Incidental Mutation 'R5540:Kdm5b'
ID 435854
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 043098-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.451) question?
Stock # R5540 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 134487916-134560621 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 134558979 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 1501 (D1501G)
Ref Sequence ENSEMBL: ENSMUSP00000038138 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047714] [ENSMUST00000112198]
AlphaFold Q80Y84
Predicted Effect probably damaging
Transcript: ENSMUST00000047714
AA Change: D1501G

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: D1501G

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 benign
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: ENSMUST00000191572
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.6%
  • 20x: 96.1%
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: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700008O03Rik A G 7: 44,012,371 (GRCm39) S15P probably damaging Het
Actl7a A T 4: 56,744,388 (GRCm39) H305L probably benign Het
Adam26b C A 8: 43,974,654 (GRCm39) C116F probably damaging Het
Adgrl2 A G 3: 148,543,198 (GRCm39) probably null Het
Akr1b10 A G 6: 34,371,047 (GRCm39) T238A probably damaging Het
Akr1c18 A G 13: 4,187,178 (GRCm39) V186A probably benign Het
Alpk3 G A 7: 80,745,184 (GRCm39) V1311M probably damaging Het
Aox1 A G 1: 58,143,569 (GRCm39) N1229S probably benign Het
Apobec3 T A 15: 79,782,120 (GRCm39) N43K probably benign Het
Arid1a A C 4: 133,407,765 (GRCm39) D2247E unknown Het
Asph A G 4: 9,635,906 (GRCm39) L77S probably damaging Het
Cd300ld T A 11: 114,878,231 (GRCm39) T94S probably damaging Het
Celf2 T C 2: 6,558,743 (GRCm39) T382A probably benign Het
Cfap54 C T 10: 92,808,470 (GRCm39) A1402T possibly damaging Het
Chrnb1 A T 11: 69,686,476 (GRCm39) V48E probably benign Het
Col6a5 T A 9: 105,739,975 (GRCm39) E2548V probably benign Het
Crebrf A G 17: 26,961,071 (GRCm39) D56G possibly damaging Het
Dctn5 A G 7: 121,734,275 (GRCm39) T40A probably benign Het
Dmxl2 A T 9: 54,301,141 (GRCm39) N2323K probably benign Het
Dync1h1 A G 12: 110,627,384 (GRCm39) Q4021R probably benign Het
Dyrk1a T G 16: 94,486,202 (GRCm39) probably null Het
Ephb3 T A 16: 21,039,610 (GRCm39) F454Y probably damaging Het
Fbxo38 A G 18: 62,647,864 (GRCm39) probably null Het
Flg T C 3: 93,184,923 (GRCm39) F15S probably damaging Het
Fndc3b G A 3: 27,555,651 (GRCm39) P301L probably damaging Het
Fpr-rs7 C T 17: 20,334,356 (GRCm39) G45R probably damaging Het
Garin3 A G 11: 46,295,715 (GRCm39) N29S probably damaging Het
Gfi1 T A 5: 107,867,991 (GRCm39) T360S probably damaging Het
Grik4 T C 9: 42,432,243 (GRCm39) H918R probably damaging Het
Hpx A G 7: 105,241,119 (GRCm39) S385P possibly damaging Het
Kif20b A T 19: 34,915,860 (GRCm39) M546L probably benign Het
Map3k9 G T 12: 81,819,587 (GRCm39) N222K probably damaging Het
Me1 A G 9: 86,561,926 (GRCm39) L53P possibly damaging Het
Mis18bp1 T C 12: 65,195,520 (GRCm39) E748G possibly damaging Het
Morc3 T A 16: 93,644,268 (GRCm39) N186K probably benign Het
Mtor A G 4: 148,539,165 (GRCm39) T221A probably benign Het
Muc6 A G 7: 141,235,850 (GRCm39) probably null Het
Myh8 C A 11: 67,177,266 (GRCm39) T444N probably benign Het
Myo7b A G 18: 32,140,143 (GRCm39) Y216H probably damaging Het
Myom1 G A 17: 71,416,782 (GRCm39) V1382M probably damaging Het
Nbeal2 A T 9: 110,460,801 (GRCm39) Y1718N probably damaging Het
Npc1l1 A G 11: 6,164,546 (GRCm39) S1168P probably damaging Het
Or4c58 A G 2: 89,675,011 (GRCm39) F102S probably damaging Het
Or4d2 T A 11: 87,784,511 (GRCm39) K80* probably null Het
Or51f5 C T 7: 102,424,136 (GRCm39) A135V probably benign Het
Or5an9 T A 19: 12,187,824 (GRCm39) I298N probably damaging Het
Or6c8b G T 10: 128,882,364 (GRCm39) D189E probably damaging Het
Pcdha4 C A 18: 37,087,890 (GRCm39) A691E probably benign Het
Pde6a T G 18: 61,364,438 (GRCm39) F165V probably damaging Het
Ptpn14 A T 1: 189,578,561 (GRCm39) M340L probably benign Het
Rnasel G T 1: 153,630,890 (GRCm39) E469* probably null Het
Rsph3a T G 17: 8,164,790 (GRCm39) L50R probably benign Het
Rusc2 A G 4: 43,423,975 (GRCm39) Y1043C probably damaging Het
Serpinb6b A T 13: 33,161,541 (GRCm39) K86* probably null Het
Serpine1 T C 5: 137,092,063 (GRCm39) T392A probably benign Het
Shcbp1 A T 8: 4,794,529 (GRCm39) D421E probably damaging Het
Slc24a1 A G 9: 64,855,863 (GRCm39) V348A unknown Het
Slc26a7 A G 4: 14,506,621 (GRCm39) F605L probably benign Het
Slc66a1 A T 4: 139,027,655 (GRCm39) L229Q probably damaging Het
Spag17 A C 3: 99,963,588 (GRCm39) E1102A possibly damaging Het
Stab2 A G 10: 86,683,989 (GRCm39) V2390A probably benign Het
Stk11 A G 10: 79,961,883 (GRCm39) I35V probably benign Het
Stk24 T C 14: 121,531,693 (GRCm39) D321G possibly damaging Het
Tbx4 A T 11: 85,801,994 (GRCm39) N209I possibly damaging Het
Tmem225 T C 9: 40,060,681 (GRCm39) L80P probably damaging Het
Tnfrsf4 C T 4: 156,098,380 (GRCm39) T17I probably benign Het
Traf3ip1 G A 1: 91,429,037 (GRCm39) R268Q probably benign Het
Trhde T A 10: 114,636,497 (GRCm39) I237F probably benign Het
Ugt2a1 A T 5: 87,633,915 (GRCm39) W231R probably damaging Het
Vash1 ACTGCTGCTGCTGCTGCTGC ACTGCTGCTGCTGCTGC 12: 86,726,831 (GRCm39) probably benign Het
Vps16 T A 2: 130,284,305 (GRCm39) D685E probably benign Het
Washc4 A G 10: 83,409,657 (GRCm39) D602G probably damaging Het
Wdr59 A G 8: 112,211,816 (GRCm39) L377P possibly damaging Het
Wdr81 T C 11: 75,339,896 (GRCm39) E1364G probably damaging 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
R5396:Kdm5b UTSW 1 134,549,836 (GRCm39) splice site 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
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'- TTTGCTTACTGTCACAGGGC -3'
(R):5'- AGCTTTGCTGAGATTGAGGAAATC -3'

Sequencing Primer
(F):5'- TTACTGTCACAGGGCAGCACTG -3'
(R):5'- GAGGAAATCTTCTTTATTGGAGTCC -3'
Posted On 2016-10-24