Incidental Mutation 'R9114:Kdm5a'
ID 692408
Institutional Source Beutler Lab
Gene Symbol Kdm5a
Ensembl Gene ENSMUSG00000030180
Gene Name lysine demethylase 5A
Synonyms Rbbp2, Jarid1a, RBP2
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9114 (G1)
Quality Score 225.009
Status Not validated
Chromosome 6
Chromosomal Location 120341085-120421535 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) T to A at 120382887 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Stop codon at position 739 (Y739*)
Ref Sequence ENSEMBL: ENSMUSP00000005108 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005108] [ENSMUST00000132009] [ENSMUST00000135802]
AlphaFold Q3UXZ9
Predicted Effect probably null
Transcript: ENSMUST00000005108
AA Change: Y739*
SMART Domains Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: Y739*

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 probably benign
Transcript: ENSMUST00000132009
SMART Domains Protein: ENSMUSP00000145375
Gene: ENSMUSG00000030180

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 null
Transcript: ENSMUST00000135802
AA Change: Y739*
SMART Domains Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180
AA Change: Y739*

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.5%
Validation Efficiency
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb1a T A 5: 8,788,702 (GRCm39) L1027* probably null Het
Actl11 T A 9: 107,808,509 (GRCm39) M944K possibly damaging Het
Afap1l2 T C 19: 56,906,427 (GRCm39) K491E probably damaging Het
Ahr A T 12: 35,561,164 (GRCm39) D150E probably damaging Het
Arhgef1 T A 7: 24,607,304 (GRCm39) L17Q probably damaging Het
Bysl A G 17: 47,915,242 (GRCm39) S169P Het
C4b A T 17: 34,948,404 (GRCm39) F1610I probably damaging Het
Chtf8 C A 8: 107,612,481 (GRCm39) A153S probably benign Het
Ciapin1 C T 8: 95,558,400 (GRCm39) probably null Het
Cnnm1 A G 19: 43,429,395 (GRCm39) E171G possibly damaging Het
Crybb3 T C 5: 113,225,407 (GRCm39) N155S probably benign Het
Dclk3 T A 9: 111,317,683 (GRCm39) M773K probably benign Het
Ddx18 A T 1: 121,489,267 (GRCm39) V260D probably damaging Het
Dmxl2 T A 9: 54,307,321 (GRCm39) N2216Y Het
Epn2 T C 11: 61,437,446 (GRCm39) E42G probably damaging Het
Esrrg C A 1: 187,878,605 (GRCm39) P229T probably benign Het
Esrrg C A 1: 187,878,606 (GRCm39) P229Q possibly damaging Het
Ethe1 G T 7: 24,305,643 (GRCm39) R130L probably benign Het
Fgl2 G A 5: 21,580,363 (GRCm39) C235Y probably damaging Het
Fmnl1 C T 11: 103,087,327 (GRCm39) T890M unknown Het
Fsip2 C G 2: 82,807,301 (GRCm39) P1207A probably benign Het
Gc C T 5: 89,593,165 (GRCm39) D85N possibly damaging Het
Gfi1 G A 5: 107,869,370 (GRCm39) R287W probably damaging Het
Gm3629 T C 14: 17,834,566 (GRCm39) probably null Het
Hapln3 A G 7: 78,771,712 (GRCm39) F59S probably benign Het
Il24 G A 1: 130,813,483 (GRCm39) T38I possibly damaging Het
Izumo1 A G 7: 45,276,583 (GRCm39) D382G probably benign Het
Kif2b T A 11: 91,466,538 (GRCm39) I582F possibly damaging Het
Klhdc1 A G 12: 69,288,783 (GRCm39) Y31C probably damaging Het
Lama1 G A 17: 68,128,669 (GRCm39) E3009K Het
Mad2l1bp G A 17: 46,458,958 (GRCm39) R191C probably damaging Het
Mark1 A C 1: 184,644,261 (GRCm39) S468A probably damaging Het
Mknk2 T A 10: 80,504,823 (GRCm39) N236Y probably damaging Het
Muc2 T A 7: 141,287,983 (GRCm39) C251* probably null Het
Nacad T C 11: 6,552,252 (GRCm39) D313G probably damaging Het
Neb G T 2: 52,099,599 (GRCm39) D4750E probably benign Het
Nlrp6 T C 7: 140,506,332 (GRCm39) S758P probably damaging Het
Nxt2 C T X: 141,020,747 (GRCm39) A118V possibly damaging Het
Or13a28 A C 7: 140,218,282 (GRCm39) I223L probably benign Het
Or51b4 T C 7: 103,530,569 (GRCm39) T294A possibly damaging Het
Or8b3b A G 9: 38,583,892 (GRCm39) F283L probably benign Het
Oxtr A G 6: 112,466,481 (GRCm39) V93A probably damaging Het
Pbx3 C A 2: 34,103,271 (GRCm39) D234Y probably damaging Het
Pde4b A T 4: 102,459,826 (GRCm39) T554S probably damaging Het
Peg10 GC GCTCC 6: 4,756,452 (GRCm39) probably benign Het
Pid1 A T 1: 84,015,955 (GRCm39) Y151N probably damaging Het
Plcd4 A G 1: 74,591,307 (GRCm39) E234G possibly damaging Het
Pou6f1 A G 15: 100,478,789 (GRCm39) V373A probably benign Het
Ppp1r12c T C 7: 4,485,792 (GRCm39) K685E possibly damaging Het
Rnf34 T A 5: 122,999,957 (GRCm39) V71D probably damaging Het
Rpap2 T G 5: 107,746,156 (GRCm39) H11Q possibly damaging Het
Skint2 A G 4: 112,496,834 (GRCm39) T247A probably benign Het
Stat5b T A 11: 100,692,350 (GRCm39) N145Y probably damaging Het
Sv2b A G 7: 74,856,017 (GRCm39) L91P probably damaging Het
Syt1 A G 10: 108,340,376 (GRCm39) I314T probably damaging Het
Tlk1 A T 2: 70,572,502 (GRCm39) N355K probably benign Het
Tnc C A 4: 63,890,973 (GRCm39) M1636I probably benign Het
Trank1 C A 9: 111,162,843 (GRCm39) A34D probably damaging Het
Unc13c A G 9: 73,719,665 (GRCm39) I1001T probably benign Het
Vdr T C 15: 97,765,136 (GRCm39) D201G probably benign Het
Vmn2r115 A T 17: 23,564,307 (GRCm39) I160L probably benign Het
Wdr81 C A 11: 75,335,250 (GRCm39) R1772L probably damaging Het
Zfp457 T C 13: 67,442,068 (GRCm39) D169G 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
R2061:Kdm5a UTSW 6 120,358,578 (GRCm39) missense probably benign
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
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'- CCATTGAAATTGGGAGTTTCTCTG -3'
(R):5'- TGTGATAGCAATGACACCAAGG -3'

Sequencing Primer
(F):5'- GGGAGTTTCTCTGATATTTTTCCC -3'
(R):5'- TCAGGTCTGCTAAGTACATGGAC -3'
Posted On 2021-12-30