Incidental Mutation 'R7687:Kdm3a'
ID |
593147 |
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 # |
R7687 (G1)
|
Quality Score |
225.009 |
Status
|
Not validated
|
Chromosome |
6 |
Chromosomal Location |
71565954-71609963 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 71576476 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Lysine to Asparagine
at position 779
(K779N)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000065716
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000065509]
[ENSMUST00000167220]
[ENSMUST00000205289]
[ENSMUST00000207023]
|
AlphaFold |
Q6PCM1 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000065509
AA Change: K779N
PolyPhen 2
Score 0.638 (Sensitivity: 0.87; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000065716 Gene: ENSMUSG00000053470 AA Change: K779N
Domain | Start | End | E-Value | Type |
low complexity region
|
853 |
859 |
N/A |
INTRINSIC |
JmjC
|
1060 |
1283 |
1.6e-56 |
SMART |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000167220
AA Change: K779N
PolyPhen 2
Score 0.638 (Sensitivity: 0.87; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000128789 Gene: ENSMUSG00000053470 AA Change: K779N
Domain | Start | End | E-Value | Type |
low complexity region
|
853 |
859 |
N/A |
INTRINSIC |
JmjC
|
1060 |
1283 |
1.6e-56 |
SMART |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000205289
AA Change: K779N
PolyPhen 2
Score 0.638 (Sensitivity: 0.87; Specificity: 0.91)
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000206916
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000207023
AA Change: K779N
PolyPhen 2
Score 0.638 (Sensitivity: 0.87; Specificity: 0.91)
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.1%
|
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: 51 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca12 |
T |
C |
1: 71,297,341 (GRCm39) |
K2383R |
probably benign |
Het |
Acly |
C |
T |
11: 100,395,680 (GRCm39) |
|
probably null |
Het |
Baiap3 |
T |
A |
17: 25,468,311 (GRCm39) |
I276F |
possibly damaging |
Het |
Cdc14b |
A |
T |
13: 64,357,007 (GRCm39) |
D419E |
probably benign |
Het |
Celsr2 |
G |
T |
3: 108,305,085 (GRCm39) |
P2165T |
probably benign |
Het |
Clk4 |
A |
G |
11: 51,172,225 (GRCm39) |
D476G |
probably benign |
Het |
Dera |
A |
G |
6: 137,813,878 (GRCm39) |
T10A |
|
Het |
Dip2c |
A |
T |
13: 9,654,617 (GRCm39) |
T742S |
probably benign |
Het |
Dohh |
C |
A |
10: 81,223,640 (GRCm39) |
A231E |
probably benign |
Het |
Dot1l |
T |
G |
10: 80,625,202 (GRCm39) |
S1150A |
possibly damaging |
Het |
Eea1 |
T |
A |
10: 95,862,460 (GRCm39) |
I794N |
probably benign |
Het |
En2 |
T |
C |
5: 28,375,287 (GRCm39) |
S277P |
probably damaging |
Het |
Erich1 |
A |
G |
8: 14,080,691 (GRCm39) |
L276P |
probably damaging |
Het |
Flnb |
A |
G |
14: 7,924,224 (GRCm38) |
N1779S |
probably damaging |
Het |
Frzb |
T |
A |
2: 80,254,979 (GRCm39) |
T186S |
probably benign |
Het |
Gdf7 |
T |
A |
12: 8,348,257 (GRCm39) |
R347* |
probably null |
Het |
Ighv9-4 |
T |
C |
12: 114,263,883 (GRCm39) |
I17V |
not run |
Het |
Ipo13 |
G |
A |
4: 117,769,088 (GRCm39) |
P235S |
probably benign |
Het |
Itga2 |
C |
A |
13: 115,002,796 (GRCm39) |
G565C |
probably damaging |
Het |
Kcnc4 |
CCCGCCGCCGCCGCCGCCGCCGC |
CCCGCCGCCGCCGCCGCCGCCGCCGC |
3: 107,365,925 (GRCm39) |
|
probably benign |
Het |
Kcnk10 |
A |
G |
12: 98,401,355 (GRCm39) |
I440T |
probably damaging |
Het |
Kmt2d |
C |
T |
15: 98,760,001 (GRCm39) |
D1086N |
unknown |
Het |
Kntc1 |
A |
G |
5: 123,897,152 (GRCm39) |
I172V |
probably benign |
Het |
Maip1 |
A |
G |
1: 57,451,003 (GRCm39) |
E215G |
probably damaging |
Het |
Mms19 |
A |
T |
19: 41,943,607 (GRCm39) |
M417K |
possibly damaging |
Het |
Mslnl |
T |
C |
17: 25,962,157 (GRCm39) |
V185A |
probably damaging |
Het |
Naa11 |
A |
T |
5: 97,539,648 (GRCm39) |
V170E |
probably benign |
Het |
Ncapg |
C |
T |
5: 45,857,227 (GRCm39) |
P980S |
probably benign |
Het |
Or2aj5 |
T |
C |
16: 19,424,485 (GRCm39) |
N310S |
probably benign |
Het |
Pbxip1 |
A |
G |
3: 89,355,506 (GRCm39) |
D675G |
probably damaging |
Het |
Pdlim5 |
A |
G |
3: 141,983,608 (GRCm39) |
S382P |
probably benign |
Het |
Pkd1l1 |
T |
A |
11: 8,804,390 (GRCm39) |
I2184F |
|
Het |
Plau |
A |
G |
14: 20,889,866 (GRCm39) |
Y237C |
probably damaging |
Het |
Ppl |
T |
C |
16: 4,915,806 (GRCm39) |
T586A |
probably benign |
Het |
Rapgef6 |
T |
G |
11: 54,551,901 (GRCm39) |
I923S |
possibly damaging |
Het |
Rbfox2 |
C |
T |
15: 77,190,694 (GRCm39) |
G17D |
unknown |
Het |
Sema3b |
T |
C |
9: 107,481,013 (GRCm39) |
D108G |
probably damaging |
Het |
Slc6a20a |
A |
G |
9: 123,485,331 (GRCm39) |
I297T |
probably damaging |
Het |
Slit1 |
A |
G |
19: 41,639,128 (GRCm39) |
F261L |
probably benign |
Het |
Tcp10a |
T |
A |
17: 7,612,507 (GRCm39) |
V433D |
probably damaging |
Het |
Tktl2 |
A |
G |
8: 66,965,753 (GRCm39) |
E437G |
probably damaging |
Het |
Tll1 |
G |
T |
8: 64,574,526 (GRCm39) |
Y109* |
probably null |
Het |
Tmem79 |
A |
G |
3: 88,239,888 (GRCm39) |
V274A |
probably damaging |
Het |
Tnfrsf23 |
G |
A |
7: 143,235,199 (GRCm39) |
S55L |
probably benign |
Het |
Ubd |
T |
C |
17: 37,504,865 (GRCm39) |
|
probably null |
Het |
Ubl3 |
C |
A |
5: 148,442,985 (GRCm39) |
R105L |
possibly damaging |
Het |
Ubl7 |
A |
T |
9: 57,821,867 (GRCm39) |
D72V |
probably damaging |
Het |
Wdr55 |
T |
C |
18: 36,895,076 (GRCm39) |
S81P |
probably damaging |
Het |
Wtip |
T |
C |
7: 33,816,044 (GRCm39) |
Y344C |
probably damaging |
Het |
Zfp488 |
A |
G |
14: 33,692,357 (GRCm39) |
S269P |
possibly damaging |
Het |
Zkscan2 |
A |
C |
7: 123,099,085 (GRCm39) |
S36A |
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 |
|
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 |
PCR Primer
(F):5'- GGGGACACTCACCCTTATTCTC -3'
(R):5'- GCTGATATGTGAGGGCAAATAC -3'
Sequencing Primer
(F):5'- CCTTGTTGACATTCCCACTGGTAAG -3'
(R):5'- GGGCAAATACCAAAGTACGTTC -3'
|
Posted On |
2019-11-12 |