Incidental Mutation 'R6236:Kdm3a'
| ID |
504942 |
| 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 |
044400-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.962)
|
| Stock # |
R6236 (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 71588641 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 456
(E456G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000145959
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000065509]
[ENSMUST00000167220]
[ENSMUST00000205289]
[ENSMUST00000207023]
|
| AlphaFold |
Q6PCM1 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000065509
AA Change: E456G
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: E456G
| 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: E456G
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: E456G
| 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: E456G
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000205470
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000206597
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000206704
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000206916
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000207023
AA Change: E456G
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| Meta Mutation Damage Score |
0.0600 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.1%
- 20x: 94.6%
|
| Validation Efficiency |
100% (57/57) |
| 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: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acap3 |
A |
G |
4: 155,989,664 (GRCm39) |
T703A |
possibly damaging |
Het |
| Acd |
C |
T |
8: 106,427,127 (GRCm39) |
A49T |
probably benign |
Het |
| Acer1 |
T |
A |
17: 57,262,231 (GRCm39) |
I224F |
probably benign |
Het |
| Acvr1 |
T |
C |
2: 58,367,678 (GRCm39) |
D161G |
probably benign |
Het |
| Catsper4 |
T |
C |
4: 133,948,887 (GRCm39) |
I111V |
probably benign |
Het |
| Cfap210 |
A |
C |
2: 69,588,385 (GRCm39) |
|
probably null |
Het |
| Chst14 |
T |
A |
2: 118,757,997 (GRCm39) |
C264S |
probably damaging |
Het |
| Clnk |
T |
C |
5: 38,870,542 (GRCm39) |
T339A |
probably benign |
Het |
| Cnot4 |
T |
C |
6: 35,045,608 (GRCm39) |
K201R |
probably benign |
Het |
| Col19a1 |
A |
G |
1: 24,319,030 (GRCm39) |
V1020A |
probably damaging |
Het |
| Cts6 |
C |
A |
13: 61,344,192 (GRCm39) |
E287* |
probably null |
Het |
| Dbf4 |
T |
C |
5: 8,448,579 (GRCm39) |
|
probably benign |
Het |
| Diaph3 |
G |
A |
14: 87,275,004 (GRCm39) |
R140* |
probably null |
Het |
| Faah |
T |
C |
4: 115,856,786 (GRCm39) |
I459V |
probably benign |
Het |
| Fbxw2 |
A |
T |
2: 34,712,845 (GRCm39) |
L72H |
probably damaging |
Het |
| Fstl4 |
G |
A |
11: 53,077,162 (GRCm39) |
G640S |
probably benign |
Het |
| Gabrb1 |
C |
T |
5: 72,265,663 (GRCm39) |
T186M |
probably damaging |
Het |
| Gata2 |
T |
C |
6: 88,179,548 (GRCm39) |
|
probably null |
Het |
| Ifi203 |
A |
G |
1: 173,761,479 (GRCm39) |
V190A |
probably benign |
Het |
| Kl |
A |
T |
5: 150,876,755 (GRCm39) |
T192S |
probably damaging |
Het |
| Klhl3 |
G |
A |
13: 58,232,876 (GRCm39) |
A77V |
probably damaging |
Het |
| Klri2 |
A |
G |
6: 129,715,858 (GRCm39) |
F114L |
probably benign |
Het |
| Lonp2 |
A |
T |
8: 87,363,215 (GRCm39) |
R278* |
probably null |
Het |
| Lrp5 |
A |
T |
19: 3,680,483 (GRCm39) |
|
probably null |
Het |
| Med13 |
T |
A |
11: 86,219,357 (GRCm39) |
H363L |
probably damaging |
Het |
| Metap1d |
T |
G |
2: 71,346,022 (GRCm39) |
F194L |
probably benign |
Het |
| Misp |
A |
G |
10: 79,662,956 (GRCm39) |
K458E |
probably benign |
Het |
| Muc6 |
G |
T |
7: 141,218,685 (GRCm39) |
T1996N |
possibly damaging |
Het |
| Myh2 |
A |
G |
11: 67,081,157 (GRCm39) |
T1258A |
probably benign |
Het |
| Nipbl |
T |
A |
15: 8,354,064 (GRCm39) |
D1691V |
possibly damaging |
Het |
| Nr1i2 |
C |
T |
16: 38,086,300 (GRCm39) |
C55Y |
probably damaging |
Het |
| Or11h7 |
T |
C |
14: 50,891,257 (GRCm39) |
S188P |
probably damaging |
Het |
| Or7g21 |
A |
T |
9: 19,032,409 (GRCm39) |
I50F |
possibly damaging |
Het |
| Pcdhgb4 |
T |
C |
18: 37,854,345 (GRCm39) |
Y247H |
probably damaging |
Het |
| Prmt6 |
T |
C |
3: 110,157,214 (GRCm39) |
I358M |
probably benign |
Het |
| Ric1 |
T |
A |
19: 29,572,826 (GRCm39) |
D755E |
possibly damaging |
Het |
| Sez6l |
G |
T |
5: 112,623,110 (GRCm39) |
T147K |
possibly damaging |
Het |
| Ski |
A |
G |
4: 155,244,001 (GRCm39) |
F451S |
probably benign |
Het |
| Slc45a2 |
C |
T |
15: 11,022,158 (GRCm39) |
T300I |
probably benign |
Het |
| Smarca2 |
T |
C |
19: 26,673,613 (GRCm39) |
V1050A |
probably benign |
Het |
| Spag1 |
T |
C |
15: 36,211,281 (GRCm39) |
S476P |
probably damaging |
Het |
| Sptbn2 |
T |
A |
19: 4,798,166 (GRCm39) |
S1964T |
probably benign |
Het |
| Sucla2 |
T |
A |
14: 73,831,190 (GRCm39) |
D434E |
probably benign |
Het |
| Tbl3 |
G |
A |
17: 24,919,717 (GRCm39) |
T779I |
probably benign |
Het |
| Tlr2 |
T |
A |
3: 83,745,438 (GRCm39) |
E215V |
probably benign |
Het |
| Tomm40 |
G |
A |
7: 19,437,281 (GRCm39) |
P227S |
probably benign |
Het |
| Tpp2 |
T |
A |
1: 44,016,477 (GRCm39) |
S711T |
probably benign |
Het |
| Traj32 |
T |
A |
14: 54,423,565 (GRCm39) |
Y2* |
probably null |
Het |
| Trim34b |
A |
G |
7: 103,985,525 (GRCm39) |
R387G |
probably damaging |
Het |
| Ttn |
A |
T |
2: 76,641,587 (GRCm39) |
L5176Q |
possibly damaging |
Het |
| Usp5 |
T |
C |
6: 124,795,441 (GRCm39) |
T651A |
probably benign |
Het |
| Vmn1r188 |
T |
C |
13: 22,272,414 (GRCm39) |
S123P |
probably damaging |
Het |
| Zdhhc14 |
T |
C |
17: 5,543,918 (GRCm39) |
L66P |
probably damaging |
Het |
| Zfp712 |
C |
T |
13: 67,188,685 (GRCm39) |
C614Y |
probably damaging |
Het |
| Zfp827 |
A |
G |
8: 79,797,105 (GRCm39) |
K397R |
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 |
|
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 |
|
|
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'- TGAGATGTGAAACACTTACGAGTC -3'
(R):5'- ACTTGAAAATTCTGAGTGAGCCC -3'
Sequencing Primer
(F):5'- CACTTACGAGTCTGGGTTTTATTAC -3'
(R):5'- TGAGCCCAAAGGTAGCTGTATCC -3'
|
| Posted On |
2018-02-28 |
Incidental Mutation