Incidental Mutation 'R7608:Kdm3a'
| ID |
588433 |
| 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 |
045678-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.961)
|
| Stock # |
R7608 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
71565954-71609963 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 71577731 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Leucine
at position 690
(M690L)
|
| 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
AA Change: M690L
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: M690L
| 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
AA Change: M690L
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: M690L
| 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
AA Change: M690L
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000206916
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000207023
AA Change: M690L
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
100% (51/51) |
| 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
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb6 |
A |
G |
1: 75,154,347 (GRCm39) |
F311S |
probably benign |
Het |
| Adamts7 |
C |
A |
9: 90,055,826 (GRCm39) |
T193N |
possibly damaging |
Het |
| Akr1b7 |
A |
G |
6: 34,397,457 (GRCm39) |
N273S |
probably damaging |
Het |
| Asz1 |
G |
A |
6: 18,077,252 (GRCm39) |
T151M |
probably damaging |
Het |
| Atosb |
A |
G |
4: 43,036,533 (GRCm39) |
L66P |
probably damaging |
Het |
| Atrnl1 |
T |
A |
19: 57,703,119 (GRCm39) |
Y1046N |
probably damaging |
Het |
| Cacna2d1 |
T |
C |
5: 16,564,022 (GRCm39) |
S902P |
probably damaging |
Het |
| Casp3 |
T |
A |
8: 47,087,368 (GRCm39) |
I105K |
probably benign |
Het |
| Ccdc146 |
C |
T |
5: 21,506,450 (GRCm39) |
V664I |
probably benign |
Het |
| Cfap61 |
G |
A |
2: 145,805,451 (GRCm39) |
C267Y |
possibly damaging |
Het |
| Dgkz |
A |
T |
2: 91,764,399 (GRCm39) |
|
probably null |
Het |
| Dnah11 |
G |
T |
12: 118,104,505 (GRCm39) |
|
probably null |
Het |
| Duox1 |
C |
A |
2: 122,156,616 (GRCm39) |
Y514* |
probably null |
Het |
| Epha7 |
C |
T |
4: 28,871,937 (GRCm39) |
S422L |
probably benign |
Het |
| Fan1 |
A |
T |
7: 64,003,979 (GRCm39) |
|
probably null |
Het |
| Fgfrl1 |
A |
T |
5: 108,853,211 (GRCm39) |
K278M |
probably damaging |
Het |
| Fign |
T |
C |
2: 63,809,063 (GRCm39) |
I736V |
possibly damaging |
Het |
| Galns |
A |
G |
8: 123,318,184 (GRCm39) |
F410S |
probably benign |
Het |
| Hspbp1 |
C |
A |
7: 4,663,821 (GRCm39) |
K341N |
possibly damaging |
Het |
| Idh3b |
A |
T |
2: 130,122,900 (GRCm39) |
S296R |
probably damaging |
Het |
| Ifi44 |
A |
G |
3: 151,438,045 (GRCm39) |
F414S |
probably damaging |
Het |
| Ldaf1 |
A |
G |
7: 119,704,011 (GRCm39) |
K19E |
probably damaging |
Het |
| Lrrc49 |
C |
T |
9: 60,510,005 (GRCm39) |
G488S |
probably null |
Het |
| Mcc |
T |
C |
18: 44,624,294 (GRCm39) |
N417S |
possibly damaging |
Het |
| Melk |
T |
A |
4: 44,325,571 (GRCm39) |
|
probably null |
Het |
| Mtcl1 |
T |
C |
17: 66,650,300 (GRCm39) |
R1722G |
probably damaging |
Het |
| Or4a79 |
A |
G |
2: 89,551,642 (GRCm39) |
V271A |
probably benign |
Het |
| Or51f23c-ps1 |
A |
G |
7: 102,431,132 (GRCm39) |
I150V |
probably benign |
Het |
| Or5b119 |
G |
A |
19: 13,456,956 (GRCm39) |
T202I |
possibly damaging |
Het |
| Or8d2 |
T |
A |
9: 38,759,806 (GRCm39) |
V132D |
possibly damaging |
Het |
| Pdzrn3 |
T |
C |
6: 101,128,713 (GRCm39) |
E651G |
probably damaging |
Het |
| Pop5 |
A |
G |
5: 115,375,931 (GRCm39) |
|
probably benign |
Het |
| Prox1 |
T |
A |
1: 189,885,642 (GRCm39) |
M602L |
probably benign |
Het |
| Prpf39 |
G |
A |
12: 65,100,220 (GRCm39) |
A298T |
probably benign |
Het |
| Scg2 |
T |
C |
1: 79,413,898 (GRCm39) |
E275G |
probably benign |
Het |
| Scn11a |
A |
T |
9: 119,644,379 (GRCm39) |
|
probably null |
Het |
| Slc16a4 |
A |
T |
3: 107,210,443 (GRCm39) |
Y371F |
probably damaging |
Het |
| Slc4a1ap |
T |
A |
5: 31,693,533 (GRCm39) |
M489K |
possibly damaging |
Het |
| Spata13 |
A |
G |
14: 60,929,956 (GRCm39) |
N505D |
possibly damaging |
Het |
| Tas2r129 |
A |
G |
6: 132,928,156 (GRCm39) |
N31S |
probably damaging |
Het |
| Tnn |
A |
T |
1: 159,915,984 (GRCm39) |
Y1508* |
probably null |
Het |
| Trim23 |
T |
C |
13: 104,328,541 (GRCm39) |
V354A |
probably benign |
Het |
| Tsc1 |
A |
T |
2: 28,548,748 (GRCm39) |
T18S |
probably benign |
Het |
| Txlnb |
A |
G |
10: 17,691,146 (GRCm39) |
K232R |
probably damaging |
Het |
| Vmn1r53 |
C |
T |
6: 90,201,104 (GRCm39) |
M73I |
probably benign |
Het |
| Vmn1r67 |
G |
A |
7: 10,181,290 (GRCm39) |
V185M |
possibly damaging |
Het |
| Vmn2r14 |
A |
G |
5: 109,369,276 (GRCm39) |
I99T |
probably benign |
Het |
| Zfp318 |
T |
G |
17: 46,710,935 (GRCm39) |
V886G |
probably damaging |
Het |
| Zfp760 |
A |
G |
17: 21,941,797 (GRCm39) |
N324S |
probably benign |
Het |
| Zfp819 |
T |
C |
7: 43,266,357 (GRCm39) |
V280A |
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 |
|
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 |
PCR Primer
(F):5'- AAGTCTTGTAGGCAGCACC -3'
(R):5'- GAACTCTAAGCACGGGAAGTC -3'
Sequencing Primer
(F):5'- GGCAGCACCTGTAAATAATGGATTTG -3'
(R):5'- GCACGGGAAGTCTCATACTC -3'
|
| Posted On |
2019-10-24 |
Incidental Mutation