRCm39) probably null Het
Kyat3 A G 3: 142,440,367 (GRCm39) K364E probably benign Het
Lars1 T A 18: 42,350,024 (GRCm39) T927S probably benign Het
Mfap1b A T 2: 121,304,371 (GRCm39) M8K probably benign Het
Mroh8 G A 2: 157,070,576 (GRCm39) P592S possibly damaging Het
Myo3b A T 2: 69,957,329 (GRCm39) I185L probably damaging Het
Or1e16 AGCGGTCGTAGGC AGC 11: 73,286,480 (GRCm39) probably null Het
Or1x6 C T 11: 50,939,297 (GRCm39) A121V probably damaging Het
Or4c110 A T 2: 88,832,540 (GRCm39) L31M probably benign Het
Or51a24 T C 7: 103,734,098 (GRCm39) Y63C probably benign Het
Pcdha8 T A 18: 37,126,787 (GRCm39) V423E probably damaging Het
Pcdhb21 G T 18: 37,648,772 (GRCm39) V634L probably benign Het
Pde8a T C 7: 80,983,170 (GRCm39) V791A probably damaging Het
Pds5a A G 5: 65,795,920 (GRCm39) S657P probably benign Het
Pes1 CGGAGGAGGAGGAGGAGGAGGAGG CGGAGGAGGAGGAGGAGGAGG 11: 3,927,719 (GRCm39) probably benign Het
Rad51d A G 11: 82,781,196 (GRCm39) V17A possibly damaging Het
Sdc1 A T 12: 8,841,743 (GRCm39) probably null Het
Sdcbp2 T A 2: 151,429,057 (GRCm39) I152N probably damaging Het
Slc4a4 G T 5: 89,194,076 (GRCm39) M141I probably benign Het
Sntb1 C G 15: 55,506,191 (GRCm39) G461R probably damaging Het
Spata6 T C 4: 111,656,315 (GRCm39) C320R probably damaging Het
Spata6l T C 19: 28,905,089 (GRCm39) H325R possibly damaging Het
Ssu2 T A 6: 112,357,957 (GRCm39) T129S probably damaging Het
Stat5a T A 11: 100,771,409 (GRCm39) W631R probably damaging Het
Sult1c2 T A 17: 54,143,939 (GRCm39) N122I possibly damaging Het
Synpo2 G A 3: 122,911,331 (GRCm39) Q105* probably null Het
Tert G A 13: 73,787,362 (GRCm39) V783I probably damaging Het
Ticam1 G T 17: 56,578,117 (GRCm39) T326K probably benign Het
Tmem63b T C 17: 45,980,888 (GRCm39) M269V possibly damaging Het
Tmem86a T A 7: 46,702,794 (GRCm39) V73E possibly damaging Het
Trpv4 G A 5: 114,761,675 (GRCm39) R818C possibly damaging Het
Tstd2 A G 4: 46,135,542 (GRCm39) S4P probably benign Het
Ttn A T 2: 76,644,715 (GRCm39) V4686E probably damaging Het
Ubash3b A G 9: 40,954,769 (GRCm39) probably null Het
Usp31 A G 7: 121,267,005 (GRCm39) probably null Het
Usp33 A G 3: 152,089,824 (GRCm39) E780G possibly damaging Het
Vapb T A 2: 173,613,336 (GRCm39) Y78* probably null Het
Vps13b G A 15: 35,887,094 (GRCm39) R3227Q probably damaging Het
Vps33a A T 5: 123,696,693 (GRCm39) I320N probably damaging Het
Wnt5a T C 14: 28,244,727 (GRCm39) C305R probably damaging Het
Zbtb38 A G 9: 96,569,696 (GRCm39) C463R probably damaging Het
Zc3h12d G A 10: 7,742,090 (GRCm39) C263Y probably damaging Het
Zfp971 G A 2: 177,675,526 (GRCm39) R375Q probably damaging Het
Znrf1 T A 8: 112,345,826 (GRCm39) probably null Het
Other mutations in Kdm5b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00230:Kdm5b APN 1 134,548,693 (GRCm39) missense probably damaging 1.00
IGL01458:Kdm5b APN 1 134,549,724 (GRCm39) missense possibly damaging 0.53
IGL01567:Kdm5b APN 1 134,530,278 (GRCm39) missense probably damaging 1.00
IGL01625:Kdm5b APN 1 134,545,706 (GRCm39) missense possibly damaging 0.74
IGL01970:Kdm5b APN 1 134,528,465 (GRCm39) missense probably damaging 1.00
IGL02183:Kdm5b APN 1 134,552,669 (GRCm39) missense probably benign 0.09
IGL02592:Kdm5b APN 1 134,552,591 (GRCm39) missense probably damaging 0.99
IGL02695:Kdm5b APN 1 134,532,223 (GRCm39) missense possibly damaging 0.94
IGL02697:Kdm5b APN 1 134,516,511 (GRCm39) splice site probably benign
IGL03036:Kdm5b APN 1 134,536,675 (GRCm39) missense probably damaging 1.00
IGL03056:Kdm5b APN 1 134,515,717 (GRCm39) missense probably damaging 0.99
IGL03206:Kdm5b APN 1 134,555,055 (GRCm39) missense probably benign
IGL03342:Kdm5b APN 1 134,530,314 (GRCm39) missense probably benign 0.00
IGL03388:Kdm5b APN 1 134,555,060 (GRCm39) missense probably benign
amaryllis UTSW 1 134,536,799 (GRCm39) critical splice donor site probably null
PIT4486001:Kdm5b UTSW 1 134,556,423 (GRCm39) missense probably damaging 1.00
R0233:Kdm5b UTSW 1 134,532,372 (GRCm39) splice site probably benign
R0334:Kdm5b UTSW 1 134,532,260 (GRCm39) missense probably damaging 0.99
R0504:Kdm5b UTSW 1 134,548,761 (GRCm39) critical splice donor site probably null
R0505:Kdm5b UTSW 1 134,530,309 (GRCm39) missense probably damaging 0.96
R0521:Kdm5b UTSW 1 134,545,771 (GRCm39) missense possibly damaging 0.65
R1004:Kdm5b UTSW 1 134,516,642 (GRCm39) missense possibly damaging 0.71
R1087:Kdm5b UTSW 1 134,528,375 (GRCm39) missense probably damaging 1.00
R1126:Kdm5b UTSW 1 134,541,729 (GRCm39) missense possibly damaging 0.90
R1221:Kdm5b UTSW 1 134,526,829 (GRCm39) missense probably damaging 0.98
R1230:Kdm5b UTSW 1 134,540,992 (GRCm39) missense probably damaging 1.00
R1345:Kdm5b UTSW 1 134,558,288 (GRCm39) missense possibly damaging 0.94
R1482:Kdm5b UTSW 1 134,552,635 (GRCm39) missense probably damaging 1.00
R1582:Kdm5b UTSW 1 134,552,591 (GRCm39) missense probably damaging 0.99
R1653:Kdm5b UTSW 1 134,530,219 (GRCm39) missense probably damaging 1.00
R1693:Kdm5b UTSW 1 134,525,314 (GRCm39) splice site probably benign
R1721:Kdm5b UTSW 1 134,540,919 (GRCm39) splice site probably benign
R1741:Kdm5b UTSW 1 134,545,755 (GRCm39) missense possibly damaging 0.82
R1762:Kdm5b UTSW 1 134,532,205 (GRCm39) nonsense probably null
R1820:Kdm5b UTSW 1 134,525,408 (GRCm39) missense possibly damaging 0.87
R1872:Kdm5b UTSW 1 134,552,732 (GRCm39) missense probably damaging 1.00
R1966:Kdm5b UTSW 1 134,541,611 (GRCm39) splice site probably null
R2056:Kdm5b UTSW 1 134,540,952 (GRCm39) missense probably benign 0.05
R2059:Kdm5b UTSW 1 134,540,952 (GRCm39) missense probably benign 0.05
R2405:Kdm5b UTSW 1 134,536,754 (GRCm39) missense probably damaging 0.97
R3417:Kdm5b UTSW 1 134,515,715 (GRCm39) missense probably damaging 1.00
R3771:Kdm5b UTSW 1 134,541,083 (GRCm39) missense probably damaging 1.00
R3783:Kdm5b UTSW 1 134,558,280 (GRCm39) missense probably benign
R3803:Kdm5b UTSW 1 134,543,679 (GRCm39) missense probably benign 0.07
R3980:Kdm5b UTSW 1 134,547,408 (GRCm39) missense probably benign 0.11
R3983:Kdm5b UTSW 1 134,559,042 (GRCm39) missense possibly damaging 0.91
R4013:Kdm5b UTSW 1 134,555,067 (GRCm39) missense possibly damaging 0.86
R4162:Kdm5b UTSW 1 134,552,899 (GRCm39) missense probably benign 0.01
R4701:Kdm5b UTSW 1 134,533,750 (GRCm39) intron probably benign
R4791:Kdm5b UTSW 1 134,558,538 (GRCm39) missense possibly damaging 0.82
R4836:Kdm5b UTSW 1 134,521,053 (GRCm39) splice site probably null
R4924:Kdm5b UTSW 1 134,559,089 (GRCm39) missense probably benign 0.00
R5135:Kdm5b UTSW 1 134,516,484 (GRCm39) intron probably benign
R5248:Kdm5b UTSW 1 134,548,735 (GRCm39) missense probably benign 0.11
R5290:Kdm5b UTSW 1 134,549,837 (GRCm39) splice site probably null
R5358:Kdm5b UTSW 1 134,535,432 (GRCm39) nonsense probably null
R5388:Kdm5b UTSW 1 134,536,635 (GRCm39) nonsense probably null
R5397:Kdm5b UTSW 1 134,549,836 (GRCm39) splice site probably null
R5398:Kdm5b UTSW 1 134,549,836 (GRCm39) splice site probably null
R5399:Kdm5b UTSW 1 134,549,836 (GRCm39) splice site probably null
R5529:Kdm5b UTSW 1 134,515,741 (GRCm39) missense probably damaging 1.00
R5540:Kdm5b UTSW 1 134,558,979 (GRCm39) missense probably damaging 0.98
R5661:Kdm5b UTSW 1 134,526,811 (GRCm39) missense probably benign 0.01
R5663:Kdm5b UTSW 1 134,558,373 (GRCm39) missense probably benign
R5822:Kdm5b UTSW 1 134,516,511 (GRCm39) splice site probably benign
R6226:Kdm5b UTSW 1 134,536,616 (GRCm39) missense probably damaging 0.99
R6368:Kdm5b UTSW 1 134,526,945 (GRCm39) missense probably damaging 1.00
R6681:Kdm5b UTSW 1 134,541,007 (GRCm39) missense possibly damaging 0.90
R6715:Kdm5b UTSW 1 134,536,799 (GRCm39) critical splice donor site probably null
R7132:Kdm5b UTSW 1 134,526,844 (GRCm39) missense probably damaging 1.00
R7202:Kdm5b UTSW 1 134,552,497 (GRCm39) missense probably benign
R7258:Kdm5b UTSW 1 134,548,759 (GRCm39) missense probably damaging 1.00
R7335:Kdm5b UTSW 1 134,488,177 (GRCm39) missense probably damaging 1.00
R7420:Kdm5b UTSW 1 134,532,235 (GRCm39) missense probably benign 0.14
R7426:Kdm5b UTSW 1 134,523,571 (GRCm39) missense probably benign 0.02
R7452:Kdm5b UTSW 1 134,552,686 (GRCm39) missense probably damaging 1.00
R7595:Kdm5b UTSW 1 134,536,704 (GRCm39) missense probably benign 0.00
R7612:Kdm5b UTSW 1 134,552,656 (GRCm39) nonsense probably null
R7704:Kdm5b UTSW 1 134,515,669 (GRCm39) missense probably damaging 1.00
R7846:Kdm5b UTSW 1 134,545,578 (GRCm39) missense probably damaging 1.00
R8115:Kdm5b UTSW 1 134,547,411 (GRCm39) missense possibly damaging 0.83
R8146:Kdm5b UTSW 1 134,552,864 (GRCm39) missense probably benign 0.05
R8160:Kdm5b UTSW 1 134,541,657 (GRCm39) missense probably damaging 1.00
R8527:Kdm5b UTSW 1 134,533,512 (GRCm39) missense possibly damaging 0.78
R8542:Kdm5b UTSW 1 134,533,512 (GRCm39) missense possibly damaging 0.78
R8930:Kdm5b UTSW 1 134,544,010 (GRCm39) missense probably damaging 1.00
R8932:Kdm5b UTSW 1 134,544,010 (GRCm39) missense probably damaging 1.00
R8950:Kdm5b UTSW 1 134,541,664 (GRCm39) missense possibly damaging 0.84
R9089:Kdm5b UTSW 1 134,535,506 (GRCm39) missense probably damaging 0.98
R9109:Kdm5b UTSW 1 134,528,493 (GRCm39) critical splice donor site probably null
R9133:Kdm5b UTSW 1 134,530,323 (GRCm39) missense probably benign
R9298:Kdm5b UTSW 1 134,528,493 (GRCm39) critical splice donor site probably null
R9423:Kdm5b UTSW 1 134,515,705 (GRCm39) missense possibly damaging 0.85
R9630:Kdm5b UTSW 1 134,512,971 (GRCm39) critical splice donor site probably null
R9670:Kdm5b UTSW 1 134,558,240 (GRCm39) nonsense probably null
X0063:Kdm5b UTSW 1 134,516,614 (GRCm39) missense probably benign 0.07
Z1176:Kdm5b UTSW 1 134,552,773 (GRCm39) missense probably damaging 1.00
Z1177:Kdm5b UTSW 1 134,523,536 (GRCm39) frame shift probably null
Predicted Primers PCR Primer
(F):5'- GAAGTCTGTTTCACCATTGGC -3'
(R):5'- CTCATTAATGCCAGGCAAGGG -3'

Sequencing Primer
(F):5'- GGCTCTGTTTTCTCTTACATTAGG -3'
(R):5'- AGGCAAGGGCTTTACCACTG -3'
Posted On 2016-09-06