Incidental Mutation 'RF053:Kdm3a'
ID |
605181 |
Institutional Source |
Beutler Lab
|
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)
|
Stock # |
RF053 (G1)
|
Quality Score |
100.457 |
Status
|
Not validated
|
Chromosome |
6 |
Chromosomal Location |
71565954-71609963 bp(-) (GRCm39) |
Type of Mutation |
critical splice donor site |
DNA Base Change (assembly) |
TTTTT to TTTTTT
at 71609033 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Ref Sequence |
ENSEMBL: ENSMUSP00000065716
(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
Domain | Start | End | E-Value | Type |
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
Domain | Start | End | E-Value | Type |
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: 99.8%
- 3x: 99.7%
- 10x: 99.3%
- 20x: 98.6%
|
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: 20 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
A030005L19Rik |
TGGCTGCTG |
TGGCTGCTGGGGCTGCTG |
1: 82,891,294 (GRCm39) |
|
probably benign |
Het |
Abra |
TGGC |
T |
15: 41,729,695 (GRCm39) |
|
probably benign |
Het |
Blm |
CTCCTCCTCCTC |
CTCCTCCTCCTCATCCTCCTCCTC |
7: 80,162,669 (GRCm39) |
|
probably benign |
Het |
Bmp5 |
TGAGGAG |
T |
9: 75,683,656 (GRCm39) |
|
probably benign |
Het |
Cngb1 |
GGCTCTGGCTCTGGCTCTGGCTCTG |
GG |
8: 96,030,276 (GRCm39) |
|
probably null |
Het |
Cyb5r4 |
GGATGTGACAGACACACTGCCCAG |
GGATGTGACAGACACACTGCCCAGCGATGTGACAGACACACTGCCCAG |
9: 86,922,475 (GRCm39) |
|
probably benign |
Het |
Ehbp1l1 |
TCACACCACC |
T |
19: 5,766,030 (GRCm39) |
|
probably benign |
Het |
Krtap28-10 |
CAGCCACCACAGC |
CAGCCACCACAGCCAAAGCCACCACAGC |
1: 83,019,999 (GRCm39) |
|
probably benign |
Het |
Mamld1 |
CA |
CAGAA |
X: 70,162,458 (GRCm39) |
|
probably benign |
Het |
Map1a |
CTCCAGCTCCAGCTCCAGCTCCAGCTCCA |
CTCCAGCTCCAGCTCCAGCTCCAGCTCCAGATCCAGCTCCAGCTCCAGCTCCAGCTCCA |
2: 121,136,771 (GRCm39) |
|
probably benign |
Het |
Med12l |
CAG |
CAGAAG |
3: 59,183,414 (GRCm39) |
|
probably benign |
Het |
Nefh |
GACTTGGCCTCACCT |
GACTTGGCCTCACCTCACCACTTGGCCTCACCT |
11: 4,891,014 (GRCm39) |
|
probably null |
Het |
Polr1has |
CACCAC |
CACCACCACCACCACCACCTCTACCAC |
17: 37,275,958 (GRCm39) |
|
probably benign |
Het |
Rap1gds1 |
TCATTTATTATGACCATAC |
TC |
3: 138,647,418 (GRCm39) |
|
probably null |
Het |
Tcof1 |
C |
CAGA |
18: 60,968,819 (GRCm39) |
|
probably benign |
Het |
Tfeb |
AGC |
AGCCGC |
17: 48,097,039 (GRCm39) |
|
probably benign |
Het |
Trappc9 |
TGCT |
TGCTGCTGCTGCTGCGGCT |
15: 72,673,177 (GRCm39) |
|
probably benign |
Het |
Usp2 |
C |
CTCATGTGACCTGTTCTTCACTTAA |
9: 44,000,426 (GRCm39) |
|
probably benign |
Het |
Zfp598 |
CCCACCACCACAACCACCACCACCACCACCAC |
CCCACCACCACCACCACAACCACCACCACCACCACCAC |
17: 24,899,735 (GRCm39) |
|
probably benign |
Het |
Zfp69 |
GTGCCAGGGGTCTCTCCATCATGGGATCCTGCTGCAGGGATGCCAGGGGTCTCTCCATCATGGGATCCTGCTGCAGGGGTGCCAGGGGTCGCTTCATCATGGGATCCTGTTGCAGTGGTGCCAGGGGTCGCTCCATCATGGGATCCTGCTGCAGGGGTGCCAGGGGTC |
GTGCCAGGGGTCTCTCCATCATGGGATCCTGCTGCAGGGGTGCCAGGGGTCGCTTCATCATGGGATCCTGTTGCAGTGGTGCCAGGGGTCGCTCCATCATGGGATCCTGCTGCAGGGGTGCCAGGGGTC |
4: 120,804,544 (GRCm39) |
|
probably benign |
Het |
|
Other mutations in Kdm3a |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
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 |
|
|
Predicted Primers |
PCR Primer
(F):5'- CCCATTTCAAAGACTTTCACGGTC -3'
(R):5'- AAACCATGGTGCTCACGCTC -3'
Sequencing Primer
(F):5'- AGACTTTCACGGTCTAGAGTTC -3'
(R):5'- CTCACGCTCGGAGAAAGTTG -3'
|
Posted On |
2019-12-04 |