Incidental Mutation 'R0326:Kdm4a'
ID 25791
Institutional Source Beutler Lab
Gene Symbol Kdm4a
Ensembl Gene ENSMUSG00000033326
Gene Name lysine (K)-specific demethylase 4A
Synonyms D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2
MMRRC Submission 038536-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.643) question?
Stock # R0326 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 117994154-118037240 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 118018903 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Glycine at position 438 (R438G)
Ref Sequence ENSEMBL: ENSMUSP00000062910 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000050288] [ENSMUST00000097911] [ENSMUST00000106403] [ENSMUST00000106406]
AlphaFold Q8BW72
Predicted Effect probably benign
Transcript: ENSMUST00000050288
AA Change: R438G

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: R438G

DomainStartEndE-ValueType
JmjN 13 55 1.01e-20 SMART
JmjC 142 308 3.57e-63 SMART
low complexity region 461 487 N/A INTRINSIC
low complexity region 502 525 N/A INTRINSIC
low complexity region 619 637 N/A INTRINSIC
PHD 709 767 4.93e-4 SMART
PHD 829 885 1.54e-5 SMART
TUDOR 897 954 2.87e-8 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000097911
AA Change: R438G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: R438G

DomainStartEndE-ValueType
JmjN 13 55 1.01e-20 SMART
JmjC 142 308 3.57e-63 SMART
low complexity region 461 487 N/A INTRINSIC
low complexity region 502 525 N/A INTRINSIC
low complexity region 619 637 N/A INTRINSIC
PHD 709 767 4.93e-4 SMART
PHD 829 885 1.54e-5 SMART
TUDOR 897 954 2.41e-10 SMART
TUDOR 955 1011 4.77e-14 SMART
low complexity region 1032 1044 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000106403
AA Change: R438G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: R438G

DomainStartEndE-ValueType
JmjN 13 55 1.01e-20 SMART
JmjC 142 308 3.57e-63 SMART
low complexity region 461 487 N/A INTRINSIC
low complexity region 502 525 N/A INTRINSIC
low complexity region 619 637 N/A INTRINSIC
PHD 709 767 4.93e-4 SMART
PHD 829 885 1.54e-5 SMART
TUDOR 897 954 2.41e-10 SMART
TUDOR 955 1011 4.77e-14 SMART
low complexity region 1032 1044 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000106406
AA Change: R438G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: R438G

DomainStartEndE-ValueType
JmjN 13 55 1.01e-20 SMART
JmjC 142 308 3.57e-63 SMART
low complexity region 461 487 N/A INTRINSIC
low complexity region 502 525 N/A INTRINSIC
low complexity region 619 637 N/A INTRINSIC
PHD 709 767 4.93e-4 SMART
PHD 829 885 1.54e-5 SMART
TUDOR 897 954 2.41e-10 SMART
TUDOR 955 1011 4.77e-14 SMART
low complexity region 1032 1044 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000157678
Predicted Effect noncoding transcript
Transcript: ENSMUST00000164821
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.0%
  • 10x: 95.8%
  • 20x: 91.8%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the Jumonji domain 2 (JMJD2) family and encodes a protein containing a JmjN domain, a JmjC domain, a JD2H domain, two TUDOR domains, and two PHD-type zinc fingers. This nuclear protein functions as a trimethylation-specific demethylase, converting specific trimethylated histone residues to the dimethylated form, and as a transcriptional repressor. [provided by RefSeq, Apr 2009]
Allele List at MGI
Other mutations in this stock
Total: 99 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
AA986860 C T 1: 130,670,635 (GRCm39) P286S possibly damaging Het
Aagab T A 9: 63,526,444 (GRCm39) S156T probably damaging Het
Abca14 T G 7: 119,823,642 (GRCm39) Y390D probably damaging Het
Abcc2 T A 19: 43,814,386 (GRCm39) I1122N possibly damaging Het
Adamts16 T C 13: 70,927,730 (GRCm39) E503G possibly damaging Het
Adamts9 A T 6: 92,835,038 (GRCm39) C697* probably null Het
Adgrv1 T C 13: 81,623,112 (GRCm39) D3837G possibly damaging Het
Ahcyl T A 16: 45,974,246 (GRCm39) D377V probably benign Het
Aire T A 10: 77,878,433 (GRCm39) R128S probably damaging Het
Alkbh2 A C 5: 114,262,011 (GRCm39) *240E probably null Het
Als2 T C 1: 59,219,742 (GRCm39) Y1191C probably damaging Het
Anapc5 A T 5: 122,952,667 (GRCm39) V186E probably benign Het
Apob C T 12: 8,040,307 (GRCm39) A548V probably damaging Het
B3galt4 A T 17: 34,169,722 (GRCm39) V172E probably damaging Het
Bbs7 A C 3: 36,646,525 (GRCm39) C432G possibly damaging Het
Cacna2d3 T A 14: 28,767,601 (GRCm39) E758V probably damaging Het
Cactin T G 10: 81,158,496 (GRCm39) L154R probably benign Het
Ccdc88a A C 11: 29,411,021 (GRCm39) R502S probably benign Het
Ccnf A T 17: 24,450,784 (GRCm39) I398N possibly damaging Het
Chd1 A T 17: 15,988,828 (GRCm39) D1527V probably damaging Het
Chd1 A T 17: 15,988,830 (GRCm39) M1528L probably benign Het
Chrac1 G A 15: 72,964,675 (GRCm39) probably null Het
Cln3 T G 7: 126,182,217 (GRCm39) M1L probably damaging Het
Cnot6 T C 11: 49,568,263 (GRCm39) Y442C probably damaging Het
Col19a1 A T 1: 24,324,132 (GRCm39) probably null Het
Col1a2 T C 6: 4,537,838 (GRCm39) F1116L unknown Het
Col1a2 G A 6: 4,518,822 (GRCm39) probably benign Het
Cops4 T G 5: 100,676,408 (GRCm39) V53G probably damaging Het
Crnkl1 A G 2: 145,761,875 (GRCm39) S561P probably benign Het
Ctnnb1 C A 9: 120,780,778 (GRCm39) Q99K probably benign Het
Cxcr5 T C 9: 44,424,578 (GRCm39) S360G probably benign Het
Dab2 G A 15: 6,447,797 (GRCm39) V60M probably damaging Het
Ddx3y A T Y: 1,263,321 (GRCm39) Y648* probably null Het
Dennd2a T A 6: 39,474,044 (GRCm39) D430V probably damaging Het
Dsp G T 13: 38,376,846 (GRCm39) E1544* probably null Het
Efcab7 A T 4: 99,719,631 (GRCm39) M38L possibly damaging Het
Fto A G 8: 92,136,155 (GRCm39) N141S probably damaging Het
Gabrp A G 11: 33,504,362 (GRCm39) F318L probably damaging Het
Gmeb1 A C 4: 131,969,663 (GRCm39) C103W probably damaging Het
Heatr9 T C 11: 83,405,365 (GRCm39) D365G probably damaging Het
Hif3a G A 7: 16,778,325 (GRCm39) R436W probably benign Het
Hint2 A G 4: 43,654,378 (GRCm39) V145A probably damaging Het
Hmcn2 T A 2: 31,313,237 (GRCm39) L3482* probably null Het
Hsd3b1 A T 3: 98,760,590 (GRCm39) Y134N probably damaging Het
Impg2 T A 16: 56,080,848 (GRCm39) V775E probably damaging Het
Ipo5 A G 14: 121,159,635 (GRCm39) I154M probably benign Het
Itgad T A 7: 127,797,550 (GRCm39) F893Y probably benign Het
Itprid1 A T 6: 55,875,228 (GRCm39) M393L possibly damaging Het
Klk1b11 T A 7: 43,425,943 (GRCm39) M1K probably null Het
Lama5 A T 2: 179,824,219 (GRCm39) V2602D possibly damaging Het
Lrch3 T C 16: 32,799,870 (GRCm39) S35P probably damaging Het
Mfn2 A G 4: 147,967,745 (GRCm39) L441P probably damaging Het
Mgat4c A T 10: 102,224,565 (GRCm39) I260F probably damaging Het
Mon1b T A 8: 114,364,375 (GRCm39) S51T probably benign Het
Myh11 T C 16: 14,036,744 (GRCm39) D993G probably benign Het
Myo1a A G 10: 127,552,166 (GRCm39) N762D probably benign Het
Nacc2 A T 2: 25,950,345 (GRCm39) Y464N probably damaging Het
Nckap1 A G 2: 80,383,714 (GRCm39) I150T probably benign Het
Ndufv2 G T 17: 66,387,816 (GRCm39) P119T probably damaging Het
Noc4l G A 5: 110,800,241 (GRCm39) R95* probably null Het
Ntng1 A T 3: 110,042,819 (GRCm39) Y2* probably null Het
Oog4 T C 4: 143,165,773 (GRCm39) N53D probably benign Het
Or10ak11 A T 4: 118,687,022 (GRCm39) V205D possibly damaging Het
Or4d11 C T 19: 12,013,525 (GRCm39) V194I probably benign Het
Or6c6c A G 10: 129,541,638 (GRCm39) E297G possibly damaging Het
Or9i1b C T 19: 13,896,873 (GRCm39) T163I probably benign Het
Phkg2 T G 7: 127,173,075 (GRCm39) L11R probably damaging Het
Pogz A G 3: 94,777,424 (GRCm39) D368G probably damaging Het
Prex2 T A 1: 11,355,289 (GRCm39) L1530Q probably damaging Het
Prmt1 C T 7: 44,628,878 (GRCm39) E144K probably damaging Het
Prss8 T A 7: 127,526,348 (GRCm39) I121F probably benign Het
Psmd13 T C 7: 140,477,624 (GRCm39) L314P probably damaging Het
Ptch2 G A 4: 116,966,081 (GRCm39) G467D probably damaging Het
Rbm20 C A 19: 53,852,596 (GRCm39) P1192Q probably damaging Het
Rpl19 T A 11: 97,919,200 (GRCm39) D45E probably benign Het
Rsph10b C T 5: 143,903,946 (GRCm39) A219V probably damaging Het
Rtraf C T 14: 19,864,600 (GRCm39) probably null Het
Scaf1 T A 7: 44,658,175 (GRCm39) T235S probably damaging Het
Shank1 T A 7: 43,968,594 (GRCm39) C296S unknown Het
Slc39a7 A T 17: 34,247,924 (GRCm39) V426D probably damaging Het
Slc41a2 A T 10: 83,119,610 (GRCm39) V384D probably damaging Het
Slco1c1 T C 6: 141,505,499 (GRCm39) L475P probably benign Het
Slco6d1 A C 1: 98,418,359 (GRCm39) K515T probably benign Het
Sos2 T C 12: 69,682,459 (GRCm39) E253G probably damaging Het
Sp6 G T 11: 96,912,361 (GRCm39) D25Y possibly damaging Het
Syt11 A C 3: 88,669,855 (GRCm39) D12E possibly damaging Het
Taf2 A G 15: 54,910,856 (GRCm39) L606P probably damaging Het
Tbc1d5 A G 17: 51,273,764 (GRCm39) Y116H probably damaging Het
Tnfrsf8 A G 4: 145,015,029 (GRCm39) I243T possibly damaging Het
Tnxb A G 17: 34,917,153 (GRCm39) S2183G probably benign Het
Trim66 T C 7: 109,059,379 (GRCm39) Y853C probably benign Het
Ttn T A 2: 76,567,839 (GRCm39) T27685S probably damaging Het
Ttn T C 2: 76,573,466 (GRCm39) E25809G probably damaging Het
Uvssa G A 5: 33,566,191 (GRCm39) G445S probably benign Het
Zfp326 T C 5: 106,058,141 (GRCm39) S427P probably damaging Het
Zfp592 A G 7: 80,674,637 (GRCm39) T534A possibly damaging Het
Zfp672 A G 11: 58,207,173 (GRCm39) S383P possibly damaging Het
Zfp799 A G 17: 33,039,700 (GRCm39) S188P possibly damaging Het
Zyg11b A C 4: 108,129,450 (GRCm39) V54G possibly damaging Het
Other mutations in Kdm4a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01670:Kdm4a APN 4 118,017,698 (GRCm39) missense probably damaging 1.00
IGL01845:Kdm4a APN 4 118,017,656 (GRCm39) missense possibly damaging 0.85
IGL02009:Kdm4a APN 4 118,017,366 (GRCm39) missense probably benign 0.01
IGL02296:Kdm4a APN 4 118,034,662 (GRCm39) missense probably damaging 1.00
IGL02366:Kdm4a APN 4 118,017,703 (GRCm39) critical splice acceptor site probably null
IGL02606:Kdm4a APN 4 118,017,486 (GRCm39) missense probably benign 0.00
IGL02673:Kdm4a APN 4 118,025,769 (GRCm39) missense probably benign 0.00
R0245:Kdm4a UTSW 4 118,032,886 (GRCm39) missense probably benign 0.05
R0551:Kdm4a UTSW 4 117,995,428 (GRCm39) makesense probably null
R0603:Kdm4a UTSW 4 117,999,708 (GRCm39) missense probably damaging 1.00
R0652:Kdm4a UTSW 4 118,032,886 (GRCm39) missense probably benign 0.05
R0799:Kdm4a UTSW 4 118,004,189 (GRCm39) splice site probably null
R0847:Kdm4a UTSW 4 118,021,695 (GRCm39) missense probably damaging 0.96
R1307:Kdm4a UTSW 4 118,032,839 (GRCm39) missense probably benign 0.02
R1572:Kdm4a UTSW 4 117,996,146 (GRCm39) missense possibly damaging 0.89
R1869:Kdm4a UTSW 4 117,996,068 (GRCm39) missense probably null 1.00
R1902:Kdm4a UTSW 4 118,017,596 (GRCm39) missense probably benign 0.38
R1903:Kdm4a UTSW 4 118,017,596 (GRCm39) missense probably benign 0.38
R2135:Kdm4a UTSW 4 117,999,656 (GRCm39) missense probably damaging 1.00
R3856:Kdm4a UTSW 4 118,010,428 (GRCm39) missense probably damaging 1.00
R4687:Kdm4a UTSW 4 118,001,280 (GRCm39) missense probably damaging 1.00
R4940:Kdm4a UTSW 4 118,018,951 (GRCm39) missense probably benign 0.00
R5115:Kdm4a UTSW 4 118,019,778 (GRCm39) missense possibly damaging 0.75
R5229:Kdm4a UTSW 4 118,003,802 (GRCm39) missense probably damaging 0.99
R5305:Kdm4a UTSW 4 118,017,698 (GRCm39) missense probably damaging 1.00
R5423:Kdm4a UTSW 4 117,996,105 (GRCm39) missense probably damaging 1.00
R5750:Kdm4a UTSW 4 117,999,396 (GRCm39) intron probably benign
R5849:Kdm4a UTSW 4 118,019,037 (GRCm39) missense probably benign 0.17
R5876:Kdm4a UTSW 4 117,996,073 (GRCm39) missense probably damaging 0.98
R6564:Kdm4a UTSW 4 118,034,636 (GRCm39) missense probably benign 0.18
R6772:Kdm4a UTSW 4 117,999,752 (GRCm39) critical splice acceptor site probably null
R6982:Kdm4a UTSW 4 118,010,636 (GRCm39) splice site probably null
R7410:Kdm4a UTSW 4 118,001,115 (GRCm39) missense possibly damaging 0.64
R7418:Kdm4a UTSW 4 118,017,440 (GRCm39) missense probably damaging 0.99
R8808:Kdm4a UTSW 4 117,999,480 (GRCm39) missense unknown
R8956:Kdm4a UTSW 4 118,019,013 (GRCm39) missense possibly damaging 0.69
R8958:Kdm4a UTSW 4 117,999,573 (GRCm39) missense probably benign 0.08
R9233:Kdm4a UTSW 4 118,004,193 (GRCm39) critical splice donor site probably null
R9281:Kdm4a UTSW 4 117,995,728 (GRCm39) missense probably damaging 1.00
R9647:Kdm4a UTSW 4 118,017,399 (GRCm39) missense probably benign
R9647:Kdm4a UTSW 4 118,003,790 (GRCm39) missense probably benign 0.01
Z1176:Kdm4a UTSW 4 118,034,699 (GRCm39) missense probably benign 0.41
Z1176:Kdm4a UTSW 4 118,010,387 (GRCm39) missense probably benign 0.00
Z1177:Kdm4a UTSW 4 118,004,366 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- AGCAGTGGAACAAGCCGTTTCCTC -3'
(R):5'- AGTCGGTGACCATACGTGCTCTTAG -3'

Sequencing Primer
(F):5'- TGTCCCCAAGCAAAGTGC -3'
(R):5'- CCATACGTGCTCTTAGGTTTGTTG -3'
Posted On 2013-04-16