Incidental Mutation 'R6715:Kdm5b'
ID 529278
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 044833-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.356) question?
Stock # R6715 (G1)
Quality Score 225.009
Status Validated
Chromosome 1
Chromosomal Location 134560171-134635285 bp(+) (GRCm38)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to A at 134609061 bp (GRCm38)
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 noncoding transcript
Transcript: ENSMUST00000112197
SMART Domains Protein: ENSMUSP00000107816
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 225 236 N/A INTRINSIC
PHD 308 354 6.15e-14 SMART
JmjC 450 595 2.6e-24 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
Meta Mutation Damage Score 0.9505 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.6%
  • 20x: 92.9%
Validation Efficiency 100% (35/35)
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: 32 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adck1 G A 12: 88,459,080 (GRCm38) R426H probably damaging Het
Arl2 G A 19: 6,137,525 (GRCm38) R98C probably damaging Het
Atm A G 9: 53,531,648 (GRCm38) I105T probably damaging Het
Cnnm2 G A 19: 46,853,973 (GRCm38) G565E probably damaging Het
Ddx60 G A 8: 61,983,890 (GRCm38) G958D probably benign Het
Fbxo2 T A 4: 148,165,769 (GRCm38) M252K probably benign Het
Filip1 C A 9: 79,818,758 (GRCm38) A860S probably benign Het
Gm11992 C A 11: 9,061,214 (GRCm38) S218R probably damaging Het
Gnb3 A G 6: 124,837,728 (GRCm38) L69P possibly damaging Het
Gpr18 T G 14: 121,911,977 (GRCm38) H212P possibly damaging Het
Iqcb1 T C 16: 36,835,629 (GRCm38) F126S probably damaging Het
Katnip C T 7: 125,761,829 (GRCm38) Q104* probably null Het
Kcnh1 A G 1: 192,337,641 (GRCm38) D425G probably benign Het
Mcm3ap C T 10: 76,489,532 (GRCm38) T989M possibly damaging Het
Mtor T C 4: 148,538,547 (GRCm38) C1999R probably benign Het
Myo1c C T 11: 75,671,635 (GRCm38) P918S probably benign Het
Myof A T 19: 37,968,346 (GRCm38) D508E probably benign Het
Or52b2 A T 7: 105,337,332 (GRCm38) I128N probably damaging Het
Or56b2j G A 7: 104,703,956 (GRCm38) V130M possibly damaging Het
Or5l13 T A 2: 87,949,991 (GRCm38) M81L probably benign Het
Osbpl7 A G 11: 97,054,599 (GRCm38) H266R probably damaging Het
Pear1 T C 3: 87,759,117 (GRCm38) Y93C probably damaging Het
Pgr A G 9: 8,964,999 (GRCm38) H881R possibly damaging Het
Rfx1 A G 8: 84,095,815 (GRCm38) E914G possibly damaging Het
Samm50 T C 15: 84,211,058 (GRCm38) I415T probably benign Het
Snx7 T C 3: 117,782,336 (GRCm38) D434G possibly damaging Het
Susd4 G A 1: 182,892,037 (GRCm38) V406M probably benign Het
Syt15 G T 14: 34,222,862 (GRCm38) G122V probably damaging Het
Tlr5 A G 1: 182,972,659 (GRCm38) probably benign Het
Ttc6 T C 12: 57,674,770 (GRCm38) probably null Het
Vmn1r211 C A 13: 22,851,779 (GRCm38) M239I probably benign Het
Vps37a G T 8: 40,540,861 (GRCm38) probably null 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
R4791:Kdm5b UTSW 1 134,630,800 (GRCm38) missense possibly damaging 0.82
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
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'- ATTATCGCTTGCTGCACCG -3'
(R):5'- TTGCTGAGCTAGAACAAAGGC -3'

Sequencing Primer
(F):5'- GCTTGCTGCACCGTTATTG -3'
(R):5'- GTGTTAATCACCTTAGCCAGCAG -3'
Posted On 2018-07-24