Incidental Mutation 'R6198:Kdm5a'
ID 503037
Institutional Source Beutler Lab
Gene Symbol Kdm5a
Ensembl Gene ENSMUSG00000030180
Gene Name lysine demethylase 5A
Synonyms Rbbp2, Jarid1a, RBP2
MMRRC Submission 044338-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6198 (G1)
Quality Score 225.009
Status Validated
Chromosome 6
Chromosomal Location 120341085-120421535 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 120415958 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 1626 (V1626E)
Ref Sequence ENSEMBL: ENSMUSP00000005108 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005108]
AlphaFold Q3UXZ9
Predicted Effect probably benign
Transcript: ENSMUST00000005108
AA Change: V1626E

PolyPhen 2 Score 0.366 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: V1626E

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: ENSMUST00000142791
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 99% (68/69)
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: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700006A11Rik A T 3: 124,210,499 (GRCm39) probably null Het
2610318N02Rik A G 16: 16,936,233 (GRCm39) S164P probably damaging Het
Acsbg3 A G 17: 57,189,679 (GRCm39) S265G probably damaging Het
Acyp2 C T 11: 30,456,354 (GRCm39) E98K possibly damaging Het
Adam19 A C 11: 46,012,329 (GRCm39) N275T probably damaging Het
Adgrg7 T A 16: 56,597,556 (GRCm39) T84S possibly damaging Het
Asl C T 5: 130,047,757 (GRCm39) V70I probably benign Het
Atp2c1 A G 9: 105,398,271 (GRCm39) S26P probably benign Het
Bcas3 A T 11: 85,400,261 (GRCm39) D410V probably damaging Het
Cc2d1b C T 4: 108,490,422 (GRCm39) R825W probably damaging Het
Ccdc15 A C 9: 37,225,581 (GRCm39) probably null Het
Cfh A G 1: 140,033,178 (GRCm39) S789P probably damaging Het
Cltc T C 11: 86,611,188 (GRCm39) N561S probably benign Het
Cnst A G 1: 179,420,430 (GRCm39) Q187R probably damaging Het
Csmd3 T C 15: 48,177,273 (GRCm39) T422A probably benign Het
Cyp2c55 A T 19: 38,995,565 (GRCm39) R26* probably null Het
Dgkb A T 12: 38,223,822 (GRCm39) M414L probably benign Het
Dgkd A G 1: 87,851,930 (GRCm39) D444G probably damaging Het
Dipk1b A G 2: 26,525,710 (GRCm39) K215E probably damaging Het
Dnmt3c T C 2: 153,561,929 (GRCm39) V544A noncoding transcript Het
Dus3l A T 17: 57,074,858 (GRCm39) T327S possibly damaging Het
Elf2 A T 3: 51,184,670 (GRCm39) L5Q probably damaging Het
Fxyd6 A G 9: 45,301,968 (GRCm39) Y30C probably damaging Het
Gcc2 A T 10: 58,128,412 (GRCm39) T1375S probably benign Het
Git2 A T 5: 114,883,556 (GRCm39) Y393* probably null Het
Gm14403 AAACCCTA AA 2: 177,201,448 (GRCm39) probably benign Het
Golgb1 T C 16: 36,713,757 (GRCm39) L246P probably damaging Het
Grp G T 18: 66,013,057 (GRCm39) Q74H possibly damaging Het
Ifi203 A T 1: 173,751,648 (GRCm39) M391K probably damaging Het
Itih2 A G 2: 10,103,352 (GRCm39) Y712H probably benign Het
Klhl40 A G 9: 121,607,833 (GRCm39) Y331C probably damaging Het
Kprp T A 3: 92,731,994 (GRCm39) Y352F probably damaging Het
Lama2 G T 10: 27,064,018 (GRCm39) H1286Q probably damaging Het
Lgi4 T A 7: 30,768,547 (GRCm39) probably null Het
Lrrc47 A T 4: 154,100,129 (GRCm39) N235I probably damaging Het
Lrrc74b T A 16: 17,366,650 (GRCm39) I308F probably damaging Het
Map7d1 T A 4: 126,135,636 (GRCm39) K135M probably damaging Het
Marchf5 A G 19: 37,188,140 (GRCm39) R36G probably damaging Het
Mtx3 C A 13: 92,989,359 (GRCm39) P299Q probably benign Het
Muc21 T A 17: 35,931,808 (GRCm39) probably benign Het
Ncapd2 C A 6: 125,156,286 (GRCm39) E500* probably null Het
Nckap5l T C 15: 99,323,869 (GRCm39) K878R probably damaging Het
Nphs1 T C 7: 30,167,340 (GRCm39) I756T probably damaging Het
Olfm4 T G 14: 80,237,813 (GRCm39) S17A probably benign Het
Or1j15 A G 2: 36,458,963 (GRCm39) M118V probably damaging Het
Or4b1 A T 2: 89,979,782 (GRCm39) D189E probably damaging Het
Pak1ip1 G T 13: 41,154,886 (GRCm39) Q27H probably benign Het
Piezo2 A T 18: 63,290,281 (GRCm39) C159* probably null Het
Pkn2 G T 3: 142,516,165 (GRCm39) T538K probably benign Het
Ppp3cc A T 14: 70,485,060 (GRCm39) M198K probably benign Het
Rrm1 T G 7: 102,095,936 (GRCm39) probably null Het
Setd3 T C 12: 108,131,427 (GRCm39) K7E possibly damaging Het
Shc1 A G 3: 89,329,414 (GRCm39) K86R probably benign Het
Slc16a7 T C 10: 125,064,084 (GRCm39) T418A probably benign Het
Spocd1 C T 4: 129,849,208 (GRCm39) P676S probably damaging Het
Spp1 A G 5: 104,587,374 (GRCm39) probably null Het
Syne1 A G 10: 5,252,269 (GRCm39) Y2462H probably damaging Het
Tiam2 T C 17: 3,464,396 (GRCm39) S42P probably benign Het
Tmem63b C T 17: 45,972,442 (GRCm39) V722I probably benign Het
Ubqln1 A G 13: 58,344,404 (GRCm39) S130P probably benign Het
Usp34 G T 11: 23,434,127 (GRCm39) L3215F probably damaging Het
Uvssa A G 5: 33,566,854 (GRCm39) Y517C probably damaging Het
Vps13d A T 4: 144,875,560 (GRCm39) F1649Y probably benign Het
Zfp236 A G 18: 82,675,278 (GRCm39) S405P probably damaging Het
Zfp9 T C 6: 118,454,282 (GRCm39) M1V probably null Het
Zfp946 A T 17: 22,673,896 (GRCm39) S217C probably damaging Het
Zfp970 T A 2: 177,167,253 (GRCm39) C276S probably damaging Het
Zswim5 T A 4: 116,735,204 (GRCm39) F183Y 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
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'- AGAGGCCTAATTTTGTGGACAC -3'
(R):5'- AACCAGACATCTGCTAACTGGTC -3'

Sequencing Primer
(F):5'- AATTTGGGGGTATTAACTTCTCAGC -3'
(R):5'- GACATCTGCTAACTGGTCTCTTTAAG -3'
Posted On 2018-02-27