Incidental Mutation 'R4420:Kdm1b'
ID |
327063 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Kdm1b
|
Ensembl Gene |
ENSMUSG00000038080 |
Gene Name |
lysine (K)-specific demethylase 1B |
Synonyms |
Aof1, 4632428N09Rik |
MMRRC Submission |
041141-MU
|
Accession Numbers |
|
Essential gene? |
Possibly non essential
(E-score: 0.406)
|
Stock # |
R4420 (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 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: 98.6%
- 10x: 97.3%
- 20x: 95.3%
|
Validation Efficiency |
96% (53/55) |
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: 48 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Arhgef17 |
G |
A |
7: 100,531,515 (GRCm39) |
|
probably benign |
Het |
Atp1b1 |
T |
C |
1: 164,281,127 (GRCm39) |
T53A |
probably damaging |
Het |
Carmil3 |
A |
G |
14: 55,731,045 (GRCm39) |
Q104R |
probably damaging |
Het |
Casz1 |
T |
G |
4: 149,033,375 (GRCm39) |
N1382K |
possibly damaging |
Het |
Chfr |
T |
A |
5: 110,318,746 (GRCm39) |
C585* |
probably null |
Het |
Chp2 |
T |
C |
7: 121,821,161 (GRCm39) |
F174S |
probably damaging |
Het |
Dclre1c |
A |
T |
2: 3,434,782 (GRCm39) |
|
probably null |
Het |
Dnah6 |
A |
G |
6: 73,168,462 (GRCm39) |
V487A |
probably benign |
Het |
Dnah9 |
T |
C |
11: 66,009,575 (GRCm39) |
R771G |
probably benign |
Het |
Duox1 |
G |
A |
2: 122,157,607 (GRCm39) |
A578T |
probably benign |
Het |
Elp3 |
G |
A |
14: 65,818,240 (GRCm39) |
A140V |
probably damaging |
Het |
Fbrsl1 |
T |
C |
5: 110,526,852 (GRCm39) |
H387R |
possibly damaging |
Het |
Gnat3 |
T |
C |
5: 18,204,799 (GRCm39) |
S151P |
probably damaging |
Het |
Gucy1a2 |
T |
A |
9: 3,634,640 (GRCm39) |
L228H |
probably damaging |
Het |
Gzmn |
A |
T |
14: 56,403,463 (GRCm39) |
H215Q |
probably benign |
Het |
Heg1 |
A |
T |
16: 33,547,805 (GRCm39) |
E864V |
probably benign |
Het |
Hoxb9 |
T |
C |
11: 96,162,807 (GRCm39) |
V147A |
probably benign |
Het |
Hsf5 |
T |
G |
11: 87,548,130 (GRCm39) |
H604Q |
probably benign |
Het |
Hus1 |
T |
C |
11: 8,950,133 (GRCm39) |
E196G |
probably damaging |
Het |
Il12rb2 |
G |
T |
6: 67,293,394 (GRCm39) |
|
probably null |
Het |
Irs1 |
T |
C |
1: 82,266,171 (GRCm39) |
S682G |
possibly damaging |
Het |
Jcad |
T |
C |
18: 4,676,032 (GRCm39) |
S1265P |
probably benign |
Het |
Matk |
A |
G |
10: 81,098,291 (GRCm39) |
S361G |
possibly damaging |
Het |
Mroh5 |
TGGAG |
TG |
15: 73,654,923 (GRCm39) |
|
probably benign |
Het |
Nceh1 |
A |
G |
3: 27,295,798 (GRCm39) |
D353G |
probably damaging |
Het |
Nqo1 |
C |
T |
8: 108,118,749 (GRCm39) |
|
probably null |
Het |
Or5t7 |
A |
G |
2: 86,507,263 (GRCm39) |
V138A |
possibly damaging |
Het |
Pcdh7 |
T |
C |
5: 58,286,512 (GRCm39) |
I1196T |
probably benign |
Het |
Pla2g4d |
A |
G |
2: 120,114,644 (GRCm39) |
V29A |
probably benign |
Het |
Ppfibp1 |
T |
A |
6: 146,927,736 (GRCm39) |
Y794* |
probably null |
Het |
Prdx5 |
C |
A |
19: 6,885,332 (GRCm39) |
|
probably null |
Het |
Psme4 |
C |
T |
11: 30,762,028 (GRCm39) |
T456I |
possibly damaging |
Het |
Ptprd |
A |
T |
4: 75,957,614 (GRCm39) |
S923R |
possibly damaging |
Het |
Samd12 |
G |
A |
15: 53,723,655 (GRCm39) |
R13W |
probably damaging |
Het |
Slc35f4 |
A |
T |
14: 49,551,034 (GRCm39) |
|
probably benign |
Het |
Smc1b |
A |
G |
15: 84,997,031 (GRCm39) |
Y530H |
probably damaging |
Het |
Spata2l |
T |
C |
8: 123,960,768 (GRCm39) |
T174A |
possibly damaging |
Het |
Sugct |
C |
T |
13: 17,627,130 (GRCm39) |
C241Y |
probably damaging |
Het |
Tarbp1 |
G |
T |
8: 127,173,819 (GRCm39) |
A965D |
possibly damaging |
Het |
Tas1r3 |
A |
G |
4: 155,946,789 (GRCm39) |
V272A |
probably damaging |
Het |
Tas2r117 |
T |
A |
6: 132,780,312 (GRCm39) |
L150* |
probably null |
Het |
Trip10 |
C |
T |
17: 57,562,448 (GRCm39) |
P322L |
probably benign |
Het |
Wdfy3 |
A |
C |
5: 102,058,850 (GRCm39) |
H1487Q |
probably damaging |
Het |
Wdr95 |
G |
A |
5: 149,456,131 (GRCm39) |
V8M |
probably damaging |
Het |
Zc3h15 |
C |
A |
2: 83,488,356 (GRCm39) |
A98E |
probably damaging |
Het |
Zfp763 |
T |
G |
17: 33,237,455 (GRCm39) |
K563N |
probably benign |
Het |
Zmym2 |
G |
A |
14: 57,194,335 (GRCm39) |
D1198N |
probably damaging |
Het |
Zp1 |
C |
T |
19: 10,892,124 (GRCm39) |
|
probably null |
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 |
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 |
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'- TGTTTTGCAAGTCCCAGCTTG -3'
(R):5'- TAGTCACCATGGCTGACGACTC -3'
Sequencing Primer
(F):5'- CAAGTCCCAGCTTGCAGAG -3'
(R):5'- AGTTAGTCACCATGGCTGAC -3'
|
Posted On |
2015-07-07 |