Incidental Mutation 'R1307:Kdm4a'
ID 157823
Institutional Source Beutler Lab
Gene Symbol Kdm4a
Ensembl Gene ENSMUSG00000033326
Gene Name lysine (K)-specific demethylase 4A
Synonyms D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2
MMRRC Submission 039373-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.643) question?
Stock # R1307 (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 118032839 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 76 (T76A)
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: T76A

PolyPhen 2 Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: T76A

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: T76A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: T76A

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: T76A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: T76A

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: T76A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: T76A

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
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 98.0%
  • 10x: 95.6%
  • 20x: 91.4%
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: 23 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ascc1 A T 10: 59,848,321 (GRCm39) I83L probably benign Het
Bcl2a1b T C 9: 89,081,543 (GRCm39) V44A probably damaging Het
Bdp1 T C 13: 100,186,271 (GRCm39) D1727G possibly damaging Het
Cabp1 A G 5: 115,310,965 (GRCm39) F294L probably damaging Het
Coq8b T A 7: 26,950,016 (GRCm39) M365K probably damaging Het
Gk2 A T 5: 97,603,268 (GRCm39) D523E probably benign Het
Havcr1 C T 11: 46,647,097 (GRCm39) T177I probably damaging Het
Lama4 A T 10: 38,946,028 (GRCm39) I804F probably benign Het
Ntn4 C T 10: 93,543,215 (GRCm39) R314W probably damaging Het
Pcdh10 A G 3: 45,336,314 (GRCm39) N876S probably benign Het
Polr3f T C 2: 144,375,113 (GRCm39) V95A probably damaging Het
Ptk2 A G 15: 73,163,895 (GRCm39) V389A probably benign Het
Rhof T C 5: 123,258,378 (GRCm39) E151G probably damaging Het
Slc25a28 T C 19: 43,655,470 (GRCm39) N135S probably benign Het
Sphk1 G A 11: 116,426,928 (GRCm39) V295I probably benign Het
Sv2b G T 7: 74,856,182 (GRCm39) T36K probably damaging Het
Sybu T C 15: 44,538,786 (GRCm39) E291G probably damaging Het
Tnc T C 4: 63,927,096 (GRCm39) E810G probably damaging Het
Uba52 T C 8: 70,961,166 (GRCm39) H68R probably damaging Het
Unc79 A G 12: 103,036,335 (GRCm39) N552S probably damaging Het
Ush2a T C 1: 188,090,164 (GRCm39) C416R probably damaging Het
Ush2a T C 1: 188,184,037 (GRCm39) V1447A probably damaging Het
Zfp985 C T 4: 147,667,704 (GRCm39) L191F 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
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
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'- TACTGGCTGAGCCTTAACTGCTGC -3'
(R):5'- TGTTCTCGTGACAGCGTGACTTCC -3'

Sequencing Primer
(F):5'- CTTAACTGCTGCGCTTGAAG -3'
(R):5'- TCTGGTAAAATGGACCGCTAGTC -3'
Posted On 2014-02-18