Incidental Mutation 'IGL01670:Kdm4a'
ID 103464
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Kdm4a
Ensembl Gene ENSMUSG00000033326
Gene Name lysine (K)-specific demethylase 4A
Synonyms D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2
Accession Numbers
Essential gene? Possibly essential (E-score: 0.643) question?
Stock # IGL01670
Quality Score
Status
Chromosome 4
Chromosomal Location 117994154-118037240 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 118017698 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 456 (Y456C)
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: Y456C

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: Y456C

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: Y456C

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: Y456C

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: Y456C

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: Y456C

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: Y456C

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: Y456C

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
Meta Mutation Damage Score 0.0747 question?
Coding Region Coverage
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: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acy1 A C 9: 106,314,006 (GRCm39) probably benign Het
Add1 C A 5: 34,777,407 (GRCm39) Q57K probably damaging Het
Alms1 A G 6: 85,655,132 (GRCm39) E3226G probably benign Het
Arl1 G T 10: 88,577,884 (GRCm39) R151L probably damaging Het
Cabs1 T A 5: 88,127,869 (GRCm39) D173E possibly damaging Het
Cdc34b T C 11: 94,632,845 (GRCm39) L15P probably benign Het
Cdyl2 A G 8: 117,351,092 (GRCm39) V13A probably damaging Het
Chd7 G T 4: 8,827,033 (GRCm39) R1026L probably damaging Het
Cldn34b4 T C X: 75,441,195 (GRCm39) S151P probably damaging Het
Col14a1 T A 15: 55,192,662 (GRCm39) I25N unknown Het
Crisp4 T A 1: 18,198,901 (GRCm39) T178S probably benign Het
Csmd2 C T 4: 128,407,164 (GRCm39) probably benign Het
Csmd3 T G 15: 47,475,225 (GRCm39) N2454H probably damaging Het
Cytip A T 2: 58,023,785 (GRCm39) I345N probably damaging Het
Frem2 A T 3: 53,564,358 (GRCm39) S50T possibly damaging Het
Gm9747 C T 1: 82,211,870 (GRCm39) probably benign Het
Gpr37 A G 6: 25,669,833 (GRCm39) F337S probably damaging Het
Herc1 A G 9: 66,394,342 (GRCm39) E4182G probably damaging Het
Isyna1 C T 8: 71,049,706 (GRCm39) P511L probably benign Het
Kera A T 10: 97,444,939 (GRCm39) R99S possibly damaging Het
Larp7-ps T C 4: 92,079,737 (GRCm39) probably null Het
Mcm2 A G 6: 88,864,614 (GRCm39) probably benign Het
Myl12a T C 17: 71,303,848 (GRCm39) T10A probably benign Het
Nav3 A G 10: 109,550,102 (GRCm39) V1876A possibly damaging Het
Nkx6-1 T A 5: 101,809,806 (GRCm39) Q247L probably benign Het
Nol8 A C 13: 49,814,784 (GRCm39) K297N possibly damaging Het
Or4c119 T A 2: 88,987,261 (GRCm39) Y86F probably benign Het
Or51e1 A T 7: 102,358,772 (GRCm39) Q102L probably damaging Het
Or5w18 A G 2: 87,633,224 (GRCm39) T164A probably benign Het
Pard3b A T 1: 62,250,807 (GRCm39) N579Y probably damaging Het
Pdcd11 T A 19: 47,094,743 (GRCm39) L509H probably damaging Het
Prss29 T C 17: 25,541,437 (GRCm39) S266P probably benign Het
Rapgef3 G T 15: 97,647,543 (GRCm39) H766N probably benign Het
Rasa1 A T 13: 85,373,609 (GRCm39) S818T probably damaging Het
Rtn4ip1 A G 10: 43,804,322 (GRCm39) M1V probably null Het
Sall1 A T 8: 89,758,199 (GRCm39) V635D probably benign Het
Slc35b4 C T 6: 34,147,484 (GRCm39) V35I probably benign Het
Slc5a11 G A 7: 122,869,172 (GRCm39) A587T probably benign Het
Slc6a21 T C 7: 44,937,557 (GRCm39) V616A possibly damaging Het
Sorl1 A G 9: 41,912,788 (GRCm39) S1398P possibly damaging Het
Srcap A G 7: 127,127,604 (GRCm39) K390E probably damaging Het
Sycp2 C T 2: 178,019,843 (GRCm39) E558K probably benign Het
Tcf20 T C 15: 82,739,564 (GRCm39) N629S possibly damaging Het
Tmem154 A G 3: 84,591,537 (GRCm39) Y29C probably damaging Het
Tmtc3 A G 10: 100,282,987 (GRCm39) I856T probably benign Het
Zswim6 A G 13: 107,865,101 (GRCm39) noncoding transcript Het
Other mutations in Kdm4a
AlleleSourceChrCoordTypePredicted EffectPPH Score
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
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
Posted On 2014-01-21