Incidental Mutation 'R4737:Kdm5a'
ID 359341
Institutional Source Beutler Lab
Gene Symbol Kdm5a
Ensembl Gene ENSMUSG00000030180
Gene Name lysine (K)-specific demethylase 5A
Synonyms Jarid1a, Rbbp2, RBP2
MMRRC Submission 042024-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4737 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 120364124-120444574 bp(+) (GRCm38)
Type of Mutation intron
DNA Base Change (assembly) T to A at 120406015 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000145021 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005108] [ENSMUST00000132009] [ENSMUST00000135802]
AlphaFold Q3UXZ9
Predicted Effect probably benign
Transcript: ENSMUST00000005108
SMART Domains Protein: ENSMUSP00000005108
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
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: ENSMUST00000124847
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 benign
Transcript: ENSMUST00000135802
SMART Domains Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180

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
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.3%
Validation Efficiency 100% (94/94)
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: 88 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A430110L20Rik A G 1: 181,227,819 (GRCm38) noncoding transcript Het
Acp2 A T 2: 91,210,723 (GRCm38) R419W probably benign Het
Actr5 A G 2: 158,628,071 (GRCm38) N207S probably damaging Het
Afap1 G A 5: 35,961,782 (GRCm38) V254M probably benign Het
Arfgef1 A T 1: 10,189,611 (GRCm38) M544K possibly damaging Het
Arhgap5 A T 12: 52,519,077 (GRCm38) M944L probably benign Het
Bnip3l-ps G A 12: 18,216,772 (GRCm38) noncoding transcript Het
Carf A G 1: 60,109,318 (GRCm38) T58A probably benign Het
Carns1 A G 19: 4,170,928 (GRCm38) probably benign Het
Ccp110 T A 7: 118,724,548 (GRCm38) I670K possibly damaging Het
Cftr T A 6: 18,299,883 (GRCm38) D1218E probably benign Het
Chrna9 A T 5: 65,967,871 (GRCm38) T52S probably damaging Het
Chst9 T C 18: 15,452,777 (GRCm38) Y243C probably damaging Het
Clk2 A T 3: 89,168,709 (GRCm38) H62L probably benign Het
Cntnap2 A T 6: 45,060,317 (GRCm38) R10W possibly damaging Het
Cpt1b C T 15: 89,421,406 (GRCm38) D369N probably benign Het
Crhr2 G T 6: 55,091,305 (GRCm38) H423Q probably damaging Het
D8Ertd738e T A 8: 84,249,521 (GRCm38) I33F probably damaging Het
Dbt T C 3: 116,539,132 (GRCm38) I200T probably damaging Het
Ddhd1 A T 14: 45,628,821 (GRCm38) probably benign Het
Ddx27 A G 2: 167,029,299 (GRCm38) I480V probably benign Het
Dpp9 A C 17: 56,198,970 (GRCm38) probably null Het
Dpy19l3 A T 7: 35,703,501 (GRCm38) M562K probably damaging Het
Dus3l T C 17: 56,767,868 (GRCm38) L330P probably damaging Het
Efcab7 C T 4: 99,831,568 (GRCm38) Q96* probably null Het
Egfr T C 11: 16,869,231 (GRCm38) F254L probably damaging Het
Eml5 C T 12: 98,798,852 (GRCm38) V1566M probably damaging Het
Entpd7 T A 19: 43,691,195 (GRCm38) Y62* probably null Het
Erbb4 T C 1: 68,343,900 (GRCm38) M313V probably damaging Het
Gm5528 A G 1: 72,004,552 (GRCm38) noncoding transcript Het
H2-M9 G T 17: 36,640,739 (GRCm38) Y281* probably null Het
Hmcn1 T G 1: 150,689,595 (GRCm38) K2260N possibly damaging Het
Hnf4a A G 2: 163,564,219 (GRCm38) I259V probably benign Het
Ick A G 9: 78,150,654 (GRCm38) T162A probably damaging Het
Insm1 A T 2: 146,222,902 (GRCm38) T213S probably benign Het
Iqca T C 1: 90,077,822 (GRCm38) D488G probably damaging Het
Kdm7a G C 6: 39,152,839 (GRCm38) L468V possibly damaging Het
Lck G A 4: 129,555,984 (GRCm38) T229I possibly damaging Het
Lig3 T C 11: 82,787,727 (GRCm38) L265P probably damaging Het
Lipa T A 19: 34,501,634 (GRCm38) K229* probably null Het
Lrrk1 C T 7: 66,306,873 (GRCm38) S418N probably benign Het
Mark2 A G 19: 7,281,232 (GRCm38) V126A probably damaging Het
Met T C 6: 17,491,541 (GRCm38) C101R probably damaging Het
Mkln1 A T 6: 31,426,799 (GRCm38) K85M probably damaging Het
Mst1 A G 9: 108,080,521 (GRCm38) R15G probably benign Het
Muc6 T G 7: 141,640,159 (GRCm38) probably benign Het
Muc6 G T 7: 141,638,772 (GRCm38) T1996N possibly damaging Het
Myo7b T C 18: 31,998,602 (GRCm38) S514G probably damaging Het
Narfl A T 17: 25,781,309 (GRCm38) H322L probably damaging Het
Nars T C 18: 64,516,427 (GRCm38) E11G probably benign Het
Ogdh T A 11: 6,297,044 (GRCm38) F23I probably benign Het
Olfr1121 T C 2: 87,372,321 (GRCm38) I263T probably damaging Het
Olfr1186 C T 2: 88,526,225 (GRCm38) S214F probably damaging Het
Olfr1238 C T 2: 89,406,486 (GRCm38) V198I probably benign Het
Olfr1272 A G 2: 90,282,381 (GRCm38) S65P probably damaging Het
Olfr584 C T 7: 103,085,914 (GRCm38) A127V probably damaging Het
Olfr825 T A 10: 130,162,838 (GRCm38) T163S probably benign Het
Olfr979 A T 9: 40,000,422 (GRCm38) D268E probably damaging Het
Otub2 T A 12: 103,392,844 (GRCm38) L64Q probably benign Het
Pappa2 T C 1: 158,957,012 (GRCm38) R143G probably benign Het
Patl2 T A 2: 122,125,306 (GRCm38) T250S probably damaging Het
Pcdhac2 C T 18: 37,145,899 (GRCm38) T644I possibly damaging Het
Pi4kb C T 3: 95,004,338 (GRCm38) T690I probably damaging Het
Pla2g4d T C 2: 120,266,790 (GRCm38) Y776C probably benign Het
Plekhh2 C T 17: 84,563,959 (GRCm38) S215L probably benign Het
Psmd2 T G 16: 20,659,815 (GRCm38) probably benign Het
Ptpn21 T C 12: 98,708,844 (GRCm38) E183G probably benign Het
Ptprg T A 14: 12,226,314 (GRCm38) D527E probably damaging Het
Rhobtb1 T A 10: 69,279,497 (GRCm38) probably null Het
Scel T A 14: 103,572,037 (GRCm38) M271K possibly damaging Het
Senp3 A T 11: 69,678,829 (GRCm38) C310* probably null Het
Slc25a3 T C 10: 91,122,188 (GRCm38) T97A possibly damaging Het
Srsf11 A T 3: 158,026,732 (GRCm38) Y82* probably null Het
Tbc1d8 G A 1: 39,402,878 (GRCm38) T211I possibly damaging Het
Tbkbp1 T C 11: 97,148,648 (GRCm38) E145G probably damaging Het
Tln1 T C 4: 43,540,588 (GRCm38) N1471S probably benign Het
Tnn T G 1: 160,146,089 (GRCm38) D236A probably damaging Het
Trmt2a C T 16: 18,251,286 (GRCm38) probably benign Het
Ttn A T 2: 76,811,243 (GRCm38) L5176Q possibly damaging Het
Ubxn10 G A 4: 138,735,948 (GRCm38) probably benign Het
Ulk4 G A 9: 121,073,872 (GRCm38) Q1180* probably null Het
Usp43 T A 11: 67,855,505 (GRCm38) K1120N probably damaging Het
Uspl1 T A 5: 149,194,339 (GRCm38) L244Q possibly damaging Het
Vmn1r32 T C 6: 66,553,645 (GRCm38) H49R probably damaging Het
Vmn2r4 T C 3: 64,409,963 (GRCm38) D118G probably damaging Het
Vwce A G 19: 10,650,579 (GRCm38) I468V probably benign Het
Zbtb7c G T 18: 76,146,154 (GRCm38) R561L probably benign Het
Zfp956 T C 6: 47,962,542 (GRCm38) S175P probably damaging Het
Other mutations in Kdm5a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00540:Kdm5a APN 6 120,385,719 (GRCm38) critical splice donor site probably null 0.00
IGL00706:Kdm5a APN 6 120,406,636 (GRCm38) missense possibly damaging 0.44
IGL01361:Kdm5a APN 6 120,399,016 (GRCm38) missense probably damaging 1.00
IGL01402:Kdm5a APN 6 120,390,679 (GRCm38) nonsense probably null 0.00
IGL01924:Kdm5a APN 6 120,394,255 (GRCm38) critical splice donor site probably null 0.00
IGL01935:Kdm5a APN 6 120,408,323 (GRCm38) missense probably benign 0.02
IGL02165:Kdm5a APN 6 120,415,290 (GRCm38) missense probably damaging 1.00
IGL02472:Kdm5a APN 6 120,406,730 (GRCm38) splice site probably benign
IGL02506:Kdm5a APN 6 120,432,149 (GRCm38) missense probably damaging 0.99
IGL02604:Kdm5a APN 6 120,431,980 (GRCm38) missense probably benign
IGL02633:Kdm5a APN 6 120,364,719 (GRCm38) missense probably damaging 1.00
IGL02876:Kdm5a APN 6 120,390,644 (GRCm38) unclassified probably benign
IGL03009:Kdm5a APN 6 120,430,086 (GRCm38) missense probably damaging 0.98
IGL03027:Kdm5a APN 6 120,374,990 (GRCm38) splice site probably null
IGL03164:Kdm5a APN 6 120,439,019 (GRCm38) missense probably damaging 1.00
IGL03236:Kdm5a APN 6 120,438,988 (GRCm38) missense probably damaging 0.98
IGL03276:Kdm5a APN 6 120,402,708 (GRCm38) splice site probably benign
Anastasia UTSW 6 120,430,231 (GRCm38) nonsense probably null
Augmented UTSW 6 120,430,016 (GRCm38) intron probably benign
Calla_lily UTSW 6 120,405,022 (GRCm38) missense probably damaging 1.00
crocus UTSW 6 120,399,038 (GRCm38) missense probably null 0.98
Magnolia UTSW 6 120,398,978 (GRCm38) missense probably damaging 0.99
Saffron UTSW 6 120,389,620 (GRCm38) missense probably benign 0.19
Selbst UTSW 6 120,388,105 (GRCm38) nonsense probably null
R0320:Kdm5a UTSW 6 120,389,620 (GRCm38) missense probably benign 0.19
R0462:Kdm5a UTSW 6 120,402,600 (GRCm38) missense probably damaging 1.00
R0601:Kdm5a UTSW 6 120,402,671 (GRCm38) missense possibly damaging 0.76
R0628:Kdm5a UTSW 6 120,415,239 (GRCm38) missense probably damaging 1.00
R1024:Kdm5a UTSW 6 120,399,038 (GRCm38) missense probably null 0.98
R2013:Kdm5a UTSW 6 120,431,990 (GRCm38) missense probably benign 0.09
R2015:Kdm5a UTSW 6 120,431,990 (GRCm38) missense probably benign 0.09
R2061:Kdm5a UTSW 6 120,381,617 (GRCm38) missense probably benign
R2188:Kdm5a UTSW 6 120,406,640 (GRCm38) missense possibly damaging 0.59
R3923:Kdm5a UTSW 6 120,381,664 (GRCm38) missense probably benign 0.01
R4013:Kdm5a UTSW 6 120,394,106 (GRCm38) missense probably damaging 1.00
R4016:Kdm5a UTSW 6 120,394,106 (GRCm38) missense probably damaging 1.00
R4017:Kdm5a UTSW 6 120,394,106 (GRCm38) missense probably damaging 1.00
R4030:Kdm5a UTSW 6 120,405,113 (GRCm38) nonsense probably null
R4646:Kdm5a UTSW 6 120,374,977 (GRCm38) missense possibly damaging 0.55
R4779:Kdm5a UTSW 6 120,369,099 (GRCm38) unclassified probably benign
R4836:Kdm5a UTSW 6 120,412,402 (GRCm38) missense probably damaging 1.00
R5129:Kdm5a UTSW 6 120,405,022 (GRCm38) missense probably damaging 1.00
R5182:Kdm5a UTSW 6 120,388,105 (GRCm38) nonsense probably null
R5183:Kdm5a UTSW 6 120,430,016 (GRCm38) intron probably benign
R5572:Kdm5a UTSW 6 120,412,375 (GRCm38) missense possibly damaging 0.69
R6110:Kdm5a UTSW 6 120,412,306 (GRCm38) missense probably damaging 1.00
R6132:Kdm5a UTSW 6 120,374,931 (GRCm38) missense probably damaging 1.00
R6198:Kdm5a UTSW 6 120,438,997 (GRCm38) missense probably benign 0.37
R6246:Kdm5a UTSW 6 120,431,910 (GRCm38) missense probably damaging 0.97
R6336:Kdm5a UTSW 6 120,398,978 (GRCm38) missense probably damaging 0.99
R6343:Kdm5a UTSW 6 120,382,933 (GRCm38) missense probably benign 0.01
R6612:Kdm5a UTSW 6 120,430,228 (GRCm38) missense probably damaging 0.99
R6647:Kdm5a UTSW 6 120,412,461 (GRCm38) missense probably benign 0.25
R7068:Kdm5a UTSW 6 120,430,215 (GRCm38) missense probably benign 0.40
R7369:Kdm5a UTSW 6 120,432,004 (GRCm38) missense possibly damaging 0.67
R7380:Kdm5a UTSW 6 120,405,918 (GRCm38) missense probably benign 0.35
R7411:Kdm5a UTSW 6 120,426,815 (GRCm38) missense probably damaging 1.00
R7521:Kdm5a UTSW 6 120,432,187 (GRCm38) nonsense probably null
R7570:Kdm5a UTSW 6 120,427,842 (GRCm38) missense probably damaging 0.99
R7647:Kdm5a UTSW 6 120,427,786 (GRCm38) missense probably benign 0.01
R7704:Kdm5a UTSW 6 120,427,064 (GRCm38) missense probably damaging 1.00
R7796:Kdm5a UTSW 6 120,390,763 (GRCm38) missense probably damaging 1.00
R7875:Kdm5a UTSW 6 120,399,018 (GRCm38) nonsense probably null
R8265:Kdm5a UTSW 6 120,406,596 (GRCm38) missense possibly damaging 0.72
R8297:Kdm5a UTSW 6 120,381,555 (GRCm38) missense probably benign 0.00
R8336:Kdm5a UTSW 6 120,419,446 (GRCm38) missense probably benign 0.00
R8471:Kdm5a UTSW 6 120,430,231 (GRCm38) nonsense probably null
R8872:Kdm5a UTSW 6 120,388,140 (GRCm38) missense probably damaging 1.00
R8890:Kdm5a UTSW 6 120,389,663 (GRCm38) missense probably damaging 1.00
R9028:Kdm5a UTSW 6 120,439,131 (GRCm38) missense probably benign
R9064:Kdm5a UTSW 6 120,426,908 (GRCm38) small deletion probably benign
R9114:Kdm5a UTSW 6 120,405,926 (GRCm38) nonsense probably null
R9316:Kdm5a UTSW 6 120,405,012 (GRCm38) missense probably damaging 1.00
R9353:Kdm5a UTSW 6 120,427,769 (GRCm38) missense probably benign 0.01
R9412:Kdm5a UTSW 6 120,389,030 (GRCm38) missense probably damaging 1.00
R9416:Kdm5a UTSW 6 120,388,095 (GRCm38) missense probably damaging 1.00
R9431:Kdm5a UTSW 6 120,415,292 (GRCm38) missense probably damaging 1.00
R9711:Kdm5a UTSW 6 120,390,697 (GRCm38) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TCCATTGAAATTGGGAGTTTCTCTG -3'
(R):5'- GGTCATGAGACTGAGGCAAC -3'

Sequencing Primer
(F):5'- GGGAGTTTCTCTGATATTTTTCCC -3'
(R):5'- TCATGAGACTGAGGCAACAAAGC -3'
Posted On 2015-11-11