Incidental Mutation 'R4419:Kdm1b'
ID |
327014 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Kdm1b
|
Ensembl Gene |
ENSMUSG00000038080 |
Gene Name |
lysine (K)-specific demethylase 1B |
Synonyms |
Aof1, 4632428N09Rik |
MMRRC Submission |
041140-MU
|
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.504)
|
Stock # |
R4419 (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: 98.6%
- 10x: 97.4%
- 20x: 95.6%
|
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: 43 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Amdhd2 |
G |
A |
17: 24,377,652 (GRCm39) |
P126L |
probably benign |
Het |
Arfip2 |
T |
C |
7: 105,288,270 (GRCm39) |
T44A |
probably damaging |
Het |
B4galt1 |
A |
G |
4: 40,853,537 (GRCm39) |
V90A |
probably benign |
Het |
Bad |
C |
A |
19: 6,928,053 (GRCm39) |
A115E |
probably benign |
Het |
Bicc1 |
A |
G |
10: 70,782,804 (GRCm39) |
L521P |
possibly damaging |
Het |
Caskin1 |
T |
C |
17: 24,723,683 (GRCm39) |
S824P |
probably damaging |
Het |
Cblb |
T |
A |
16: 51,867,621 (GRCm39) |
D76E |
possibly damaging |
Het |
Celsr3 |
G |
T |
9: 108,720,443 (GRCm39) |
A2572S |
possibly damaging |
Het |
Csmd3 |
T |
C |
15: 47,567,707 (GRCm39) |
Q2152R |
probably damaging |
Het |
D2hgdh |
T |
A |
1: 93,757,535 (GRCm39) |
V150E |
probably damaging |
Het |
Ddn |
C |
A |
15: 98,703,492 (GRCm39) |
W600L |
probably benign |
Het |
Dicer1 |
A |
T |
12: 104,671,373 (GRCm39) |
Y966N |
probably damaging |
Het |
Dsp |
T |
A |
13: 38,379,108 (GRCm39) |
I1352N |
probably damaging |
Het |
Duox1 |
G |
A |
2: 122,157,607 (GRCm39) |
A578T |
probably benign |
Het |
Dysf |
T |
C |
6: 84,184,224 (GRCm39) |
|
probably null |
Het |
Elmo2 |
T |
C |
2: 165,153,675 (GRCm39) |
|
probably null |
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 |
Ky |
G |
A |
9: 102,419,909 (GRCm39) |
V639I |
probably damaging |
Het |
Med16 |
G |
A |
10: 79,734,216 (GRCm39) |
A566V |
probably benign |
Het |
Mettl17 |
G |
T |
14: 52,124,729 (GRCm39) |
G167C |
possibly damaging |
Het |
Mgat4b |
T |
C |
11: 50,123,813 (GRCm39) |
F318L |
probably damaging |
Het |
Mug2 |
C |
A |
6: 122,056,589 (GRCm39) |
A1178D |
probably damaging |
Het |
Myo3b |
A |
G |
2: 69,926,706 (GRCm39) |
D51G |
probably damaging |
Het |
Naip2 |
T |
C |
13: 100,297,133 (GRCm39) |
N968D |
probably benign |
Het |
Nbea |
T |
C |
3: 55,917,021 (GRCm39) |
H820R |
probably damaging |
Het |
Nqo1 |
C |
T |
8: 108,118,749 (GRCm39) |
|
probably null |
Het |
Or10ak7 |
A |
T |
4: 118,791,586 (GRCm39) |
I153N |
possibly damaging |
Het |
Or6c68 |
T |
C |
10: 129,157,684 (GRCm39) |
F64S |
possibly damaging |
Het |
Or8b51 |
C |
T |
9: 38,569,365 (GRCm39) |
V108I |
probably benign |
Het |
Ppargc1a |
T |
C |
5: 51,652,044 (GRCm39) |
D218G |
probably damaging |
Het |
Rras |
A |
G |
7: 44,670,003 (GRCm39) |
D145G |
probably damaging |
Het |
Scn3a |
C |
A |
2: 65,297,304 (GRCm39) |
G1452C |
probably damaging |
Het |
Slc22a2 |
C |
A |
17: 12,831,473 (GRCm39) |
S421* |
probably null |
Het |
Slc39a10 |
A |
G |
1: 46,849,226 (GRCm39) |
F797L |
probably benign |
Het |
Spta1 |
T |
A |
1: 174,074,990 (GRCm39) |
Y2405* |
probably null |
Het |
Ss18 |
A |
G |
18: 14,766,662 (GRCm39) |
Y359H |
unknown |
Het |
St14 |
C |
T |
9: 31,008,224 (GRCm39) |
C537Y |
probably damaging |
Het |
Tmem252 |
T |
A |
19: 24,654,910 (GRCm39) |
Y96N |
probably damaging |
Het |
Trafd1 |
T |
C |
5: 121,511,396 (GRCm39) |
D474G |
probably benign |
Het |
Trmt1l |
A |
G |
1: 151,316,559 (GRCm39) |
I20M |
probably damaging |
Het |
Ulk1 |
C |
T |
5: 110,937,223 (GRCm39) |
R691Q |
probably benign |
Het |
Vmn1r43 |
A |
G |
6: 89,846,629 (GRCm39) |
S286P |
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 |
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 |
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'- GTTTTGCAAGTCCCAGCTTG -3'
(R):5'- TAGTCACCATGGCTGACGAC -3'
Sequencing Primer
(F):5'- CAAGTCCCAGCTTGCAGAG -3'
(R):5'- AGTTAGTCACCATGGCTGAC -3'
|
Posted On |
2015-07-07 |