Incidental Mutation 'R0603:Kdm4a'
ID 55539
Institutional Source Beutler Lab
Gene Symbol Kdm4a
Ensembl Gene ENSMUSG00000033326
Gene Name lysine (K)-specific demethylase 4A
Synonyms D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2
MMRRC Submission 038792-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.643) question?
Stock # R0603 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 117994154-118037240 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 117999708 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Isoleucine at position 905 (V905I)
Ref Sequence ENSEMBL: ENSMUSP00000102014 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000050288] [ENSMUST00000097911] [ENSMUST00000106403] [ENSMUST00000106406]
AlphaFold Q8BW72
Predicted Effect probably damaging
Transcript: ENSMUST00000050288
AA Change: V905I

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: V905I

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 damaging
Transcript: ENSMUST00000097911
AA Change: V905I

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: V905I

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 damaging
Transcript: ENSMUST00000106403
AA Change: V905I

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: V905I

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 damaging
Transcript: ENSMUST00000106406
AA Change: V905I

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: V905I

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: ENSMUST00000152808
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.9%
  • 10x: 97.6%
  • 20x: 95.3%
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: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Anapc7 A G 5: 122,578,233 (GRCm39) N406S probably benign Het
Arhgap4 C T X: 72,950,389 (GRCm39) R54Q probably damaging Het
Asb15 T A 6: 24,556,556 (GRCm39) I17N probably damaging Het
Atp8a1 T C 5: 67,914,039 (GRCm39) probably null Het
Caprin1 A G 2: 103,627,146 (GRCm39) V47A probably benign Het
Col4a2 T C 8: 11,464,779 (GRCm39) V348A probably benign Het
Disp2 A G 2: 118,622,487 (GRCm39) K1073R probably damaging Het
Dmxl2 G A 9: 54,313,190 (GRCm39) H1686Y possibly damaging Het
Dzank1 C T 2: 144,353,432 (GRCm39) V152I probably benign Het
Elp1 A T 4: 56,792,105 (GRCm39) I221N possibly damaging Het
Evl T A 12: 108,614,681 (GRCm39) I25N probably damaging Het
Fam117a A G 11: 95,271,699 (GRCm39) K424E probably damaging Het
Gm17732 C T 18: 62,795,823 (GRCm39) probably benign Het
Gpr158 T C 2: 21,820,480 (GRCm39) I659T possibly damaging Het
Hectd4 T A 5: 121,442,400 (GRCm39) V1280E possibly damaging Het
Irs4 T C X: 140,508,071 (GRCm39) T42A probably damaging Het
Lmtk3 T A 7: 45,444,980 (GRCm39) probably benign Het
Lsp1 G A 7: 142,043,115 (GRCm39) R221H probably damaging Het
Marf1 C T 16: 13,960,398 (GRCm39) A549T probably damaging Het
Mmut A T 17: 41,258,057 (GRCm39) I408F probably damaging Het
Nckap1 A T 2: 80,343,073 (GRCm39) V942E probably benign Het
Neto1 T A 18: 86,491,785 (GRCm39) C229S possibly damaging Het
Nipal2 A G 15: 34,650,544 (GRCm39) I63T probably damaging Het
Or11g2 T C 14: 50,855,967 (GRCm39) I96T probably damaging Het
Or1af1 G A 2: 37,110,118 (GRCm39) V206I probably damaging Het
Or4k49 A T 2: 111,495,225 (GRCm39) Y218F probably damaging Het
Or7e165 A T 9: 19,695,235 (GRCm39) R269W probably damaging Het
Or8g36 C A 9: 39,422,810 (GRCm39) V69F possibly damaging Het
Pgpep1 T C 8: 71,103,283 (GRCm39) E120G probably benign Het
Pkhd1 A T 1: 20,187,397 (GRCm39) M3637K probably benign Het
Pkm T C 9: 59,573,164 (GRCm39) V58A probably damaging Het
Ppp2r1b C A 9: 50,772,985 (GRCm39) T154K probably damaging Het
Rgs18 T A 1: 144,631,818 (GRCm39) D98V possibly damaging Het
Rsph6a G T 7: 18,799,886 (GRCm39) A506S possibly damaging Het
Selenop T A 15: 3,305,183 (GRCm39) V113E probably damaging Het
Slc6a11 G A 6: 114,221,851 (GRCm39) V514M probably benign Het
Srsf9 C T 5: 115,470,696 (GRCm39) S132L probably damaging Het
Tchh G A 3: 93,351,088 (GRCm39) R176H possibly damaging Het
Tcp11 T C 17: 28,286,784 (GRCm39) N405S probably damaging Het
Tle1 A C 4: 72,036,584 (GRCm39) D760E probably damaging Het
Tmem178 A G 17: 81,252,488 (GRCm39) D124G possibly damaging Het
Trabd G A 15: 88,966,929 (GRCm39) E118K probably damaging Het
Ttc39a A G 4: 109,283,499 (GRCm39) D115G probably damaging Het
Uaca T A 9: 60,778,379 (GRCm39) M920K possibly damaging Het
Uba2 A T 7: 33,861,038 (GRCm39) M5K probably damaging Het
Unc5c C T 3: 141,476,863 (GRCm39) P343L probably damaging Het
Wdhd1 T C 14: 47,501,043 (GRCm39) D453G probably damaging Het
Wfdc8 A G 2: 164,445,145 (GRCm39) Y157H probably damaging Het
Zbbx T G 3: 74,985,757 (GRCm39) K432Q probably benign Het
Zeb2 G A 2: 44,907,438 (GRCm39) T169M probably benign Het
Zfp956 A G 6: 47,932,962 (GRCm39) E79G probably damaging Het
Zzef1 G A 11: 72,708,895 (GRCm39) V165I probably benign 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
R0326:Kdm4a UTSW 4 118,018,903 (GRCm39) missense probably benign 0.00
R0551:Kdm4a UTSW 4 117,995,428 (GRCm39) makesense probably null
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'- CCAGAAGCCGCTTTCAGACATTACC -3'
(R):5'- ATAGGCTGAGGCAGGACATTGCTG -3'

Sequencing Primer
(F):5'- CCACTATGTCCTCAGGATAAAGGTTG -3'
(R):5'- GCAGGACATTGCTGTAAATTGG -3'
Posted On 2013-07-11