Incidental Mutation 'IGL01670:Kdm4a'
ID103464
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Kdm4a
Ensembl Gene ENSMUSG00000033326
Gene Namelysine (K)-specific demethylase 4A
SynonymsJmjd2, D4Ertd222e, JHDM3A, Jmjd2a
Accession Numbers
Is this an essential gene? Possibly essential (E-score: 0.712) question?
Stock #IGL01670
Quality Score
Status
Chromosome4
Chromosomal Location118136957-118180043 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 118160501 bp
ZygosityHeterozygous
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]
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: 106,436,807 probably benign Het
Add1 C A 5: 34,620,063 Q57K probably damaging Het
Alms1 A G 6: 85,678,150 E3226G probably benign Het
Arl1 G T 10: 88,742,022 R151L probably damaging Het
Cabs1 T A 5: 87,980,010 D173E possibly damaging Het
Cdc34b T C 11: 94,742,019 L15P probably benign Het
Cdyl2 A G 8: 116,624,353 V13A probably damaging Het
Chd7 G T 4: 8,827,033 R1026L probably damaging Het
Cldn34b4 T C X: 76,397,589 S151P probably damaging Het
Col14a1 T A 15: 55,329,266 I25N unknown Het
Crisp4 T A 1: 18,128,677 T178S probably benign Het
Csmd2 C T 4: 128,513,371 probably benign Het
Csmd3 T G 15: 47,611,829 N2454H probably damaging Het
Cytip A T 2: 58,133,773 I345N probably damaging Het
Frem2 A T 3: 53,656,937 S50T possibly damaging Het
Gm12666 T C 4: 92,191,500 probably null Het
Gm9747 C T 1: 82,234,149 probably benign Het
Gpr37 A G 6: 25,669,834 F337S probably damaging Het
Herc1 A G 9: 66,487,060 E4182G probably damaging Het
Isyna1 C T 8: 70,597,056 P511L probably benign Het
Kera A T 10: 97,609,077 R99S possibly damaging Het
Mcm2 A G 6: 88,887,632 probably benign Het
Myl12a T C 17: 70,996,853 T10A probably benign Het
Nav3 A G 10: 109,714,241 V1876A possibly damaging Het
Nkx6-1 T A 5: 101,661,940 Q247L probably benign Het
Nol8 A C 13: 49,661,308 K297N possibly damaging Het
Olfr1143 A G 2: 87,802,880 T164A probably benign Het
Olfr1224-ps1 T A 2: 89,156,917 Y86F probably benign Het
Olfr558 A T 7: 102,709,565 Q102L probably damaging Het
Pard3b A T 1: 62,211,648 N579Y probably damaging Het
Pdcd11 T A 19: 47,106,304 L509H probably damaging Het
Prss29 T C 17: 25,322,463 S266P probably benign Het
Rapgef3 G T 15: 97,749,662 H766N probably benign Het
Rasa1 A T 13: 85,225,490 S818T probably damaging Het
Rtn4ip1 A G 10: 43,928,326 M1V probably null Het
Sall1 A T 8: 89,031,571 V635D probably benign Het
Slc35b4 C T 6: 34,170,549 V35I probably benign Het
Slc5a11 G A 7: 123,269,949 A587T probably benign Het
Slc6a21 T C 7: 45,288,133 V616A possibly damaging Het
Sorl1 A G 9: 42,001,492 S1398P possibly damaging Het
Srcap A G 7: 127,528,432 K390E probably damaging Het
Sycp2 C T 2: 178,378,050 E558K probably benign Het
Tcf20 T C 15: 82,855,363 N629S possibly damaging Het
Tmem154 A G 3: 84,684,230 Y29C probably damaging Het
Tmtc3 A G 10: 100,447,125 I856T probably benign Het
Zswim6 A G 13: 107,728,566 noncoding transcript Het
Other mutations in Kdm4a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01845:Kdm4a APN 4 118160459 missense possibly damaging 0.85
IGL02009:Kdm4a APN 4 118160169 missense probably benign 0.01
IGL02296:Kdm4a APN 4 118177465 missense probably damaging 1.00
IGL02366:Kdm4a APN 4 118160506 critical splice acceptor site probably null
IGL02606:Kdm4a APN 4 118160289 missense probably benign 0.00
IGL02673:Kdm4a APN 4 118168572 missense probably benign 0.00
R0245:Kdm4a UTSW 4 118175689 missense probably benign 0.05
R0326:Kdm4a UTSW 4 118161706 missense probably benign 0.00
R0551:Kdm4a UTSW 4 118138231 makesense probably null
R0603:Kdm4a UTSW 4 118142511 missense probably damaging 1.00
R0652:Kdm4a UTSW 4 118175689 missense probably benign 0.05
R0799:Kdm4a UTSW 4 118146992 splice site probably null
R0847:Kdm4a UTSW 4 118164498 missense probably damaging 0.96
R1307:Kdm4a UTSW 4 118175642 missense probably benign 0.02
R1572:Kdm4a UTSW 4 118138949 missense possibly damaging 0.89
R1869:Kdm4a UTSW 4 118138871 missense probably null 1.00
R1902:Kdm4a UTSW 4 118160399 missense probably benign 0.38
R1903:Kdm4a UTSW 4 118160399 missense probably benign 0.38
R2135:Kdm4a UTSW 4 118142459 missense probably damaging 1.00
R3856:Kdm4a UTSW 4 118153231 missense probably damaging 1.00
R4687:Kdm4a UTSW 4 118144083 missense probably damaging 1.00
R4940:Kdm4a UTSW 4 118161754 missense probably benign 0.00
R5115:Kdm4a UTSW 4 118162581 missense possibly damaging 0.75
R5229:Kdm4a UTSW 4 118146605 missense probably damaging 0.99
R5305:Kdm4a UTSW 4 118160501 missense probably damaging 1.00
R5423:Kdm4a UTSW 4 118138908 missense probably damaging 1.00
R5750:Kdm4a UTSW 4 118142199 intron probably benign
R5849:Kdm4a UTSW 4 118161840 missense probably benign 0.17
R5876:Kdm4a UTSW 4 118138876 missense probably damaging 0.98
R6564:Kdm4a UTSW 4 118177439 missense probably benign 0.18
R6772:Kdm4a UTSW 4 118142555 critical splice acceptor site probably null
R6982:Kdm4a UTSW 4 118153439 intron probably null
R7410:Kdm4a UTSW 4 118143918 missense possibly damaging 0.64
R7418:Kdm4a UTSW 4 118160243 missense probably damaging 0.99
Z1176:Kdm4a UTSW 4 118153190 missense probably benign 0.00
Z1176:Kdm4a UTSW 4 118177502 missense probably benign 0.41
Z1177:Kdm4a UTSW 4 118147169 missense probably benign
Posted On2014-01-21