Incidental Mutation 'R1175:Kdm3a'
ID 99934
Institutional Source Beutler Lab
Gene Symbol Kdm3a
Ensembl Gene ENSMUSG00000053470
Gene Name lysine (K)-specific demethylase 3A
Synonyms 1700105C21Rik, Jmjd1, Jmjd1a, Tsga, C230043E16Rik
MMRRC Submission 039248-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.961) question?
Stock # R1175 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 71565954-71609963 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 71577011 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 768 (E768G)
Ref Sequence ENSEMBL: ENSMUSP00000145719 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000065509] [ENSMUST00000167220] [ENSMUST00000205289] [ENSMUST00000207023]
AlphaFold Q6PCM1
Predicted Effect possibly damaging
Transcript: ENSMUST00000065509
AA Change: E768G

PolyPhen 2 Score 0.675 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: E768G

DomainStartEndE-ValueType
low complexity region 853 859 N/A INTRINSIC
JmjC 1060 1283 1.6e-56 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000167220
AA Change: E768G

PolyPhen 2 Score 0.675 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: E768G

DomainStartEndE-ValueType
low complexity region 853 859 N/A INTRINSIC
JmjC 1060 1283 1.6e-56 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000205289
AA Change: E768G

PolyPhen 2 Score 0.945 (Sensitivity: 0.80; Specificity: 0.95)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205470
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205505
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206050
Predicted Effect possibly damaging
Transcript: ENSMUST00000207023
AA Change: E768G

PolyPhen 2 Score 0.675 (Sensitivity: 0.86; Specificity: 0.92)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206339
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206704
Predicted Effect probably benign
Transcript: ENSMUST00000206916
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206798
Meta Mutation Damage Score 0.0599 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.8%
  • 10x: 94.7%
  • 20x: 88.0%
Validation Efficiency 100% (74/74)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a zinc finger protein that contains a jumonji domain and may play a role in hormone-dependent transcriptional activation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
PHENOTYPE: Male mice homozygous for a hypomorphic allele display infertility, oligoasthenoteratozoospermia, small testis, and impaired spermiogenesis. Mice homozygous for a null allele exhibit abnormal spermatogenesis and obesity associated with hyperlipidemia. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610318N02Rik T A 16: 16,935,446 (GRCm39) H214L probably benign Het
Abca17 T C 17: 24,508,325 (GRCm39) E1070G possibly damaging Het
Accsl A T 2: 93,696,589 (GRCm39) probably benign Het
Akp3 G A 1: 87,055,593 (GRCm39) G547R unknown Het
Anapc1 C A 2: 128,522,108 (GRCm39) C150F probably damaging Het
Aoc1l3 C A 6: 48,967,173 (GRCm39) P707H probably damaging Het
Arhgef18 T A 8: 3,439,023 (GRCm39) probably benign Het
Borcs5 T A 6: 134,687,096 (GRCm39) N150K probably damaging Het
C9orf72 C A 4: 35,218,630 (GRCm39) E76D probably damaging Het
Cdh20 G A 1: 109,988,862 (GRCm39) V255I probably benign Het
Cntnap5c C A 17: 58,671,241 (GRCm39) T1143K possibly damaging Het
Col7a1 A C 9: 108,784,402 (GRCm39) T137P unknown Het
Defb8 C T 8: 19,495,910 (GRCm39) G50E probably damaging Het
Dimt1 T A 13: 107,086,193 (GRCm39) probably benign Het
Dnajb11 T A 16: 22,689,423 (GRCm39) D281E probably damaging Het
Eci2 G T 13: 35,177,087 (GRCm39) N24K probably damaging Het
Fbn1 A T 2: 125,236,607 (GRCm39) C358S probably benign Het
Fbxl13 A T 5: 21,825,602 (GRCm39) probably benign Het
Fbxw11 T C 11: 32,661,922 (GRCm39) C121R probably damaging Het
Fsd2 T C 7: 81,209,518 (GRCm39) D108G probably benign Het
Gab1 C A 8: 81,511,471 (GRCm39) R458L probably damaging Het
Ghrhr T A 6: 55,365,254 (GRCm39) L416* probably null Het
Glipr1l2 C A 10: 111,919,371 (GRCm39) L31I possibly damaging Het
Gm1818 A G 12: 48,602,982 (GRCm39) noncoding transcript Het
Gm19965 T A 1: 116,748,550 (GRCm39) probably benign Het
Gpr149 A G 3: 62,511,888 (GRCm39) L37P probably damaging Het
Hoxa9 A G 6: 52,202,693 (GRCm39) I131T probably damaging Het
Itpkc T C 7: 26,927,195 (GRCm39) I240V probably benign Het
Jakmip3 A G 7: 138,629,515 (GRCm39) D552G probably damaging Het
Kank4 T C 4: 98,653,806 (GRCm39) Y874C probably damaging Het
Klf6 A G 13: 5,911,711 (GRCm39) D25G probably benign Het
Lamc1 T C 1: 153,122,977 (GRCm39) probably benign Het
Laptm4a T C 12: 8,986,716 (GRCm39) V258A probably damaging Het
Map3k19 A G 1: 127,751,617 (GRCm39) V578A probably benign Het
Mast1 T C 8: 85,651,956 (GRCm39) E342G probably benign Het
Mgat5b T C 11: 116,868,622 (GRCm39) L515P probably damaging Het
Mink1 A G 11: 70,502,166 (GRCm39) D985G probably benign Het
Mphosph9 A G 5: 124,453,739 (GRCm39) V191A possibly damaging Het
Muc6 C T 7: 141,234,368 (GRCm39) G708S probably damaging Het
Pcnt A T 10: 76,228,878 (GRCm39) probably null Het
Psmd8 A T 7: 28,875,598 (GRCm39) Y174N probably damaging Het
Ptgdr2 C A 19: 10,918,292 (GRCm39) R270S possibly damaging Het
Rasal2 A G 1: 156,975,218 (GRCm39) M1172T probably damaging Het
Rif1 A G 2: 51,997,640 (GRCm39) probably benign Het
Rnf123 C T 9: 107,954,572 (GRCm39) R48H probably benign Het
Rsrc1 T C 3: 67,263,551 (GRCm39) probably benign Het
Rxfp2 T C 5: 149,975,021 (GRCm39) V210A probably benign Het
Serpinb9d C T 13: 33,384,608 (GRCm39) P195L probably benign Het
Sis A G 3: 72,865,437 (GRCm39) probably benign Het
Skint4 T C 4: 111,981,793 (GRCm39) M246T probably benign Het
Snrnp200 C A 2: 127,070,997 (GRCm39) R1093S probably damaging Het
Sp100 A G 1: 85,629,141 (GRCm39) N471D possibly damaging Het
Spmip4 T A 6: 50,566,121 (GRCm39) K118M probably damaging Het
Ssxb8 T G X: 8,556,062 (GRCm39) H88P probably damaging Het
Sufu T C 19: 46,389,703 (GRCm39) probably null Het
Synpo2l G A 14: 20,718,235 (GRCm39) T10I possibly damaging Het
Tdo2 A T 3: 81,881,683 (GRCm39) S40R probably damaging Het
Tent4b T A 8: 88,978,635 (GRCm39) F445L probably damaging Het
Terb1 G A 8: 105,210,938 (GRCm39) T363I probably benign Het
Timd4 C T 11: 46,708,498 (GRCm39) P175S probably damaging Het
Tlr3 C A 8: 45,850,171 (GRCm39) V833L probably damaging Het
Tpst2 T A 5: 112,455,911 (GRCm39) M150K probably damaging Het
Trim67 T A 8: 125,543,774 (GRCm39) V378E probably damaging Het
Tyrp1 C T 4: 80,763,105 (GRCm39) Q331* probably null Het
Ubap2l A T 3: 89,930,807 (GRCm39) S413T probably benign Het
Uimc1 G A 13: 55,176,415 (GRCm39) T701I possibly damaging Het
Vangl2 G T 1: 171,832,353 (GRCm39) T501N probably damaging Het
Vmn1r60 A G 7: 5,547,621 (GRCm39) S160P probably benign Het
Vmn2r66 G T 7: 84,654,799 (GRCm39) D503E probably benign Het
Vmn2r72 T A 7: 85,401,152 (GRCm39) E89V probably damaging Het
Zfp457 G A 13: 67,441,748 (GRCm39) P180S probably damaging Het
Other mutations in Kdm3a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02168:Kdm3a APN 6 71,577,101 (GRCm39) missense probably damaging 1.00
IGL02219:Kdm3a APN 6 71,577,718 (GRCm39) missense probably benign 0.01
IGL02423:Kdm3a APN 6 71,590,987 (GRCm39) splice site probably benign
IGL02427:Kdm3a APN 6 71,569,184 (GRCm39) splice site probably benign
IGL02519:Kdm3a APN 6 71,588,570 (GRCm39) missense probably benign 0.04
IGL03143:Kdm3a APN 6 71,573,845 (GRCm39) missense probably damaging 0.98
IGL03279:Kdm3a APN 6 71,588,659 (GRCm39) missense probably benign
R0194:Kdm3a UTSW 6 71,601,578 (GRCm39) missense probably null 0.44
R0408:Kdm3a UTSW 6 71,588,663 (GRCm39) missense probably benign 0.00
R0426:Kdm3a UTSW 6 71,577,739 (GRCm39) missense probably damaging 1.00
R0608:Kdm3a UTSW 6 71,597,030 (GRCm39) missense probably benign 0.01
R1835:Kdm3a UTSW 6 71,590,940 (GRCm39) missense probably benign 0.14
R3821:Kdm3a UTSW 6 71,588,661 (GRCm39) missense probably benign 0.00
R5083:Kdm3a UTSW 6 71,598,346 (GRCm39) missense probably damaging 1.00
R5536:Kdm3a UTSW 6 71,588,920 (GRCm39) missense probably benign 0.31
R5903:Kdm3a UTSW 6 71,609,234 (GRCm39) start gained probably benign
R5965:Kdm3a UTSW 6 71,598,364 (GRCm39) missense probably benign 0.21
R6236:Kdm3a UTSW 6 71,588,641 (GRCm39) missense probably benign 0.00
R6541:Kdm3a UTSW 6 71,571,517 (GRCm39) missense possibly damaging 0.69
R6666:Kdm3a UTSW 6 71,588,974 (GRCm39) missense probably benign 0.00
R7090:Kdm3a UTSW 6 71,572,529 (GRCm39) missense possibly damaging 0.69
R7112:Kdm3a UTSW 6 71,609,154 (GRCm39) missense probably benign
R7136:Kdm3a UTSW 6 71,588,764 (GRCm39) missense probably benign 0.00
R7163:Kdm3a UTSW 6 71,609,061 (GRCm39) missense probably damaging 1.00
R7608:Kdm3a UTSW 6 71,577,731 (GRCm39) missense probably benign 0.01
R7614:Kdm3a UTSW 6 71,568,937 (GRCm39) missense possibly damaging 0.82
R7683:Kdm3a UTSW 6 71,576,438 (GRCm39) missense probably benign
R7687:Kdm3a UTSW 6 71,576,476 (GRCm39) missense possibly damaging 0.64
R7868:Kdm3a UTSW 6 71,572,473 (GRCm39) missense probably benign 0.31
R8447:Kdm3a UTSW 6 71,588,881 (GRCm39) missense probably benign
R8476:Kdm3a UTSW 6 71,588,693 (GRCm39) missense probably damaging 0.98
R8933:Kdm3a UTSW 6 71,577,092 (GRCm39) missense probably benign 0.00
R9046:Kdm3a UTSW 6 71,572,540 (GRCm39) missense probably damaging 1.00
R9211:Kdm3a UTSW 6 71,573,674 (GRCm39) missense probably benign 0.07
R9569:Kdm3a UTSW 6 71,584,434 (GRCm39) missense probably benign 0.02
R9727:Kdm3a UTSW 6 71,569,094 (GRCm39) nonsense probably null
RF053:Kdm3a UTSW 6 71,609,033 (GRCm39) critical splice donor site probably benign
Predicted Primers
Posted On 2014-01-15