Incidental Mutation 'IGL03143:Kdm3a'
ID 410784
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Kdm3a
Ensembl Gene ENSMUSG00000053470
Gene Name lysine (K)-specific demethylase 3A
Synonyms 1700105C21Rik, Jmjd1, Jmjd1a, Tsga, C230043E16Rik
Accession Numbers
Essential gene? Probably essential (E-score: 0.961) question?
Stock # IGL03143
Quality Score
Status
Chromosome 6
Chromosomal Location 71565954-71609963 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 71573845 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 906 (I906N)
Ref Sequence ENSEMBL: ENSMUSP00000145959 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000065509] [ENSMUST00000167220] [ENSMUST00000205289] [ENSMUST00000207023]
AlphaFold Q6PCM1
Predicted Effect probably damaging
Transcript: ENSMUST00000065509
AA Change: I906N

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: I906N

DomainStartEndE-ValueType
low complexity region 853 859 N/A INTRINSIC
JmjC 1060 1283 1.6e-56 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000167220
AA Change: I906N

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: I906N

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 noncoding transcript
Transcript: ENSMUST00000205470
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205505
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206339
Predicted Effect probably damaging
Transcript: ENSMUST00000207023
AA Change: I906N

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206798
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206357
Predicted Effect probably benign
Transcript: ENSMUST00000206916
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206582
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 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: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ackr2 T G 9: 121,738,333 (GRCm39) L236R probably damaging Het
Agbl1 C T 7: 76,069,793 (GRCm39) Q442* probably null Het
Ahrr G A 13: 74,405,614 (GRCm39) Q108* probably null Het
Ankrd23 T C 1: 36,570,726 (GRCm39) probably benign Het
Art5 A G 7: 101,747,104 (GRCm39) I225T probably damaging Het
Asxl3 T C 18: 22,656,031 (GRCm39) V1347A probably benign Het
Birc6 A G 17: 74,905,994 (GRCm39) M1326V possibly damaging Het
Bpifb6 A C 2: 153,744,655 (GRCm39) N32T probably damaging Het
Brip1 T A 11: 85,952,653 (GRCm39) T1043S possibly damaging Het
Cbx5 A T 15: 103,121,532 (GRCm39) V35E probably damaging Het
Ccdc175 T A 12: 72,182,832 (GRCm39) M396L probably benign Het
Ceacam3 G T 7: 16,892,045 (GRCm39) E263* probably null Het
Cyp4a12a A G 4: 115,159,200 (GRCm39) T157A probably benign Het
Dennd11 A T 6: 40,399,828 (GRCm39) probably benign Het
Derl3 T C 10: 75,730,324 (GRCm39) V129A possibly damaging Het
Dnajb1 T C 8: 84,335,103 (GRCm39) I48T probably damaging Het
Dop1b G A 16: 93,556,543 (GRCm39) E349K probably benign Het
Fkbp10 A T 11: 100,313,580 (GRCm39) I285F probably benign Het
Frrs1 A T 3: 116,692,836 (GRCm39) T37S probably damaging Het
Gata2 A G 6: 88,181,677 (GRCm39) Y377C probably damaging Het
Gm9789 T A 16: 88,954,883 (GRCm39) probably benign Het
Itpkb T A 1: 180,160,933 (GRCm39) V353D probably benign Het
Kcng4 T C 8: 120,352,509 (GRCm39) E467G probably damaging Het
Lama1 G A 17: 68,111,531 (GRCm39) G2261R probably damaging Het
Lamc1 A T 1: 153,208,020 (GRCm39) L89Q probably benign Het
Lef1 G T 3: 130,993,965 (GRCm39) E314* probably null Het
Lpin3 T C 2: 160,745,518 (GRCm39) probably benign Het
Mrtfb A G 16: 13,218,676 (GRCm39) N452D possibly damaging Het
Naaladl1 C T 19: 6,164,896 (GRCm39) T628I possibly damaging Het
Nell1 C T 7: 49,929,281 (GRCm39) Q259* probably null Het
Neu2 G T 1: 87,524,698 (GRCm39) E228* probably null Het
Or5b119 A T 19: 13,456,835 (GRCm39) H242Q probably damaging Het
Or5k15 A G 16: 58,709,824 (GRCm39) F253S probably damaging Het
Or8g21 T G 9: 38,906,732 (GRCm39) probably benign Het
Or8k20 T C 2: 86,106,580 (GRCm39) N84D probably benign Het
Osbpl6 T A 2: 76,378,716 (GRCm39) D124E probably damaging Het
Palm T C 10: 79,652,617 (GRCm39) probably benign Het
Parp8 C A 13: 117,047,497 (GRCm39) probably benign Het
Pax7 A G 4: 139,556,798 (GRCm39) probably benign Het
Pcnx3 G A 19: 5,735,423 (GRCm39) R468W probably damaging Het
Pds5b T A 5: 150,702,722 (GRCm39) V818D probably damaging Het
Piezo2 C T 18: 63,241,147 (GRCm39) V694I probably damaging Het
Plk1 A G 7: 121,760,877 (GRCm39) probably benign Het
Polb T C 8: 23,130,367 (GRCm39) probably benign Het
Rad54b A G 4: 11,599,755 (GRCm39) T320A probably damaging Het
Reg3b G A 6: 78,349,183 (GRCm39) W103* probably null Het
Slc17a3 T G 13: 24,039,962 (GRCm39) probably null Het
Snrnp200 C T 2: 127,071,962 (GRCm39) probably benign Het
Stox2 T A 8: 47,646,839 (GRCm39) H207L possibly damaging Het
Tbx15 A C 3: 99,259,514 (GRCm39) M462L possibly damaging Het
Tcirg1 G A 19: 3,948,811 (GRCm39) T458I probably damaging Het
Tnfrsf25 A G 4: 152,201,384 (GRCm39) probably benign Het
Trank1 A G 9: 111,195,155 (GRCm39) K1060E probably damaging Het
Ttc16 T C 2: 32,664,457 (GRCm39) D3G possibly damaging Het
Vmn1r199 A C 13: 22,567,299 (GRCm39) N155H probably damaging Het
Vmn1r202 G A 13: 22,685,640 (GRCm39) T259I probably benign 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
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
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
Posted On 2016-08-02