Incidental Mutation 'R1175:Kdm3a'
ID99934
Institutional Source Beutler Lab
Gene Symbol Kdm3a
Ensembl Gene ENSMUSG00000053470
Gene Namelysine (K)-specific demethylase 3A
SynonymsC230043E16Rik, Jmjd1a, Tsga, 1700105C21Rik, Jmjd1
MMRRC Submission 039248-MU
Accession Numbers
Is this an essential gene? Probably essential (E-score: 0.957) question?
Stock #R1175 (G1)
Quality Score225
Status Validated
Chromosome6
Chromosomal Location71588972-71632990 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 71600027 bp
ZygosityHeterozygous
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]
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 noncoding transcript
Transcript: ENSMUST00000206339
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206704
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206798
Predicted Effect probably benign
Transcript: ENSMUST00000206916
Predicted Effect possibly damaging
Transcript: ENSMUST00000207023
AA Change: E768G

PolyPhen 2 Score 0.675 (Sensitivity: 0.86; Specificity: 0.92)
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: 17,117,582 H214L probably benign Het
3110043O21Rik C A 4: 35,218,630 E76D probably damaging Het
4921507P07Rik T A 6: 50,589,141 K118M probably damaging Het
A430078G23Rik T A 8: 3,389,023 probably benign Het
Abca17 T C 17: 24,289,351 E1070G possibly damaging Het
Accsl A T 2: 93,866,244 probably benign Het
Akp3 G A 1: 87,127,871 G547R unknown Het
Anapc1 C A 2: 128,680,188 C150F probably damaging Het
Borcs5 T A 6: 134,710,133 N150K probably damaging Het
Cdh7 G A 1: 110,061,132 V255I probably benign Het
Cntnap5c C A 17: 58,364,246 T1143K possibly damaging Het
Col7a1 A C 9: 108,955,334 T137P unknown Het
Defb8 C T 8: 19,445,894 G50E probably damaging Het
Dimt1 T A 13: 106,949,685 probably benign Het
Dnajb11 T A 16: 22,870,673 D281E probably damaging Het
Eci2 G T 13: 34,993,104 N24K probably damaging Het
Fbn1 A T 2: 125,394,687 C358S probably benign Het
Fbxl13 A T 5: 21,620,604 probably benign Het
Fbxw11 T C 11: 32,711,922 C121R probably damaging Het
Fsd2 T C 7: 81,559,770 D108G probably benign Het
Gab1 C A 8: 80,784,842 R458L probably damaging Het
Ghrhr T A 6: 55,388,269 L416* probably null Het
Glipr1l2 C A 10: 112,083,466 L31I possibly damaging Het
Gm1818 A G 12: 48,556,199 noncoding transcript Het
Gm19965 T A 1: 116,820,820 probably benign Het
Gpr149 A G 3: 62,604,467 L37P probably damaging Het
Hoxa9 A G 6: 52,225,713 I131T probably damaging Het
Itpkc T C 7: 27,227,770 I240V probably benign Het
Jakmip3 A G 7: 139,027,786 D552G probably damaging Het
Kank4 T C 4: 98,765,569 Y874C probably damaging Het
Klf6 A G 13: 5,861,712 D25G probably benign Het
Lamc1 T C 1: 153,247,231 probably benign Het
Laptm4a T C 12: 8,936,716 V258A probably damaging Het
Map3k19 A G 1: 127,823,880 V578A probably benign Het
Mast1 T C 8: 84,925,327 E342G probably benign Het
Mgat5b T C 11: 116,977,796 L515P probably damaging Het
Mink1 A G 11: 70,611,340 D985G probably benign Het
Mphosph9 A G 5: 124,315,676 V191A possibly damaging Het
Muc6 C T 7: 141,648,101 G708S probably damaging Het
Papd5 T A 8: 88,252,007 F445L probably damaging Het
Pcnt A T 10: 76,393,044 probably null Het
Psmd8 A T 7: 29,176,173 Y174N probably damaging Het
Ptgdr2 C A 19: 10,940,928 R270S possibly damaging Het
Rasal2 A G 1: 157,147,648 M1172T probably damaging Het
Rif1 A G 2: 52,107,628 probably benign Het
Rnf123 C T 9: 108,077,373 R48H probably benign Het
Rsrc1 T C 3: 67,356,218 probably benign Het
Rxfp2 T C 5: 150,051,556 V210A probably benign Het
Serpinb9d C T 13: 33,200,625 P195L probably benign Het
Sis A G 3: 72,958,104 probably benign Het
Skint4 T C 4: 112,124,596 M246T probably benign Het
Snrnp200 C A 2: 127,229,077 R1093S probably damaging Het
Sp100 A G 1: 85,701,420 N471D possibly damaging Het
Ssxb8 T G X: 8,689,823 H88P probably damaging Het
Sufu T C 19: 46,401,264 probably null Het
Svs1 C A 6: 48,990,239 P707H probably damaging Het
Synpo2l G A 14: 20,668,167 T10I possibly damaging Het
Tdo2 A T 3: 81,974,376 S40R probably damaging Het
Terb1 G A 8: 104,484,306 T363I probably benign Het
Timd4 C T 11: 46,817,671 P175S probably damaging Het
Tlr3 C A 8: 45,397,134 V833L probably damaging Het
Tpst2 T A 5: 112,308,045 M150K probably damaging Het
Trim67 T A 8: 124,817,035 V378E probably damaging Het
Tyrp1 C T 4: 80,844,868 Q331* probably null Het
Ubap2l A T 3: 90,023,500 S413T probably benign Het
Uimc1 G A 13: 55,028,602 T701I possibly damaging Het
Vangl2 G T 1: 172,004,786 T501N probably damaging Het
Vmn1r60 A G 7: 5,544,622 S160P probably benign Het
Vmn2r66 G T 7: 85,005,591 D503E probably benign Het
Vmn2r72 T A 7: 85,751,944 E89V probably damaging Het
Zfp457 G A 13: 67,293,684 P180S probably damaging Het
Other mutations in Kdm3a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02168:Kdm3a APN 6 71600117 missense probably damaging 1.00
IGL02219:Kdm3a APN 6 71600734 missense probably benign 0.01
IGL02423:Kdm3a APN 6 71614003 splice site probably benign
IGL02427:Kdm3a APN 6 71592200 splice site probably benign
IGL02519:Kdm3a APN 6 71611586 missense probably benign 0.04
IGL03143:Kdm3a APN 6 71596861 missense probably damaging 0.98
IGL03279:Kdm3a APN 6 71611675 missense probably benign
R0194:Kdm3a UTSW 6 71624594 missense probably null 0.44
R0408:Kdm3a UTSW 6 71611679 missense probably benign 0.00
R0426:Kdm3a UTSW 6 71600755 missense probably damaging 1.00
R0608:Kdm3a UTSW 6 71620046 missense probably benign 0.01
R1835:Kdm3a UTSW 6 71613956 missense probably benign 0.14
R3821:Kdm3a UTSW 6 71611677 missense probably benign 0.00
R5083:Kdm3a UTSW 6 71621362 missense probably damaging 1.00
R5536:Kdm3a UTSW 6 71611936 missense probably benign 0.31
R5903:Kdm3a UTSW 6 71632250 start gained probably benign
R5965:Kdm3a UTSW 6 71621380 missense probably benign 0.21
R6236:Kdm3a UTSW 6 71611657 missense probably benign 0.00
R6541:Kdm3a UTSW 6 71594533 missense possibly damaging 0.69
R6666:Kdm3a UTSW 6 71611990 missense probably benign 0.00
R7090:Kdm3a UTSW 6 71595545 missense possibly damaging 0.69
R7112:Kdm3a UTSW 6 71632170 missense probably benign
R7136:Kdm3a UTSW 6 71611780 missense probably benign 0.00
R7163:Kdm3a UTSW 6 71632077 missense probably damaging 1.00
R7608:Kdm3a UTSW 6 71600747 missense probably benign 0.01
R7614:Kdm3a UTSW 6 71591953 missense possibly damaging 0.82
R7683:Kdm3a UTSW 6 71599454 missense probably benign
R7687:Kdm3a UTSW 6 71599492 missense possibly damaging 0.64
R7868:Kdm3a UTSW 6 71595489 missense probably benign 0.31
R8447:Kdm3a UTSW 6 71611897 missense probably benign
RF053:Kdm3a UTSW 6 71632049 critical splice donor site probably benign
Predicted Primers
Posted On2014-01-15