Incidental Mutation 'R7614:Kdm3a'
| ID |
588764 |
| 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 |
045682-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.961)
|
| Stock # |
R7614 (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 C
at 71568937 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 1161
(T1161A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000065716
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000065509]
[ENSMUST00000167220]
[ENSMUST00000207023]
|
| AlphaFold |
Q6PCM1 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000065509
AA Change: T1161A
PolyPhen 2
Score 0.820 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: T1161A
| 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: T1161A
PolyPhen 2
Score 0.820 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: T1161A
| 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: ENSMUST00000207023
AA Change: T1161A
PolyPhen 2
Score 0.820 (Sensitivity: 0.84; Specificity: 0.93)
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
100% (53/53) |
| 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: 53 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abl2 |
A |
G |
1: 156,464,429 (GRCm39) |
T535A |
possibly damaging |
Het |
| Adcy9 |
A |
T |
16: 4,236,088 (GRCm39) |
L441Q |
probably damaging |
Het |
| Adgrv1 |
A |
T |
13: 81,668,780 (GRCm39) |
V2592E |
probably damaging |
Het |
| Ahdc1 |
A |
G |
4: 132,790,825 (GRCm39) |
S689G |
probably benign |
Het |
| Ankrd24 |
G |
A |
10: 81,474,523 (GRCm39) |
G229E |
unknown |
Het |
| Ankrd34c |
T |
A |
9: 89,610,914 (GRCm39) |
I476F |
probably damaging |
Het |
| Arhgef19 |
A |
G |
4: 140,984,090 (GRCm39) |
H770R |
possibly damaging |
Het |
| Arhgef4 |
T |
G |
1: 34,771,316 (GRCm39) |
S1208A |
possibly damaging |
Het |
| Arid1a |
A |
T |
4: 133,418,466 (GRCm39) |
M654K |
unknown |
Het |
| Atp11b |
T |
A |
3: 35,864,259 (GRCm39) |
|
probably null |
Het |
| Cadps |
A |
G |
14: 12,454,260 (GRCm38) |
I1086T |
probably damaging |
Het |
| Ccng2 |
C |
G |
5: 93,421,202 (GRCm39) |
S237R |
probably benign |
Het |
| Cfap276 |
T |
A |
3: 108,449,848 (GRCm39) |
D42E |
probably benign |
Het |
| Cntn3 |
T |
C |
6: 102,142,337 (GRCm39) |
H1010R |
probably benign |
Het |
| Cyp2c66 |
T |
A |
19: 39,159,472 (GRCm39) |
Y308N |
probably damaging |
Het |
| Dok6 |
T |
A |
18: 89,492,067 (GRCm39) |
H170L |
probably damaging |
Het |
| Eefsec |
C |
T |
6: 88,258,576 (GRCm39) |
D506N |
possibly damaging |
Het |
| Fam181a |
C |
T |
12: 103,282,805 (GRCm39) |
P237S |
probably damaging |
Het |
| Fam186b |
T |
C |
15: 99,184,867 (GRCm39) |
I19V |
probably damaging |
Het |
| Gm3285 |
A |
T |
10: 77,697,865 (GRCm39) |
T5S |
unknown |
Het |
| Heg1 |
A |
G |
16: 33,547,733 (GRCm39) |
E864G |
probably benign |
Het |
| Herc2 |
T |
A |
7: 55,803,023 (GRCm39) |
L2124* |
probably null |
Het |
| Hexa |
T |
C |
9: 59,469,230 (GRCm39) |
S331P |
probably damaging |
Het |
| Hspb1 |
A |
T |
5: 135,917,223 (GRCm39) |
D104V |
probably damaging |
Het |
| Ikzf1 |
A |
T |
11: 11,719,019 (GRCm39) |
Q329L |
probably damaging |
Het |
| Kcnf1 |
C |
A |
12: 17,224,787 (GRCm39) |
R478L |
probably benign |
Het |
| Krtap31-2 |
T |
C |
11: 99,827,429 (GRCm39) |
I87T |
possibly damaging |
Het |
| Lars2 |
T |
C |
9: 123,224,176 (GRCm39) |
S116P |
|
Het |
| Lrrk2 |
A |
G |
15: 91,657,061 (GRCm39) |
D1785G |
probably damaging |
Het |
| Myo10 |
A |
G |
15: 25,701,709 (GRCm39) |
H61R |
probably benign |
Het |
| Or10x4 |
T |
G |
1: 174,219,220 (GRCm39) |
F195C |
probably damaging |
Het |
| Or9s13 |
A |
G |
1: 92,548,183 (GRCm39) |
Y185C |
probably damaging |
Het |
| Pcdhb4 |
C |
A |
18: 37,442,602 (GRCm39) |
H637Q |
probably benign |
Het |
| Pcsk9 |
T |
A |
4: 106,304,763 (GRCm39) |
D435V |
probably benign |
Het |
| Prickle2 |
T |
A |
6: 92,402,631 (GRCm39) |
Y119F |
possibly damaging |
Het |
| Prr5 |
A |
G |
15: 84,641,276 (GRCm39) |
T181A |
probably benign |
Het |
| Psd |
T |
A |
19: 46,301,877 (GRCm39) |
Q903L |
probably damaging |
Het |
| Ptpn13 |
T |
A |
5: 103,649,331 (GRCm39) |
S245T |
probably benign |
Het |
| Resp18 |
T |
C |
1: 75,254,882 (GRCm39) |
S24G |
probably damaging |
Het |
| Slc17a4 |
T |
C |
13: 24,090,580 (GRCm39) |
T89A |
probably benign |
Het |
| Slc9a9 |
A |
G |
9: 94,737,792 (GRCm39) |
Y233C |
probably damaging |
Het |
| Slit1 |
T |
A |
19: 41,622,639 (GRCm39) |
I707F |
probably damaging |
Het |
| Sp4 |
T |
C |
12: 118,218,174 (GRCm39) |
E691G |
possibly damaging |
Het |
| Sun2 |
G |
T |
15: 79,623,225 (GRCm39) |
|
probably null |
Het |
| Syne3 |
T |
C |
12: 104,912,901 (GRCm39) |
T723A |
not run |
Het |
| Tcp1 |
T |
A |
17: 13,141,540 (GRCm39) |
F340I |
possibly damaging |
Het |
| Tmem39b |
A |
T |
4: 129,587,694 (GRCm39) |
V39D |
probably damaging |
Het |
| Tmtc3 |
A |
T |
10: 100,286,214 (GRCm39) |
Y536* |
probably null |
Het |
| Tnfrsf11a |
A |
T |
1: 105,755,094 (GRCm39) |
T389S |
probably damaging |
Het |
| Ttn |
T |
C |
2: 76,598,873 (GRCm39) |
T19347A |
possibly damaging |
Het |
| Vmn1r68 |
A |
G |
7: 10,261,553 (GRCm39) |
S182P |
probably benign |
Het |
| Vmn2r95 |
A |
G |
17: 18,660,352 (GRCm39) |
T255A |
probably benign |
Het |
| Wdr59 |
T |
C |
8: 112,219,394 (GRCm39) |
Y221C |
|
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 |
|
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'- TCTTAGCAACTACTGACAGCCC -3'
(R):5'- GATGTATCTGATGCAGCCAATGTC -3'
Sequencing Primer
(F):5'- CAGCCCATCCAATTGATACGGATTTG -3'
(R):5'- ATGCAGCCAATGTCATGGTTTATG -3'
|
| Posted On |
2019-10-24 |
Incidental Mutation