Incidental Mutation 'R2061:Kdm5a'
ID 316243
Institutional Source Beutler Lab
Gene Symbol Kdm5a
Ensembl Gene ENSMUSG00000030180
Gene Name lysine demethylase 5A
Synonyms Rbbp2, Jarid1a, RBP2
MMRRC Submission 040066-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2061 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 120341085-120421535 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 120358578 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Leucine at position 207 (R207L)
Ref Sequence ENSEMBL: ENSMUSP00000145021 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005108] [ENSMUST00000132009] [ENSMUST00000135802] [ENSMUST00000203373]
AlphaFold Q3UXZ9
Predicted Effect probably benign
Transcript: ENSMUST00000005108
AA Change: R207L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: R207L

DomainStartEndE-ValueType
JmjN 18 59 4.06e-20 SMART
ARID 81 170 4.76e-35 SMART
BRIGHT 85 175 2.48e-31 SMART
PHD 295 341 1.16e-14 SMART
Blast:JmjC 384 436 2e-22 BLAST
JmjC 437 603 5.88e-73 SMART
low complexity region 638 651 N/A INTRINSIC
Pfam:zf-C5HC2 676 729 1.3e-21 PFAM
Pfam:PLU-1 740 1072 1.2e-104 PFAM
low complexity region 1091 1119 N/A INTRINSIC
PHD 1163 1216 1.37e-11 SMART
low complexity region 1269 1280 N/A INTRINSIC
low complexity region 1337 1351 N/A INTRINSIC
low complexity region 1403 1414 N/A INTRINSIC
low complexity region 1494 1512 N/A INTRINSIC
coiled coil region 1534 1579 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000122505
Predicted Effect probably benign
Transcript: ENSMUST00000132009
AA Change: R207L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000145375
Gene: ENSMUSG00000030180
AA Change: R207L

DomainStartEndE-ValueType
JmjN 18 59 4.06e-20 SMART
ARID 81 170 4.76e-35 SMART
BRIGHT 85 175 2.48e-31 SMART
PHD 295 341 1.16e-14 SMART
JmjC 437 603 1.47e-64 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000135802
AA Change: R207L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180
AA Change: R207L

DomainStartEndE-ValueType
JmjN 18 59 1.7e-22 SMART
ARID 81 170 3.6e-39 SMART
BRIGHT 85 175 1.2e-33 SMART
PHD 295 341 7.3e-17 SMART
Blast:JmjC 384 436 2e-22 BLAST
JmjC 437 603 2.2e-75 SMART
low complexity region 638 651 N/A INTRINSIC
Pfam:zf-C5HC2 676 728 6.3e-15 PFAM
Pfam:PLU-1 741 811 9.8e-16 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000203373
SMART Domains Protein: ENSMUSP00000144720
Gene: ENSMUSG00000030180

DomainStartEndE-ValueType
BRIGHT 1 53 8.4e-4 SMART
Blast:JmjC 58 153 3e-56 BLAST
PDB:2E6R|A 121 152 4e-9 PDB
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.9%
Validation Efficiency 99% (124/125)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the Jumonji, AT-rich interactive domain 1 (JARID1) histone demethylase protein family. The encoded protein plays a role in gene regulation through the histone code by specifically demethylating lysine 4 of histone H3. The encoded protein interacts with many other proteins, including retinoblastoma protein, and is implicated in the transcriptional regulation of Hox genes and cytokines. This gene may play a role in tumor progression. [provided by RefSeq, Aug 2013]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit reduced body size, abnormal involuntary movement and quantitative changes in the hematopoietic stem cell and myeloid progenitor compartments, consistent with enhanced survival and increased cycling. Neonatalsurvival is sensitive to genetic background. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 122 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A4gnt T C 9: 99,502,412 (GRCm39) S191P probably damaging Het
Ak2 C T 4: 128,901,990 (GRCm39) A221V probably damaging Het
Akap9 T A 5: 4,011,010 (GRCm39) V571E probably damaging Het
Amph G T 13: 19,309,205 (GRCm39) E428* probably null Het
Armh3 C T 19: 45,967,106 (GRCm39) R12Q probably damaging Het
Arnt2 T A 7: 83,993,078 (GRCm39) D154V probably damaging Het
Arrdc1 G A 2: 24,816,364 (GRCm39) Q202* probably null Het
Ate1 A G 7: 130,112,643 (GRCm39) C72R probably damaging Het
Atox1 A G 11: 55,345,724 (GRCm39) V22A possibly damaging Het
Bbs12 A T 3: 37,373,215 (GRCm39) M3L probably damaging Het
Bfsp1 A G 2: 143,704,598 (GRCm39) V85A probably benign Het
Bltp2 T A 11: 78,159,575 (GRCm39) C541* probably null Het
Caskin2 C A 11: 115,694,456 (GRCm39) V382F probably benign Het
Ccdc39 T A 3: 33,874,045 (GRCm39) M596L probably damaging Het
Cd22 C T 7: 30,569,530 (GRCm39) V529M probably damaging Het
Cd22 A C 7: 30,575,581 (GRCm39) Y154D probably benign Het
Cdadc1 T A 14: 59,818,783 (GRCm39) E348D probably damaging Het
Cdhr2 T C 13: 54,868,631 (GRCm39) V531A probably damaging Het
Cdk11b A G 4: 155,726,061 (GRCm39) probably benign Het
Cebpa G T 7: 34,818,947 (GRCm39) R35L probably damaging Het
Chat T C 14: 32,168,830 (GRCm39) N235S probably benign Het
Col12a1 T A 9: 79,524,987 (GRCm39) I2725F possibly damaging Het
Cracr2b A G 7: 141,045,193 (GRCm39) E231G probably damaging Het
Cryaa G T 17: 31,900,029 (GRCm39) A151S probably benign Het
Cspg4b T A 13: 113,454,628 (GRCm39) W225R probably damaging Het
Dab1 A T 4: 104,535,938 (GRCm39) I116F probably damaging Het
Ddx43 C A 9: 78,303,386 (GRCm39) N75K probably benign Het
Dmbt1 T G 7: 130,700,863 (GRCm39) C1014G possibly damaging Het
Dner C A 1: 84,383,710 (GRCm39) C558F probably damaging Het
Dsc2 A G 18: 20,165,456 (GRCm39) V839A possibly damaging Het
Dsg3 C T 18: 20,660,794 (GRCm39) R378* probably null Het
Ecpas G T 4: 58,824,270 (GRCm39) P1116T probably damaging Het
Emilin1 C T 5: 31,075,082 (GRCm39) P441L possibly damaging Het
Epha6 T C 16: 59,476,160 (GRCm39) M1069V probably damaging Het
F930017D23Rik A C 10: 43,480,416 (GRCm39) noncoding transcript Het
Faf1 A T 4: 109,568,005 (GRCm39) N22Y probably damaging Het
Flrt3 A T 2: 140,503,373 (GRCm39) V85E probably damaging Het
Gadl1 T A 9: 115,770,448 (GRCm39) I87N probably damaging Het
Galnt14 A G 17: 73,819,148 (GRCm39) F314S probably damaging Het
Gba2 A T 4: 43,574,029 (GRCm39) Y141* probably null Het
Gdap1 A T 1: 17,215,689 (GRCm39) probably benign Het
Gfod1 A T 13: 43,456,719 (GRCm39) probably null Het
Gm14295 C T 2: 176,502,474 (GRCm39) R655* probably null Het
Gm4353 A G 7: 115,682,934 (GRCm39) S216P probably damaging Het
Gm6605 T A 7: 38,147,706 (GRCm39) noncoding transcript Het
Hectd1 A T 12: 51,841,227 (GRCm39) D634E probably damaging Het
Helz2 A G 2: 180,882,337 (GRCm39) I152T probably damaging Het
Hivep1 A G 13: 42,313,600 (GRCm39) K1947E possibly damaging Het
Ifrd1 A T 12: 40,263,244 (GRCm39) F144L probably benign Het
Inhca T C 9: 103,145,513 (GRCm39) M395V probably benign Het
Itgae A T 11: 73,009,448 (GRCm39) Q544L probably benign Het
Jmjd1c A T 10: 67,054,205 (GRCm39) E323D probably damaging Het
Kif5b C T 18: 6,226,377 (GRCm39) probably null Het
Lbp T C 2: 158,166,499 (GRCm39) V351A probably benign Het
Lss A T 10: 76,381,932 (GRCm39) probably null Het
Madd A C 2: 90,991,831 (GRCm39) probably benign Het
Map6 G A 7: 98,966,679 (GRCm39) V503I probably damaging Het
Mark1 A G 1: 184,660,260 (GRCm39) L22P probably damaging Het
Mcfd2 T C 17: 87,563,404 (GRCm39) N130D probably damaging Het
Mcm3ap A G 10: 76,305,902 (GRCm39) N5S probably benign Het
Mdm4 A T 1: 132,940,389 (GRCm39) F48I probably damaging Het
Mga A T 2: 119,795,461 (GRCm39) probably benign Het
Mknk2 A T 10: 80,507,391 (GRCm39) probably null Het
Mmp15 T C 8: 96,097,407 (GRCm39) Y459H possibly damaging Het
Mthfd1l A G 10: 4,053,288 (GRCm39) K879R probably benign Het
Mycbp2 T C 14: 103,524,696 (GRCm39) K655E probably damaging Het
Nasp T C 4: 116,468,323 (GRCm39) N221D probably benign Het
Ndc80 T C 17: 71,821,213 (GRCm39) E245G probably benign Het
Nmral1 C T 16: 4,534,193 (GRCm39) E83K probably damaging Het
Noa1 T A 5: 77,452,034 (GRCm39) Q550L possibly damaging Het
Nutm1 A T 2: 112,086,097 (GRCm39) Y211* probably null Het
Or10n1 G T 9: 39,525,071 (GRCm39) M69I probably benign Het
Or10v1 T A 19: 11,873,921 (GRCm39) Y179N probably damaging Het
Or2ag18 A C 7: 106,404,975 (GRCm39) H231Q probably benign Het
Or4l1 T C 14: 50,166,478 (GRCm39) I174M possibly damaging Het
Or5b118 A G 19: 13,448,605 (GRCm39) I90M probably damaging Het
Otoa T C 7: 120,730,551 (GRCm39) F584L probably damaging Het
Palb2 G A 7: 121,723,748 (GRCm39) T304I possibly damaging Het
Pcolce2 A T 9: 95,552,229 (GRCm39) M121L probably benign Het
Pcsk5 T C 19: 17,432,236 (GRCm39) T1460A probably benign Het
Pdzrn4 A T 15: 92,668,041 (GRCm39) D731V probably damaging Het
Pex11b C A 3: 96,543,037 (GRCm39) Q12K possibly damaging Het
Pigw G C 11: 84,768,136 (GRCm39) Q398E probably benign Het
Pkd1 A G 17: 24,788,888 (GRCm39) E882G possibly damaging Het
Pkhd1 A T 1: 20,683,036 (GRCm39) N55K possibly damaging Het
Plch2 A T 4: 155,127,298 (GRCm39) probably benign Het
Plcl1 T A 1: 55,790,504 (GRCm39) L1058Q probably benign Het
Ppfia2 T C 10: 106,673,190 (GRCm39) S511P possibly damaging Het
Ppfibp2 T C 7: 107,338,437 (GRCm39) L676P probably damaging Het
Ppp6c T G 2: 39,116,186 (GRCm39) D23A probably damaging Het
Prss30 G A 17: 24,193,642 (GRCm39) probably benign Het
Ptprz1 T C 6: 23,049,674 (GRCm39) probably null Het
Rec114 T A 9: 58,560,188 (GRCm39) probably benign Het
Ryr2 T C 13: 11,680,764 (GRCm39) probably null Het
Ryr3 A T 2: 112,493,349 (GRCm39) I3715N possibly damaging Het
Scin T C 12: 40,130,947 (GRCm39) Y322C probably damaging Het
Scn3a A G 2: 65,291,652 (GRCm39) V1698A probably damaging Het
Scn5a G A 9: 119,314,717 (GRCm39) S1996L probably damaging Het
Serpinb2 A G 1: 107,450,525 (GRCm39) K174R possibly damaging Het
Slc16a4 T C 3: 107,208,027 (GRCm39) I179T probably benign Het
Slc35b1 T G 11: 95,276,718 (GRCm39) F102V possibly damaging Het
Slc66a2 G T 18: 80,334,930 (GRCm39) A232S probably benign Het
Slc6a15 A G 10: 103,245,595 (GRCm39) D526G probably benign Het
Spata16 A G 3: 26,978,519 (GRCm39) D495G probably damaging Het
Stk11ip G A 1: 75,506,228 (GRCm39) E583K possibly damaging Het
Stk-ps1 T G 17: 36,709,044 (GRCm39) noncoding transcript Het
Sufu T A 19: 46,385,651 (GRCm39) I37N probably damaging Het
Tacr1 C T 6: 82,469,535 (GRCm39) P140S probably damaging Het
Tas1r3 G A 4: 155,944,927 (GRCm39) R765C probably damaging Het
Tenm3 C T 8: 48,795,291 (GRCm39) probably null Het
Tex36 A T 7: 133,196,952 (GRCm39) I55N probably damaging Het
Tmem150c T C 5: 100,227,887 (GRCm39) Y192C probably damaging Het
Tmem237 A G 1: 59,159,445 (GRCm39) probably benign Het
Trim11 A G 11: 58,872,889 (GRCm39) E191G probably damaging Het
Ttll3 C T 6: 113,386,003 (GRCm39) A612V possibly damaging Het
Ttn G A 2: 76,807,466 (GRCm39) A89V probably damaging Het
Usp37 A G 1: 74,507,431 (GRCm39) F529L probably damaging Het
Vmn1r217 A C 13: 23,298,698 (GRCm39) V68G probably benign Het
Vwf T C 6: 125,568,151 (GRCm39) S349P probably damaging Het
Wt1 G A 2: 104,961,502 (GRCm39) probably null Het
Zcchc7 T A 4: 44,895,838 (GRCm39) L262H probably damaging Het
Zfp873 A G 10: 81,895,991 (GRCm39) S241G probably benign Het
Other mutations in Kdm5a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00540:Kdm5a APN 6 120,362,680 (GRCm39) critical splice donor site probably null 0.00
IGL00706:Kdm5a APN 6 120,383,597 (GRCm39) missense possibly damaging 0.44
IGL01361:Kdm5a APN 6 120,375,977 (GRCm39) missense probably damaging 1.00
IGL01402:Kdm5a APN 6 120,367,640 (GRCm39) nonsense probably null 0.00
IGL01924:Kdm5a APN 6 120,371,216 (GRCm39) critical splice donor site probably null 0.00
IGL01935:Kdm5a APN 6 120,385,284 (GRCm39) missense probably benign 0.02
IGL02165:Kdm5a APN 6 120,392,251 (GRCm39) missense probably damaging 1.00
IGL02472:Kdm5a APN 6 120,383,691 (GRCm39) splice site probably benign
IGL02506:Kdm5a APN 6 120,409,110 (GRCm39) missense probably damaging 0.99
IGL02604:Kdm5a APN 6 120,408,941 (GRCm39) missense probably benign
IGL02633:Kdm5a APN 6 120,341,680 (GRCm39) missense probably damaging 1.00
IGL02876:Kdm5a APN 6 120,367,605 (GRCm39) unclassified probably benign
IGL03009:Kdm5a APN 6 120,407,047 (GRCm39) missense probably damaging 0.98
IGL03027:Kdm5a APN 6 120,351,951 (GRCm39) splice site probably null
IGL03164:Kdm5a APN 6 120,415,980 (GRCm39) missense probably damaging 1.00
IGL03236:Kdm5a APN 6 120,415,949 (GRCm39) missense probably damaging 0.98
IGL03276:Kdm5a APN 6 120,379,669 (GRCm39) splice site probably benign
Anastasia UTSW 6 120,407,192 (GRCm39) nonsense probably null
Augmented UTSW 6 120,406,977 (GRCm39) intron probably benign
Calla_lily UTSW 6 120,381,983 (GRCm39) missense probably damaging 1.00
crocus UTSW 6 120,375,999 (GRCm39) missense probably null 0.98
Magnolia UTSW 6 120,375,939 (GRCm39) missense probably damaging 0.99
Saffron UTSW 6 120,366,581 (GRCm39) missense probably benign 0.19
Selbst UTSW 6 120,365,066 (GRCm39) nonsense probably null
R0320:Kdm5a UTSW 6 120,366,581 (GRCm39) missense probably benign 0.19
R0462:Kdm5a UTSW 6 120,379,561 (GRCm39) missense probably damaging 1.00
R0601:Kdm5a UTSW 6 120,379,632 (GRCm39) missense possibly damaging 0.76
R0628:Kdm5a UTSW 6 120,392,200 (GRCm39) missense probably damaging 1.00
R1024:Kdm5a UTSW 6 120,375,999 (GRCm39) missense probably null 0.98
R2013:Kdm5a UTSW 6 120,408,951 (GRCm39) missense probably benign 0.09
R2015:Kdm5a UTSW 6 120,408,951 (GRCm39) missense probably benign 0.09
R2188:Kdm5a UTSW 6 120,383,601 (GRCm39) missense possibly damaging 0.59
R3923:Kdm5a UTSW 6 120,358,625 (GRCm39) missense probably benign 0.01
R4013:Kdm5a UTSW 6 120,371,067 (GRCm39) missense probably damaging 1.00
R4016:Kdm5a UTSW 6 120,371,067 (GRCm39) missense probably damaging 1.00
R4017:Kdm5a UTSW 6 120,371,067 (GRCm39) missense probably damaging 1.00
R4030:Kdm5a UTSW 6 120,382,074 (GRCm39) nonsense probably null
R4646:Kdm5a UTSW 6 120,351,938 (GRCm39) missense possibly damaging 0.55
R4737:Kdm5a UTSW 6 120,382,976 (GRCm39) intron probably benign
R4779:Kdm5a UTSW 6 120,346,060 (GRCm39) unclassified probably benign
R4836:Kdm5a UTSW 6 120,389,363 (GRCm39) missense probably damaging 1.00
R5129:Kdm5a UTSW 6 120,381,983 (GRCm39) missense probably damaging 1.00
R5182:Kdm5a UTSW 6 120,365,066 (GRCm39) nonsense probably null
R5183:Kdm5a UTSW 6 120,406,977 (GRCm39) intron probably benign
R5572:Kdm5a UTSW 6 120,389,336 (GRCm39) missense possibly damaging 0.69
R6110:Kdm5a UTSW 6 120,389,267 (GRCm39) missense probably damaging 1.00
R6132:Kdm5a UTSW 6 120,351,892 (GRCm39) missense probably damaging 1.00
R6198:Kdm5a UTSW 6 120,415,958 (GRCm39) missense probably benign 0.37
R6246:Kdm5a UTSW 6 120,408,871 (GRCm39) missense probably damaging 0.97
R6336:Kdm5a UTSW 6 120,375,939 (GRCm39) missense probably damaging 0.99
R6343:Kdm5a UTSW 6 120,359,894 (GRCm39) missense probably benign 0.01
R6612:Kdm5a UTSW 6 120,407,189 (GRCm39) missense probably damaging 0.99
R6647:Kdm5a UTSW 6 120,389,422 (GRCm39) missense probably benign 0.25
R7068:Kdm5a UTSW 6 120,407,176 (GRCm39) missense probably benign 0.40
R7369:Kdm5a UTSW 6 120,408,965 (GRCm39) missense possibly damaging 0.67
R7380:Kdm5a UTSW 6 120,382,879 (GRCm39) missense probably benign 0.35
R7411:Kdm5a UTSW 6 120,403,776 (GRCm39) missense probably damaging 1.00
R7521:Kdm5a UTSW 6 120,409,148 (GRCm39) nonsense probably null
R7570:Kdm5a UTSW 6 120,404,803 (GRCm39) missense probably damaging 0.99
R7647:Kdm5a UTSW 6 120,404,747 (GRCm39) missense probably benign 0.01
R7704:Kdm5a UTSW 6 120,404,025 (GRCm39) missense probably damaging 1.00
R7796:Kdm5a UTSW 6 120,367,724 (GRCm39) missense probably damaging 1.00
R7875:Kdm5a UTSW 6 120,375,979 (GRCm39) nonsense probably null
R8265:Kdm5a UTSW 6 120,383,557 (GRCm39) missense possibly damaging 0.72
R8297:Kdm5a UTSW 6 120,358,516 (GRCm39) missense probably benign 0.00
R8336:Kdm5a UTSW 6 120,396,407 (GRCm39) missense probably benign 0.00
R8471:Kdm5a UTSW 6 120,407,192 (GRCm39) nonsense probably null
R8872:Kdm5a UTSW 6 120,365,101 (GRCm39) missense probably damaging 1.00
R8890:Kdm5a UTSW 6 120,366,624 (GRCm39) missense probably damaging 1.00
R9028:Kdm5a UTSW 6 120,416,092 (GRCm39) missense probably benign
R9064:Kdm5a UTSW 6 120,403,869 (GRCm39) small deletion probably benign
R9114:Kdm5a UTSW 6 120,382,887 (GRCm39) nonsense probably null
R9316:Kdm5a UTSW 6 120,381,973 (GRCm39) missense probably damaging 1.00
R9353:Kdm5a UTSW 6 120,404,730 (GRCm39) missense probably benign 0.01
R9412:Kdm5a UTSW 6 120,365,991 (GRCm39) missense probably damaging 1.00
R9416:Kdm5a UTSW 6 120,365,056 (GRCm39) missense probably damaging 1.00
R9431:Kdm5a UTSW 6 120,392,253 (GRCm39) missense probably damaging 1.00
R9711:Kdm5a UTSW 6 120,367,658 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GTTAGGGACTTATCTGGAAACTTG -3'
(R):5'- CCCCAAATGATTAAGTTCATGAGATCC -3'

Sequencing Primer
(F):5'- CTGGAAACTTGCTAATTTTTCTACTC -3'
(R):5'- TGACAGCCAAAGTTGTGTCC -3'
Posted On 2015-05-15