Incidental Mutation 'R2239:Kdm1b'
| ID |
240563 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm1b
|
| Ensembl Gene |
ENSMUSG00000038080 |
| Gene Name |
lysine (K)-specific demethylase 1B |
| Synonyms |
Aof1, 4632428N09Rik |
| MMRRC Submission |
040239-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.504)
|
| Stock # |
R2239 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
47196849-47238085 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 47227231 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Leucine
at position 574
(F574L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000038373
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
|
| AlphaFold |
Q8CIG3 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000037025
AA Change: F574L
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: F574L
| 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 |
noncoding transcript
Transcript: ENSMUST00000128977
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000131120
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000143518
AA Change: F190L
|
| SMART Domains |
Protein: ENSMUSP00000114999
Gene: ENSMUSG00000038080
AA Change: F190L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SWIRM
|
3 |
86 |
1.1e-12 |
PFAM |
|
Pfam:Thi4
|
91 |
163 |
3.5e-10 |
PFAM |
|
Pfam:FAD_binding_3
|
105 |
140 |
3.5e-7 |
PFAM |
|
Pfam:HI0933_like
|
106 |
145 |
1.7e-7 |
PFAM |
|
Pfam:Pyr_redox_2
|
106 |
251 |
1.5e-10 |
PFAM |
|
Pfam:FAD_binding_2
|
107 |
150 |
5.7e-7 |
PFAM |
|
Pfam:Pyr_redox
|
107 |
158 |
6.4e-8 |
PFAM |
|
Pfam:Pyr_redox_3
|
109 |
288 |
1.2e-13 |
PFAM |
|
Pfam:NAD_binding_8
|
110 |
177 |
2.3e-13 |
PFAM |
|
Pfam:Amino_oxidase
|
115 |
181 |
8.6e-19 |
PFAM |
|
Pfam:Amino_oxidase
|
178 |
441 |
4.5e-63 |
PFAM |
|
| Meta Mutation Damage Score |
0.4719 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.9%
|
| Validation Efficiency |
94% (68/72) |
| 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: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam18 |
T |
C |
8: 25,136,303 (GRCm39) |
E406G |
probably benign |
Het |
| Ago3 |
G |
A |
4: 126,262,315 (GRCm39) |
R412C |
probably damaging |
Het |
| Arhgap36 |
G |
T |
X: 48,582,282 (GRCm39) |
V60L |
possibly damaging |
Het |
| Arl10 |
G |
T |
13: 54,722,962 (GRCm39) |
V19L |
probably benign |
Het |
| Aspm |
T |
A |
1: 139,384,584 (GRCm39) |
I127K |
possibly damaging |
Het |
| Atp8b3 |
A |
G |
10: 80,366,822 (GRCm39) |
C259R |
probably damaging |
Het |
| Camk2g |
A |
G |
14: 20,789,455 (GRCm39) |
I205T |
probably damaging |
Het |
| Ccdc47 |
G |
T |
11: 106,092,960 (GRCm39) |
N100K |
possibly damaging |
Het |
| Cd200r4 |
T |
A |
16: 44,641,260 (GRCm39) |
M1K |
probably null |
Het |
| Cdc37 |
G |
A |
9: 21,053,829 (GRCm39) |
Q176* |
probably null |
Het |
| Cdh5 |
C |
A |
8: 104,852,304 (GRCm39) |
H140N |
possibly damaging |
Het |
| Cep128 |
T |
C |
12: 91,314,341 (GRCm39) |
T146A |
probably benign |
Het |
| Cnnm4 |
T |
A |
1: 36,544,759 (GRCm39) |
S673T |
probably benign |
Het |
| Cnot1 |
T |
C |
8: 96,496,149 (GRCm39) |
I342V |
probably benign |
Het |
| Cog8 |
C |
A |
8: 107,782,993 (GRCm39) |
G99W |
probably damaging |
Het |
| Dars2 |
T |
C |
1: 160,890,852 (GRCm39) |
T120A |
possibly damaging |
Het |
| Dnah7b |
C |
A |
1: 46,240,344 (GRCm39) |
|
probably benign |
Het |
| Emilin2 |
T |
A |
17: 71,617,219 (GRCm39) |
Q64L |
probably benign |
Het |
| Eomes |
A |
G |
9: 118,311,359 (GRCm39) |
D394G |
probably damaging |
Het |
| Epn1 |
A |
G |
7: 5,100,601 (GRCm39) |
N518S |
probably damaging |
Het |
| Exoc1 |
T |
C |
5: 76,707,557 (GRCm39) |
|
probably benign |
Het |
| Fam186a |
C |
T |
15: 99,852,745 (GRCm39) |
V158M |
unknown |
Het |
| Fryl |
A |
G |
5: 73,265,890 (GRCm39) |
L477P |
probably damaging |
Het |
| Gbf1 |
T |
C |
19: 46,152,057 (GRCm39) |
I30T |
probably benign |
Het |
| Hsd17b1 |
A |
T |
11: 100,969,289 (GRCm39) |
I8F |
probably damaging |
Het |
| Htatsf1 |
G |
T |
X: 56,111,864 (GRCm39) |
D642Y |
unknown |
Het |
| Ift88 |
A |
G |
14: 57,692,961 (GRCm39) |
I387V |
probably damaging |
Het |
| Kcnh5 |
T |
A |
12: 75,054,493 (GRCm39) |
M484L |
probably benign |
Het |
| Kdm6a |
T |
C |
X: 18,065,476 (GRCm39) |
F104S |
probably damaging |
Het |
| Kntc1 |
T |
C |
5: 123,941,733 (GRCm39) |
V1809A |
possibly damaging |
Het |
| Lgr4 |
T |
C |
2: 109,842,738 (GRCm39) |
Y908H |
probably damaging |
Het |
| Ltbp3 |
C |
A |
19: 5,801,551 (GRCm39) |
C698* |
probably null |
Het |
| Map3k1 |
A |
C |
13: 111,885,478 (GRCm39) |
S1480A |
probably benign |
Het |
| Map7 |
A |
T |
10: 20,154,028 (GRCm39) |
N715Y |
unknown |
Het |
| Morn4 |
A |
G |
19: 42,066,471 (GRCm39) |
Y39H |
possibly damaging |
Het |
| Myh14 |
A |
T |
7: 44,314,607 (GRCm39) |
D105E |
probably damaging |
Het |
| Nfasc |
T |
C |
1: 132,510,760 (GRCm39) |
|
probably benign |
Het |
| Nfe2l2 |
G |
A |
2: 75,506,898 (GRCm39) |
P401S |
probably benign |
Het |
| Nt5c1b |
C |
A |
12: 10,425,558 (GRCm39) |
T309K |
probably damaging |
Het |
| Or10v5 |
T |
C |
19: 11,805,814 (GRCm39) |
D192G |
probably damaging |
Het |
| Or2aa1 |
A |
G |
11: 59,480,097 (GRCm39) |
S273P |
possibly damaging |
Het |
| Or5ac23 |
T |
A |
16: 59,149,738 (GRCm39) |
I45F |
probably damaging |
Het |
| Or5b109 |
T |
C |
19: 13,212,085 (GRCm39) |
V157A |
probably benign |
Het |
| Or5l13 |
T |
C |
2: 87,779,741 (GRCm39) |
T279A |
probably damaging |
Het |
| P4hb |
A |
G |
11: 120,454,108 (GRCm39) |
Y329H |
probably damaging |
Het |
| Papolg |
A |
G |
11: 23,826,378 (GRCm39) |
Y259H |
probably damaging |
Het |
| Pcgf5 |
A |
T |
19: 36,414,754 (GRCm39) |
N105I |
probably damaging |
Het |
| Pde4a |
G |
A |
9: 21,122,564 (GRCm39) |
C820Y |
probably damaging |
Het |
| Phka2 |
A |
G |
X: 159,324,408 (GRCm39) |
E254G |
probably damaging |
Het |
| Phrf1 |
A |
G |
7: 140,817,605 (GRCm39) |
E138G |
probably damaging |
Het |
| Rgs3 |
A |
T |
4: 62,544,124 (GRCm39) |
T299S |
probably benign |
Het |
| Skint5 |
G |
A |
4: 113,403,733 (GRCm39) |
T1163I |
unknown |
Het |
| Slc16a8 |
T |
C |
15: 79,137,147 (GRCm39) |
M88V |
probably damaging |
Het |
| Slc35f4 |
A |
G |
14: 49,543,660 (GRCm39) |
|
probably null |
Het |
| Smr2l |
T |
G |
5: 88,430,413 (GRCm39) |
M103R |
probably benign |
Het |
| Spata4 |
A |
C |
8: 55,055,664 (GRCm39) |
K185T |
probably benign |
Het |
| Spin2c |
A |
G |
X: 152,616,672 (GRCm39) |
I162V |
probably damaging |
Het |
| Stac |
G |
A |
9: 111,519,190 (GRCm39) |
|
probably benign |
Het |
| Tet1 |
T |
C |
10: 62,715,513 (GRCm39) |
D94G |
probably benign |
Het |
| Tnfsf11 |
A |
T |
14: 78,537,421 (GRCm39) |
S81T |
possibly damaging |
Het |
| Topaz1 |
C |
T |
9: 122,600,212 (GRCm39) |
T984I |
probably benign |
Het |
| Trmt5 |
A |
G |
12: 73,331,888 (GRCm39) |
I4T |
probably benign |
Het |
| Ttc7b |
A |
G |
12: 100,321,260 (GRCm39) |
|
probably null |
Het |
| Ugcg |
C |
T |
4: 59,207,798 (GRCm39) |
P46S |
probably benign |
Het |
| Ush2a |
C |
A |
1: 188,308,411 (GRCm39) |
T2020K |
probably benign |
Het |
| Zan |
G |
A |
5: 137,456,099 (GRCm39) |
Q1354* |
probably null |
Het |
| Zpld2 |
A |
C |
4: 133,929,516 (GRCm39) |
M263R |
unknown |
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 |
|
R0319:Kdm1b
|
UTSW |
13 |
47,207,195 (GRCm39) |
missense |
probably benign |
|
|
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 |
|
|
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'- TGTGTCAAATAGTTTGCCTTCC -3'
(R):5'- ACTGGCTGACTGTCCAAACC -3'
Sequencing Primer
(F):5'- AAATAGTTTGCCTTCCCCAGACG -3'
(R):5'- GCCCATCTCCTAAGCATCACATG -3'
|
| Posted On |
2014-10-15 |
Incidental Mutation