Incidental Mutation 'R0319:Kdm1b'
| ID |
25579 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm1b
|
| Ensembl Gene |
ENSMUSG00000038080 |
| Gene Name |
lysine (K)-specific demethylase 1B |
| Synonyms |
Aof1, 4632428N09Rik |
| MMRRC Submission |
038529-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.504)
|
| Stock # |
R0319 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
47196849-47238085 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 47207195 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Proline to Leucine
at position 173
(P173L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000117793
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
[ENSMUST00000143868]
|
| AlphaFold |
Q8CIG3 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000037025
AA Change: P173L
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: P173L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:zf-CW
|
138 |
191 |
2.6e-13 |
PFAM |
|
low complexity region
|
235 |
253 |
N/A |
INTRINSIC |
|
Pfam:SWIRM
|
286 |
369 |
6e-12 |
PFAM |
|
Pfam:Pyr_redox_2
|
368 |
490 |
3.1e-8 |
PFAM |
|
Pfam:Thi4
|
375 |
446 |
2.2e-10 |
PFAM |
|
Pfam:FAD_binding_3
|
388 |
423 |
4.1e-7 |
PFAM |
|
Pfam:HI0933_like
|
389 |
428 |
1.6e-7 |
PFAM |
|
Pfam:FAD_binding_2
|
390 |
428 |
1.6e-6 |
PFAM |
|
Pfam:Pyr_redox
|
390 |
438 |
8e-8 |
PFAM |
|
Pfam:NAD_binding_8
|
393 |
460 |
1.6e-13 |
PFAM |
|
Pfam:Amino_oxidase
|
398 |
824 |
3.7e-86 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000143868
AA Change: P173L
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000117793
Gene: ENSMUSG00000038080
AA Change: P173L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:zf-CW
|
137 |
175 |
3.6e-13 |
PFAM |
|
| Meta Mutation Damage Score |
0.1513 |
| Coding Region Coverage |
- 1x: 98.9%
- 3x: 97.8%
- 10x: 95.0%
- 20x: 89.1%
|
| Validation Efficiency |
100% (58/58) |
| MGI Phenotype |
PHENOTYPE: Homozygous null mice of both sexes are viable, grossly normal and male mice are fertile; however, heterozygous progeny of homozygous null mothers display severe placental defects, embryonic growth impairment, neural tube defects and pericardial edema, and do not survive past E10.5. [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 |
|---|
| 9130023H24Rik |
A |
C |
7: 127,836,362 (GRCm39) |
V77G |
probably benign |
Het |
| Abcb1b |
A |
G |
5: 8,877,428 (GRCm39) |
R663G |
probably benign |
Het |
| Acly |
A |
G |
11: 100,395,808 (GRCm39) |
V404A |
probably damaging |
Het |
| Actg2 |
T |
A |
6: 83,497,725 (GRCm39) |
I103F |
probably damaging |
Het |
| Anapc5 |
A |
G |
5: 122,956,919 (GRCm39) |
V120A |
probably damaging |
Het |
| Ankk1 |
T |
G |
9: 49,327,371 (GRCm39) |
T603P |
probably damaging |
Het |
| Ankmy2 |
T |
C |
12: 36,215,898 (GRCm39) |
S33P |
possibly damaging |
Het |
| Arhgef19 |
A |
T |
4: 140,983,710 (GRCm39) |
T748S |
possibly damaging |
Het |
| Atad5 |
T |
A |
11: 80,011,616 (GRCm39) |
|
probably benign |
Het |
| Atxn10 |
T |
C |
15: 85,249,483 (GRCm39) |
L105P |
probably damaging |
Het |
| Cacna1s |
T |
C |
1: 135,998,455 (GRCm39) |
V161A |
probably damaging |
Het |
| Col6a3 |
T |
C |
1: 90,735,426 (GRCm39) |
E741G |
possibly damaging |
Het |
| Cpne9 |
G |
A |
6: 113,271,654 (GRCm39) |
G338E |
probably damaging |
Het |
| Cyp3a13 |
G |
A |
5: 137,897,124 (GRCm39) |
P397S |
probably damaging |
Het |
| Dbn1 |
C |
T |
13: 55,622,729 (GRCm39) |
E585K |
probably damaging |
Het |
| Draxin |
A |
G |
4: 148,200,429 (GRCm39) |
L7P |
probably benign |
Het |
| Exosc7 |
T |
A |
9: 122,960,025 (GRCm39) |
|
probably benign |
Het |
| Far2 |
A |
G |
6: 148,058,968 (GRCm39) |
E218G |
probably damaging |
Het |
| Ggps1 |
A |
C |
13: 14,228,462 (GRCm39) |
N240K |
possibly damaging |
Het |
| Kcnip1 |
T |
C |
11: 33,601,529 (GRCm39) |
|
probably benign |
Het |
| Kcnv2 |
A |
T |
19: 27,301,424 (GRCm39) |
Y425F |
probably benign |
Het |
| Kdelr2 |
T |
A |
5: 143,398,272 (GRCm39) |
F40I |
probably damaging |
Het |
| Kif20b |
G |
A |
19: 34,925,132 (GRCm39) |
|
probably benign |
Het |
| Klhl9 |
A |
T |
4: 88,638,691 (GRCm39) |
Y517N |
possibly damaging |
Het |
| Lgals3bp |
A |
G |
11: 118,284,347 (GRCm39) |
S411P |
probably damaging |
Het |
| Lmo3 |
G |
A |
6: 138,354,309 (GRCm39) |
T85M |
probably damaging |
Het |
| Lvrn |
C |
A |
18: 46,997,820 (GRCm39) |
T256N |
probably damaging |
Het |
| Malt1 |
T |
C |
18: 65,595,986 (GRCm39) |
|
probably null |
Het |
| Mgst1 |
A |
G |
6: 138,133,155 (GRCm39) |
I157V |
possibly damaging |
Het |
| Mob3a |
A |
T |
10: 80,525,819 (GRCm39) |
V164E |
possibly damaging |
Het |
| Mprip |
T |
A |
11: 59,587,864 (GRCm39) |
|
probably benign |
Het |
| Mst1 |
A |
G |
9: 107,959,712 (GRCm39) |
N276S |
probably benign |
Het |
| Or5an1b |
A |
T |
19: 12,299,680 (GRCm39) |
C170* |
probably null |
Het |
| P3h2 |
T |
A |
16: 25,789,681 (GRCm39) |
I529F |
possibly damaging |
Het |
| Pikfyve |
T |
A |
1: 65,285,490 (GRCm39) |
S865T |
probably benign |
Het |
| Rcbtb2 |
G |
A |
14: 73,415,909 (GRCm39) |
R474Q |
probably benign |
Het |
| Rpl27 |
G |
A |
11: 101,334,321 (GRCm39) |
|
probably benign |
Het |
| Rtp1 |
G |
A |
16: 23,250,210 (GRCm39) |
E192K |
probably damaging |
Het |
| Sgk2 |
T |
C |
2: 162,837,592 (GRCm39) |
|
probably benign |
Het |
| Slc17a3 |
C |
T |
13: 24,039,841 (GRCm39) |
S293F |
probably damaging |
Het |
| Slc49a4 |
T |
C |
16: 35,570,884 (GRCm39) |
D140G |
probably benign |
Het |
| Spdl1 |
T |
C |
11: 34,714,347 (GRCm39) |
N114S |
possibly damaging |
Het |
| Syne2 |
C |
T |
12: 76,110,936 (GRCm39) |
R5756W |
probably damaging |
Het |
| Tor1aip1 |
T |
C |
1: 155,882,927 (GRCm39) |
E307G |
probably damaging |
Het |
| Tpd52 |
T |
C |
3: 9,018,749 (GRCm39) |
T44A |
probably benign |
Het |
| Trim67 |
A |
T |
8: 125,549,966 (GRCm39) |
Y532F |
probably damaging |
Het |
| Ttll9 |
C |
A |
2: 152,842,018 (GRCm39) |
|
probably null |
Het |
| Ush2a |
T |
C |
1: 188,680,571 (GRCm39) |
|
probably benign |
Het |
| Vcam1 |
T |
C |
3: 115,909,709 (GRCm39) |
I539M |
probably benign |
Het |
| Vmn1r19 |
T |
A |
6: 57,381,600 (GRCm39) |
M51K |
possibly damaging |
Het |
| Vmn2r61 |
T |
A |
7: 41,949,941 (GRCm39) |
M787K |
probably damaging |
Het |
| Xdh |
T |
A |
17: 74,213,096 (GRCm39) |
|
probably benign |
Het |
| Zfp109 |
A |
T |
7: 23,933,895 (GRCm39) |
V8E |
probably damaging |
Het |
| Zfp595 |
G |
A |
13: 67,464,577 (GRCm39) |
A562V |
possibly damaging |
Het |
| Zfp759 |
A |
G |
13: 67,288,356 (GRCm39) |
T636A |
probably benign |
Het |
|
| Other mutations in Kdm1b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00587:Kdm1b
|
APN |
13 |
47,222,016 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL00924:Kdm1b
|
APN |
13 |
47,221,956 (GRCm39) |
missense |
probably benign |
|
|
IGL01553:Kdm1b
|
APN |
13 |
47,234,024 (GRCm39) |
missense |
probably damaging |
0.96 |
|
IGL01663:Kdm1b
|
APN |
13 |
47,227,213 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02385:Kdm1b
|
APN |
13 |
47,221,982 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
IGL02505:Kdm1b
|
APN |
13 |
47,214,331 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02826:Kdm1b
|
APN |
13 |
47,233,943 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03257:Kdm1b
|
APN |
13 |
47,202,742 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0052:Kdm1b
|
UTSW |
13 |
47,217,593 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0426:Kdm1b
|
UTSW |
13 |
47,217,720 (GRCm39) |
splice site |
probably benign |
|
|
R0599:Kdm1b
|
UTSW |
13 |
47,212,286 (GRCm39) |
missense |
possibly damaging |
0.47 |
|
R0764:Kdm1b
|
UTSW |
13 |
47,222,079 (GRCm39) |
missense |
possibly damaging |
0.70 |
|
R1163:Kdm1b
|
UTSW |
13 |
47,225,398 (GRCm39) |
missense |
probably benign |
0.02 |
|
R1543:Kdm1b
|
UTSW |
13 |
47,221,997 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1584:Kdm1b
|
UTSW |
13 |
47,217,530 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1627:Kdm1b
|
UTSW |
13 |
47,217,707 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1669:Kdm1b
|
UTSW |
13 |
47,222,024 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1758:Kdm1b
|
UTSW |
13 |
47,214,244 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1860:Kdm1b
|
UTSW |
13 |
47,202,666 (GRCm39) |
missense |
probably benign |
0.03 |
|
R1907:Kdm1b
|
UTSW |
13 |
47,217,596 (GRCm39) |
missense |
probably benign |
0.00 |
|
R2225:Kdm1b
|
UTSW |
13 |
47,217,564 (GRCm39) |
frame shift |
probably null |
|
|
R2239:Kdm1b
|
UTSW |
13 |
47,227,231 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2271:Kdm1b
|
UTSW |
13 |
47,217,564 (GRCm39) |
frame shift |
probably null |
|
|
R2302:Kdm1b
|
UTSW |
13 |
47,217,564 (GRCm39) |
frame shift |
probably null |
|
|
R2303:Kdm1b
|
UTSW |
13 |
47,217,564 (GRCm39) |
frame shift |
probably null |
|
|
R2380:Kdm1b
|
UTSW |
13 |
47,227,231 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2442:Kdm1b
|
UTSW |
13 |
47,216,451 (GRCm39) |
missense |
probably benign |
0.32 |
|
R3022:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3054:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3545:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3546:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3548:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4094:Kdm1b
|
UTSW |
13 |
47,216,496 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4419:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4420:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4502:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4547:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4548:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4785:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4793:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4804:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4882:Kdm1b
|
UTSW |
13 |
47,214,369 (GRCm39) |
missense |
probably benign |
|
|
R4906:Kdm1b
|
UTSW |
13 |
47,216,620 (GRCm39) |
critical splice donor site |
probably null |
|
|
R4965:Kdm1b
|
UTSW |
13 |
47,227,843 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5039:Kdm1b
|
UTSW |
13 |
47,230,962 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5098:Kdm1b
|
UTSW |
13 |
47,216,467 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5265:Kdm1b
|
UTSW |
13 |
47,216,445 (GRCm39) |
missense |
probably benign |
0.35 |
|
R5541:Kdm1b
|
UTSW |
13 |
47,232,672 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5814:Kdm1b
|
UTSW |
13 |
47,216,622 (GRCm39) |
splice site |
probably null |
|
|
R6046:Kdm1b
|
UTSW |
13 |
47,232,729 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R6798:Kdm1b
|
UTSW |
13 |
47,222,012 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6903:Kdm1b
|
UTSW |
13 |
47,227,880 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7831:Kdm1b
|
UTSW |
13 |
47,204,098 (GRCm39) |
missense |
probably benign |
0.17 |
|
R7973:Kdm1b
|
UTSW |
13 |
47,230,922 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8181:Kdm1b
|
UTSW |
13 |
47,205,377 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8248:Kdm1b
|
UTSW |
13 |
47,225,354 (GRCm39) |
intron |
probably benign |
|
|
R8821:Kdm1b
|
UTSW |
13 |
47,217,617 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R8831:Kdm1b
|
UTSW |
13 |
47,217,617 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R8842:Kdm1b
|
UTSW |
13 |
47,231,832 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8861:Kdm1b
|
UTSW |
13 |
47,217,582 (GRCm39) |
missense |
probably benign |
0.02 |
|
R8885:Kdm1b
|
UTSW |
13 |
47,207,184 (GRCm39) |
nonsense |
probably null |
|
|
R9038:Kdm1b
|
UTSW |
13 |
47,202,770 (GRCm39) |
missense |
probably benign |
0.07 |
|
R9132:Kdm1b
|
UTSW |
13 |
47,225,458 (GRCm39) |
missense |
probably benign |
0.05 |
|
R9268:Kdm1b
|
UTSW |
13 |
47,217,705 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9616:Kdm1b
|
UTSW |
13 |
47,234,030 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GCAGTTTGCTACCATGCACAACAC -3'
(R):5'- GGAATACGGCATCCACCTTGTCAC -3'
Sequencing Primer
(F):5'- TTCCTTGAGTCAAAAAACACGG -3'
(R):5'- GGGCAACTGTTCCTGGATAAC -3'
|
| Posted On |
2013-04-16 |
Incidental Mutation