Incidental Mutation 'R8476:Kdm3a'
| ID |
657257 |
| 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 |
067920-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.961)
|
| Stock # |
R8476 (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 71588693 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Glutamic Acid
at position 439
(K439E)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000145959
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000065509]
[ENSMUST00000167220]
[ENSMUST00000205289]
[ENSMUST00000207023]
|
| AlphaFold |
Q6PCM1 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000065509
AA Change: K439E
PolyPhen 2
Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: K439E
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
853 |
859 |
N/A |
INTRINSIC |
|
JmjC
|
1060 |
1283 |
1.6e-56 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000167220
AA Change: K439E
PolyPhen 2
Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: K439E
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
853 |
859 |
N/A |
INTRINSIC |
|
JmjC
|
1060 |
1283 |
1.6e-56 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000205289
AA Change: K439E
PolyPhen 2
Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000206916
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000207023
AA Change: K439E
PolyPhen 2
Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.7%
|
| Validation Efficiency |
100% (34/34) |
| 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: 34 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2210408I21Rik |
A |
T |
13: 77,410,020 (GRCm39) |
I176F |
possibly damaging |
Het |
| Aen |
A |
G |
7: 78,556,947 (GRCm39) |
Y123C |
probably damaging |
Het |
| Ahnak2 |
C |
T |
12: 112,747,100 (GRCm39) |
|
probably benign |
Het |
| Anks1 |
T |
A |
17: 28,273,292 (GRCm39) |
D970E |
probably damaging |
Het |
| Atn1 |
C |
A |
6: 124,723,416 (GRCm39) |
|
probably benign |
Het |
| Bola1 |
G |
A |
3: 96,104,573 (GRCm39) |
A7V |
probably benign |
Het |
| Ccdc172 |
T |
A |
19: 58,541,270 (GRCm39) |
|
probably null |
Het |
| Ceacam11 |
T |
C |
7: 17,707,618 (GRCm39) |
I134T |
probably benign |
Het |
| Clec4e |
A |
G |
6: 123,263,235 (GRCm39) |
S73P |
probably benign |
Het |
| Dchs1 |
A |
G |
7: 105,408,015 (GRCm39) |
I1939T |
probably benign |
Het |
| Dclk1 |
A |
T |
3: 55,441,100 (GRCm39) |
E432V |
probably damaging |
Het |
| Gba2 |
C |
T |
4: 43,569,944 (GRCm39) |
R423Q |
probably damaging |
Het |
| Gpr165 |
C |
A |
X: 95,757,623 (GRCm39) |
D7E |
probably benign |
Het |
| Klhdc7a |
A |
C |
4: 139,693,051 (GRCm39) |
I632S |
probably damaging |
Het |
| Krt72 |
A |
T |
15: 101,686,701 (GRCm39) |
M415K |
probably damaging |
Het |
| Lax1 |
T |
A |
1: 133,611,326 (GRCm39) |
H82L |
probably benign |
Het |
| Morc2b |
T |
A |
17: 33,354,833 (GRCm39) |
T980S |
possibly damaging |
Het |
| Mta2 |
T |
A |
19: 8,928,352 (GRCm39) |
N550K |
probably benign |
Het |
| Or51f1 |
A |
T |
7: 102,506,152 (GRCm39) |
F112L |
probably benign |
Het |
| Or6d13 |
T |
A |
6: 116,517,507 (GRCm39) |
I31N |
probably benign |
Het |
| Pask |
A |
G |
1: 93,249,361 (GRCm39) |
W680R |
probably benign |
Het |
| Pcdhb13 |
A |
T |
18: 37,577,137 (GRCm39) |
N505I |
probably damaging |
Het |
| Pik3cd |
A |
T |
4: 149,736,277 (GRCm39) |
M984K |
probably damaging |
Het |
| Ptprm |
T |
C |
17: 67,251,317 (GRCm39) |
Y520C |
probably damaging |
Het |
| Pum1 |
A |
G |
4: 130,480,024 (GRCm39) |
S547G |
possibly damaging |
Het |
| Rabep2 |
C |
T |
7: 126,034,915 (GRCm39) |
R64* |
probably null |
Het |
| Rfxank |
T |
C |
8: 70,590,828 (GRCm39) |
N13S |
probably benign |
Het |
| Sall3 |
G |
T |
18: 81,015,333 (GRCm39) |
S865* |
probably null |
Het |
| Scaper |
T |
A |
9: 55,669,575 (GRCm39) |
D854V |
probably damaging |
Het |
| Slit3 |
G |
A |
11: 35,520,596 (GRCm39) |
D578N |
possibly damaging |
Het |
| Smarcd1 |
G |
T |
15: 99,600,305 (GRCm39) |
G35W |
probably damaging |
Het |
| Trim24 |
C |
T |
6: 37,922,578 (GRCm39) |
Q462* |
probably null |
Het |
| Ube3a |
C |
T |
7: 58,954,575 (GRCm39) |
T837I |
probably damaging |
Het |
| Vps13a |
T |
C |
19: 16,699,821 (GRCm39) |
I740M |
possibly 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 |
|
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 |
|
|
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'- TGTGAAACACTTACGAGTCTGGG -3'
(R):5'- TGGAGACTTGAAAATTCTGAGTGAG -3'
Sequencing Primer
(F):5'- CACTTACGAGTCTGGGTTTTATTAC -3'
(R):5'- TGAGCCCAAAGGTAGCTGTATCC -3'
|
| Posted On |
2021-01-18 |
Incidental Mutation