Incidental Mutation 'R3054:Kdm1b'
| ID |
265088 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm1b
|
| Ensembl Gene |
ENSMUSG00000038080 |
| Gene Name |
lysine (K)-specific demethylase 1B |
| Synonyms |
Aof1, 4632428N09Rik |
| MMRRC Submission |
040563-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.406)
|
| Stock # |
R3054 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
13 |
| Chromosomal Location |
47196849-47238085 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 47216553 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Tryptophan
at position 308
(R308W)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000038373
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
|
| AlphaFold |
Q8CIG3 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000037025
AA Change: R308W
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: R308W
| 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: R24W
|
| SMART Domains |
Protein: ENSMUSP00000114999
Gene: ENSMUSG00000038080
AA Change: R24W
| 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 |
0.6467 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.5%
|
| Validation Efficiency |
|
| 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: 41 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5730596B20Rik |
A |
T |
6: 52,156,108 (GRCm39) |
|
probably benign |
Het |
| Aldh1l2 |
T |
C |
10: 83,338,336 (GRCm39) |
K528E |
probably benign |
Het |
| Als2 |
A |
G |
1: 59,254,653 (GRCm39) |
C235R |
probably damaging |
Het |
| Armc6 |
C |
A |
8: 70,677,799 (GRCm39) |
V177L |
probably benign |
Het |
| Asb7 |
A |
T |
7: 66,328,959 (GRCm39) |
V27D |
probably damaging |
Het |
| Bard1 |
A |
G |
1: 71,127,390 (GRCm39) |
V73A |
possibly damaging |
Het |
| Ccdc150 |
A |
G |
1: 54,328,001 (GRCm39) |
N361S |
possibly damaging |
Het |
| Cntn5 |
A |
G |
9: 10,419,076 (GRCm39) |
L7P |
probably benign |
Het |
| Cst3 |
A |
G |
2: 148,713,951 (GRCm39) |
S118P |
probably damaging |
Het |
| Cyp2a22 |
T |
C |
7: 26,638,254 (GRCm39) |
D84G |
probably damaging |
Het |
| Ddo |
A |
G |
10: 40,507,738 (GRCm39) |
N45S |
probably benign |
Het |
| Drd4 |
T |
C |
7: 140,874,392 (GRCm39) |
V319A |
probably damaging |
Het |
| Fat3 |
C |
T |
9: 15,871,792 (GRCm39) |
R3533H |
probably benign |
Het |
| Fras1 |
A |
T |
5: 96,912,802 (GRCm39) |
I3369F |
probably damaging |
Het |
| Gm5591 |
T |
C |
7: 38,220,058 (GRCm39) |
S272G |
probably benign |
Het |
| Gm8444 |
A |
T |
15: 81,727,845 (GRCm39) |
|
probably benign |
Het |
| Gm9776 |
A |
G |
13: 94,495,158 (GRCm39) |
|
probably benign |
Het |
| Larp1b |
A |
T |
3: 40,918,535 (GRCm39) |
I59F |
probably benign |
Het |
| Ltn1 |
C |
T |
16: 87,200,961 (GRCm39) |
A1092T |
probably benign |
Het |
| Map1b |
A |
G |
13: 99,569,250 (GRCm39) |
V1157A |
unknown |
Het |
| Mboat1 |
A |
T |
13: 30,379,724 (GRCm39) |
M92L |
probably benign |
Het |
| Meis3 |
G |
T |
7: 15,916,378 (GRCm39) |
L284F |
probably damaging |
Het |
| Muc20 |
T |
C |
16: 32,599,403 (GRCm39) |
F3317L |
probably benign |
Het |
| Muc5b |
G |
T |
7: 141,417,778 (GRCm39) |
V3575F |
probably damaging |
Het |
| Polr1e |
C |
T |
4: 45,018,724 (GRCm39) |
T18I |
possibly damaging |
Het |
| Ppp4r1 |
G |
T |
17: 66,143,074 (GRCm39) |
A764S |
probably damaging |
Het |
| Psg29 |
A |
G |
7: 16,942,727 (GRCm39) |
T243A |
probably benign |
Het |
| Ptprn2 |
T |
C |
12: 116,685,753 (GRCm39) |
Y71H |
probably damaging |
Het |
| Radx |
T |
A |
X: 138,412,306 (GRCm39) |
V439E |
possibly damaging |
Het |
| Rufy4 |
T |
C |
1: 74,186,822 (GRCm39) |
C537R |
probably damaging |
Het |
| Sh3bp1 |
C |
T |
15: 78,795,622 (GRCm39) |
P584S |
probably benign |
Het |
| Slc4a4 |
T |
C |
5: 89,373,807 (GRCm39) |
V971A |
probably damaging |
Het |
| Stil |
T |
A |
4: 114,862,163 (GRCm39) |
H35Q |
probably damaging |
Het |
| Strn |
A |
T |
17: 78,990,321 (GRCm39) |
V65D |
probably damaging |
Het |
| Sumf1 |
T |
C |
6: 108,130,165 (GRCm39) |
N185D |
probably benign |
Het |
| Timm29 |
T |
C |
9: 21,504,887 (GRCm39) |
M185T |
probably damaging |
Het |
| Tjp3 |
T |
C |
10: 81,116,341 (GRCm39) |
K251R |
probably benign |
Het |
| Tubgcp6 |
A |
T |
15: 89,006,806 (GRCm39) |
M72K |
probably damaging |
Het |
| Utp14b |
T |
A |
1: 78,642,442 (GRCm39) |
D113E |
possibly damaging |
Het |
| Vps13b |
A |
G |
15: 35,646,507 (GRCm39) |
E1537G |
probably damaging |
Het |
| Zfr |
A |
G |
15: 12,154,593 (GRCm39) |
N592S |
probably damaging |
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 |
|
|
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 |
|
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'- CTGTTTTGCAAGTCCCAGC -3'
(R):5'- TAGTCACCATGGCTGACGAC -3'
Sequencing Primer
(F):5'- CAAGTCCCAGCTTGCAGAG -3'
(R):5'- AGTTAGTCACCATGGCTGAC -3'
|
| Posted On |
2015-02-05 |
Incidental Mutation