Incidental Mutation 'R6541:Kdm3a'
| ID |
520752 |
| 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 |
044667-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.961)
|
| Stock # |
R6541 (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 71571517 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Valine
at position 1060
(M1060V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000145959
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000065509]
[ENSMUST00000167220]
[ENSMUST00000205289]
[ENSMUST00000207023]
|
| AlphaFold |
Q6PCM1 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000065509
AA Change: M1060V
PolyPhen 2
Score 0.693 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: M1060V
| 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: M1060V
PolyPhen 2
Score 0.693 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: M1060V
| 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 |
noncoding transcript
Transcript: ENSMUST00000205470
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000205505
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000206339
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000206357
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000207023
AA Change: M1060V
PolyPhen 2
Score 0.693 (Sensitivity: 0.86; Specificity: 0.92)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000206582
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000206798
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.4%
- 20x: 97.8%
|
| Validation Efficiency |
97% (36/37) |
| 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: 36 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ass1 |
T |
C |
2: 31,400,245 (GRCm39) |
V321A |
probably damaging |
Het |
| BC028528 |
T |
A |
3: 95,795,530 (GRCm39) |
M91L |
probably benign |
Het |
| Bicra |
T |
C |
7: 15,713,054 (GRCm39) |
T998A |
probably benign |
Het |
| Cdkl3 |
T |
G |
11: 51,913,571 (GRCm39) |
L220R |
probably damaging |
Het |
| Cluh |
A |
G |
11: 74,548,040 (GRCm39) |
D117G |
probably damaging |
Het |
| Cplane1 |
T |
C |
15: 8,248,779 (GRCm39) |
V1776A |
possibly damaging |
Het |
| Crygf |
T |
C |
1: 65,967,224 (GRCm39) |
F116S |
probably damaging |
Het |
| Ergic2 |
T |
A |
6: 148,084,648 (GRCm39) |
Y20F |
probably damaging |
Het |
| Esf1 |
A |
G |
2: 140,009,799 (GRCm39) |
V179A |
probably benign |
Het |
| Gm28360 |
T |
C |
1: 117,758,047 (GRCm39) |
|
probably benign |
Het |
| Hhatl |
C |
T |
9: 121,614,210 (GRCm39) |
V385I |
probably damaging |
Het |
| Iba57 |
A |
T |
11: 59,049,689 (GRCm39) |
D219E |
possibly damaging |
Het |
| Il36b |
T |
A |
2: 24,049,827 (GRCm39) |
V146D |
probably damaging |
Het |
| Itgal |
T |
A |
7: 126,910,734 (GRCm39) |
V176E |
probably damaging |
Het |
| Kif18b |
T |
C |
11: 102,805,092 (GRCm39) |
K351R |
probably damaging |
Het |
| Mroh9 |
A |
G |
1: 162,885,607 (GRCm39) |
F342L |
possibly damaging |
Het |
| Ndufa11 |
T |
A |
17: 57,024,867 (GRCm39) |
S10T |
probably benign |
Het |
| Or2bd2 |
A |
T |
7: 6,443,492 (GRCm39) |
N198Y |
probably benign |
Het |
| Or5w19 |
T |
C |
2: 87,698,638 (GRCm39) |
F101S |
probably benign |
Het |
| Or6b6 |
A |
T |
7: 106,571,410 (GRCm39) |
F47Y |
probably benign |
Het |
| Or7h8 |
T |
A |
9: 20,123,695 (GRCm39) |
F17I |
probably benign |
Het |
| Pacsin3 |
A |
G |
2: 91,093,129 (GRCm39) |
E207G |
probably damaging |
Het |
| Pcsk1 |
T |
A |
13: 75,274,103 (GRCm39) |
L136Q |
probably damaging |
Het |
| Prr18 |
G |
T |
17: 8,560,168 (GRCm39) |
R108L |
possibly damaging |
Het |
| Rdh5 |
A |
G |
10: 128,753,977 (GRCm39) |
V44A |
possibly damaging |
Het |
| Rnd2 |
C |
T |
11: 101,359,825 (GRCm39) |
L57F |
probably damaging |
Het |
| Sh2d4b |
T |
C |
14: 40,542,748 (GRCm39) |
T343A |
probably benign |
Het |
| Slc16a10 |
T |
C |
10: 39,913,268 (GRCm39) |
N480S |
probably benign |
Het |
| Spaca7b |
T |
A |
8: 11,712,613 (GRCm39) |
Q79L |
probably benign |
Het |
| Sval3 |
A |
T |
6: 41,949,380 (GRCm39) |
N73Y |
probably damaging |
Het |
| Taar7d |
T |
C |
10: 23,904,129 (GRCm39) |
I337T |
probably benign |
Het |
| Ttn |
T |
A |
2: 76,577,039 (GRCm39) |
Q24618L |
possibly damaging |
Het |
| Ugt1a9 |
T |
A |
1: 87,999,318 (GRCm39) |
V256E |
probably damaging |
Het |
| Vmn2r108 |
T |
A |
17: 20,701,480 (GRCm39) |
I7F |
probably benign |
Het |
| Vmn2r55 |
A |
G |
7: 12,404,939 (GRCm39) |
S155P |
probably damaging |
Het |
| Vwa3b |
T |
A |
1: 37,090,842 (GRCm39) |
V169E |
probably damaging |
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 |
|
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 |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TACCTATCTCCTAAAGGTGTGCATAC -3'
(R):5'- AGTGAAGTAGTGTTTGTATGCCAAG -3'
Sequencing Primer
(F):5'- TTGGCATTCCCCAAGTGA -3'
(R):5'- CCTGGTCTACAAAGTGAGTTCCAG -3'
|
| Posted On |
2018-06-06 |
Incidental Mutation