Incidental Mutation 'R5903:Kdm3a'
ID 456441
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 044101-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.961) question?
Stock # R5903 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 71565954-71609963 bp(-) (GRCm39)
Type of Mutation start gained
DNA Base Change (assembly) C to A at 71609234 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000145959 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000065509] [ENSMUST00000167220] [ENSMUST00000205289] [ENSMUST00000207023]
AlphaFold Q6PCM1
Predicted Effect probably benign
Transcript: ENSMUST00000065509
SMART Domains Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470

DomainStartEndE-ValueType
low complexity region 853 859 N/A INTRINSIC
JmjC 1060 1283 1.6e-56 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000167220
SMART Domains Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470

DomainStartEndE-ValueType
low complexity region 853 859 N/A INTRINSIC
JmjC 1060 1283 1.6e-56 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000205289
Predicted Effect probably benign
Transcript: ENSMUST00000207023
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.6%
  • 20x: 92.8%
Validation Efficiency 98% (58/59)
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: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9130230L23Rik A G 5: 66,145,661 (GRCm39) V150A unknown Het
Abraxas1 T C 5: 100,965,824 (GRCm39) probably null Het
Actl7a G T 4: 56,743,827 (GRCm39) R118L probably damaging Het
Atg2b T C 12: 105,605,618 (GRCm39) D1449G possibly damaging Het
Atg7 G A 6: 114,683,254 (GRCm39) W439* probably null Het
Atp6v0a2 T A 5: 124,789,343 (GRCm39) I370N probably damaging Het
B4galt1 T C 4: 40,807,760 (GRCm39) D347G probably damaging Het
Baz2b C T 2: 59,790,233 (GRCm39) C660Y probably damaging Het
Ccdc88c T C 12: 100,896,801 (GRCm39) Y1390C probably damaging Het
Cdcp1 G A 9: 123,002,837 (GRCm39) Q745* probably null Het
Cep97 G A 16: 55,739,889 (GRCm39) S185L probably damaging Het
Clec4d A G 6: 123,244,020 (GRCm39) H43R probably damaging Het
Cntn3 T A 6: 102,219,094 (GRCm39) M509L probably benign Het
Cntrob A C 11: 69,200,201 (GRCm39) S564R possibly damaging Het
Cyp2j8 T A 4: 96,395,514 (GRCm39) N37I possibly damaging Het
Edc4 A G 8: 106,617,219 (GRCm39) T1029A probably benign Het
Fhip2b A T 14: 70,829,121 (GRCm39) V64E probably damaging Het
Fmnl1 G T 11: 103,062,270 (GRCm39) probably null Het
Fzd6 T A 15: 38,870,783 (GRCm39) M1K probably null Het
Gle1 C A 2: 29,830,293 (GRCm39) T283N probably benign Het
Hsd17b14 T C 7: 45,215,386 (GRCm39) V161A probably damaging Het
Hsf2 T C 10: 57,380,819 (GRCm39) S218P probably benign Het
Ipo7 T A 7: 109,650,020 (GRCm39) C736S probably damaging Het
Itpkb G T 1: 180,241,540 (GRCm39) V737L probably damaging Het
Itpr1 T C 6: 108,466,758 (GRCm39) probably benign Het
Kcnh8 G T 17: 53,110,364 (GRCm39) V192L possibly damaging Het
Kctd10 G A 5: 114,518,523 (GRCm39) probably benign Het
Kif5a T A 10: 127,066,447 (GRCm39) M990L probably benign Het
Klf12 A G 14: 100,260,124 (GRCm39) S202P probably damaging Het
Krt81 T G 15: 101,358,083 (GRCm39) Q390P probably damaging Het
Lrig3 T C 10: 125,844,347 (GRCm39) S604P probably damaging Het
Ms4a1 A T 19: 11,235,612 (GRCm39) V48D probably damaging Het
Mta1 C T 12: 113,100,239 (GRCm39) P688L probably damaging Het
Oas1h T C 5: 121,009,040 (GRCm39) V250A probably damaging Het
Or10c1 A T 17: 37,521,912 (GRCm39) Y277* probably null Het
Or52z13 G T 7: 103,247,128 (GRCm39) G202* probably null Het
P2rx3 T C 2: 84,831,071 (GRCm39) E265G possibly damaging Het
Pdzd8 A G 19: 59,333,718 (GRCm39) I101T possibly damaging Het
Psme4 A T 11: 30,791,589 (GRCm39) N1148I probably benign Het
Rnf213 T C 11: 119,312,195 (GRCm39) L874P probably damaging Het
Sart3 T C 5: 113,889,300 (GRCm39) Y508C probably damaging Het
Sez6l2 T C 7: 126,569,305 (GRCm39) probably benign Het
Slc9b1 C T 3: 135,098,655 (GRCm39) probably benign Het
Stmn3 T C 2: 180,950,573 (GRCm39) K78E possibly damaging Het
Thsd4 T A 9: 60,301,389 (GRCm39) N302I possibly damaging Het
Trdv5 A T 14: 54,386,242 (GRCm39) H74Q probably benign Het
Tubb4b C T 2: 25,113,993 (GRCm39) R77H probably benign Het
Ugt1a6a C T 1: 88,142,845 (GRCm39) P113L probably damaging Het
Unc5a T A 13: 55,147,503 (GRCm39) C438S possibly damaging Het
Zan C A 5: 137,440,396 (GRCm39) C1946F unknown 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
R1175:Kdm3a UTSW 6 71,577,011 (GRCm39) missense possibly damaging 0.94
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
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 2017-02-15