Incidental Mutation 'R2015:Kdm5a'
ID 222786
Institutional Source Beutler Lab
Gene Symbol Kdm5a
Ensembl Gene ENSMUSG00000030180
Gene Name lysine demethylase 5A
Synonyms Rbbp2, Jarid1a, RBP2
MMRRC Submission 040024-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2015 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 120341085-120421535 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 120408951 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 1545 (S1545P)
Ref Sequence ENSEMBL: ENSMUSP00000005108 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005108]
AlphaFold Q3UXZ9
Predicted Effect probably benign
Transcript: ENSMUST00000005108
AA Change: S1545P

PolyPhen 2 Score 0.094 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: S1545P

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: ENSMUST00000100996
AA Change: S1545P

PolyPhen 2 Score 0.094 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000098558
Gene: ENSMUSG00000030180
AA Change: S1545P

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 676 728 3.6e-17 PFAM
Pfam:PLU-1 741 1072 5e-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
PHD 1614 1659 1.27e-6 SMART
low complexity region 1662 1674 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124525
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132599
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142791
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.7%
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: 94 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca9 A T 11: 110,022,672 (GRCm39) M1022K probably benign Het
Abhd4 T A 14: 54,500,289 (GRCm39) H74Q probably damaging Het
Actg1 A G 11: 120,237,636 (GRCm39) S49P possibly damaging Het
Adcy8 C T 15: 64,639,727 (GRCm39) G678S probably benign Het
Aire T C 10: 77,878,792 (GRCm39) D85G probably damaging Het
Akr1c18 T A 13: 4,195,308 (GRCm39) D50V probably damaging Het
Ankrd13a C A 5: 114,930,170 (GRCm39) A185E probably damaging Het
Apc A G 18: 34,448,644 (GRCm39) I1813V probably damaging Het
Armc8 A T 9: 99,365,158 (GRCm39) C661* probably null Het
Bbs10 C T 10: 111,136,716 (GRCm39) Q610* probably null Het
Blm T C 7: 80,152,147 (GRCm39) E600G probably damaging Het
Bpifb9a T C 2: 154,110,120 (GRCm39) probably null Het
Cdk14 T C 5: 5,430,082 (GRCm39) K15R probably benign Het
Cdr1 A G X: 60,228,420 (GRCm39) F249L probably benign Het
Cep250 A C 2: 155,823,373 (GRCm39) H1009P probably damaging Het
Cfap97d1 C A 11: 101,878,044 (GRCm39) H35Q probably damaging Het
Clasp2 A G 9: 113,740,568 (GRCm39) T495A possibly damaging Het
Col19a1 C G 1: 24,598,834 (GRCm39) G53A unknown Het
Cpne1 G A 2: 155,920,308 (GRCm39) R166C probably damaging Het
Dtx3l G A 16: 35,756,797 (GRCm39) H129Y probably benign Het
Ercc3 A G 18: 32,381,482 (GRCm39) T433A probably benign Het
Gm9936 T A 5: 114,995,482 (GRCm39) probably benign Het
Grina T C 15: 76,132,734 (GRCm39) V167A probably damaging Het
H2ac25 T A 11: 58,845,754 (GRCm39) L64Q probably damaging Het
Hcfc2 A G 10: 82,574,814 (GRCm39) N618D probably benign Het
Herpud1 T C 8: 95,118,834 (GRCm39) V196A probably benign Het
Hlcs A G 16: 94,063,599 (GRCm39) V487A probably benign Het
Hspa9 A T 18: 35,079,701 (GRCm39) Y243N probably damaging Het
Igll1 A G 16: 16,681,639 (GRCm39) S39P probably benign Het
Klra8 C A 6: 130,092,536 (GRCm39) C255F probably damaging Het
Krtap4-6 A T 11: 99,556,398 (GRCm39) C110S unknown Het
Lef1 T A 3: 130,905,236 (GRCm39) I39N probably damaging Het
Lnpep G A 17: 17,799,325 (GRCm39) T110I probably damaging Het
Lrp1 T A 10: 127,376,563 (GRCm39) T4282S probably benign Het
Lrp6 A G 6: 134,457,337 (GRCm39) probably null Het
Ly6g5b A C 17: 35,333,654 (GRCm39) S53A possibly damaging Het
M6pr T G 6: 122,290,332 (GRCm39) N98K probably damaging Het
Mal2 T C 15: 54,464,136 (GRCm39) *176Q probably null Het
Mansc1 T C 6: 134,587,274 (GRCm39) D301G possibly damaging Het
Marchf1 C A 8: 66,574,473 (GRCm39) N11K probably damaging Het
Mast3 T A 8: 71,240,007 (GRCm39) I338F probably benign Het
Mcm3 A G 1: 20,873,804 (GRCm39) L772P probably damaging Het
Mib2 C T 4: 155,742,337 (GRCm39) G176D probably damaging Het
Mier2 A T 10: 79,377,036 (GRCm39) probably null Het
Mogs C T 6: 83,094,631 (GRCm39) R483* probably null Het
Msl2 G T 9: 100,957,304 (GRCm39) probably benign Het
Naa16 A T 14: 79,582,499 (GRCm39) M530K probably damaging Het
Nde1 A T 16: 13,987,321 (GRCm39) probably benign Het
Ndufb10 T C 17: 24,941,503 (GRCm39) probably null Het
Nhsl1 A T 10: 18,387,340 (GRCm39) R205W probably damaging Het
Npffr2 T A 5: 89,730,751 (GRCm39) I227N probably damaging Het
Nup210l T A 3: 90,092,739 (GRCm39) L1231Q probably damaging Het
Or2f1 A G 6: 42,721,784 (GRCm39) E271G probably damaging Het
Or7a39 T C 10: 78,715,222 (GRCm39) I72T possibly damaging Het
Pclo C A 5: 14,571,515 (GRCm39) P300Q probably damaging Het
Pik3c2a T A 7: 115,950,166 (GRCm39) probably null Het
Plekha5 T A 6: 140,480,290 (GRCm39) probably null Het
Pls1 A G 9: 95,643,418 (GRCm39) V527A possibly damaging Het
Ppfia2 T C 10: 106,310,538 (GRCm39) M15T probably benign Het
Prkd2 T A 7: 16,581,602 (GRCm39) C152* probably null Het
Ptprq T G 10: 107,503,283 (GRCm39) K792Q probably damaging Het
Pttg1ip2 T A 5: 5,505,964 (GRCm39) I106L probably benign Het
Rbbp8 T C 18: 11,853,681 (GRCm39) M296T probably benign Het
Rfc3 T C 5: 151,571,003 (GRCm39) probably null Het
Rnf17 A G 14: 56,724,426 (GRCm39) N1090S probably benign Het
Sash1 A T 10: 8,605,177 (GRCm39) V1071D probably benign Het
Sdsl G A 5: 120,601,218 (GRCm39) T18M probably damaging Het
Sepsecs T A 5: 52,804,966 (GRCm39) Q365L probably benign Het
Sgta A T 10: 80,887,130 (GRCm39) V45E probably damaging Het
Slc25a46 A T 18: 31,742,778 (GRCm39) H29Q probably benign Het
Slc2a8 A C 2: 32,871,392 (GRCm39) V136G probably benign Het
Smg7 A T 1: 152,736,259 (GRCm39) N166K probably damaging Het
Spata21 C T 4: 140,834,640 (GRCm39) Q505* probably null Het
Strn4 T C 7: 16,566,953 (GRCm39) S458P possibly damaging Het
Tbc1d22a C T 15: 86,183,885 (GRCm39) T248M probably damaging Het
Trabd T A 15: 88,968,929 (GRCm39) M149K possibly damaging Het
Trpv3 A T 11: 73,170,653 (GRCm39) N178Y probably damaging Het
Try5 C T 6: 41,291,585 (GRCm39) probably null Het
Tsg101 C T 7: 46,558,652 (GRCm39) probably null Het
Ube3b A G 5: 114,549,210 (GRCm39) E738G probably damaging Het
Unc13d A G 11: 115,959,581 (GRCm39) S631P probably damaging Het
Unc5d T C 8: 29,249,007 (GRCm39) T297A probably damaging Het
Usp18 A T 6: 121,245,509 (GRCm39) E1V probably damaging Het
Vapb C A 2: 173,613,391 (GRCm39) P97T probably benign Het
Vmn1r33 T A 6: 66,589,356 (GRCm39) D66V probably benign Het
Vmn2r19 T A 6: 123,292,954 (GRCm39) M332K probably benign Het
Vmn2r71 T A 7: 85,269,845 (GRCm39) M452K probably benign Het
Vps13b T C 15: 35,607,288 (GRCm39) S1074P probably damaging Het
Vwde C A 6: 13,208,337 (GRCm39) G182C possibly damaging Het
Wdfy3 A C 5: 102,008,352 (GRCm39) S2778A probably null Het
Zbtb2 T A 10: 4,319,757 (GRCm39) I90F possibly damaging Het
Zfp518b C A 5: 38,829,345 (GRCm39) V887F probably benign Het
Zfp790 A G 7: 29,528,286 (GRCm39) T324A probably benign Het
Zup1 A G 10: 33,805,820 (GRCm39) V437A possibly damaging 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
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
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'- TGTAATCATCCCAAACAGGAAATCG -3'
(R):5'- CAGTTTTGGGCTGCACACAC -3'

Sequencing Primer
(F):5'- TTTTGAAGGATGATAGCATAGAAGAG -3'
(R):5'- AGCATTCTCATCATCAGACTCC -3'
Posted On 2014-08-25