Incidental Mutation 'R5265:Kdm1b'
ID |
401670 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Kdm1b
|
Ensembl Gene |
ENSMUSG00000038080 |
Gene Name |
lysine (K)-specific demethylase 1B |
Synonyms |
Aof1, 4632428N09Rik |
MMRRC Submission |
042833-MU
|
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.504)
|
Stock # |
R5265 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
13 |
Chromosomal Location |
47196849-47238085 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 47216445 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Asparagine to Aspartic acid
at position 272
(N272D)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000038373
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
|
AlphaFold |
Q8CIG3 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000037025
AA Change: N272D
PolyPhen 2
Score 0.355 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000038373 Gene: ENSMUSG00000038080 AA Change: N272D
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 |
probably benign
Transcript: ENSMUST00000143518
|
SMART Domains |
Protein: ENSMUSP00000114999 Gene: ENSMUSG00000038080
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 |
0.0610 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.7%
|
Validation Efficiency |
100% (59/59) |
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: 56 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700017B05Rik |
A |
G |
9: 57,166,177 (GRCm39) |
W66R |
probably damaging |
Het |
Adamts3 |
A |
G |
5: 90,009,411 (GRCm39) |
V84A |
possibly damaging |
Het |
Caap1 |
C |
A |
4: 94,389,465 (GRCm39) |
E290* |
probably null |
Het |
Cant1 |
G |
A |
11: 118,298,876 (GRCm39) |
R296C |
probably damaging |
Het |
Cdh5 |
A |
T |
8: 104,869,371 (GRCm39) |
H699L |
probably benign |
Het |
Cfdp1 |
T |
C |
8: 112,557,617 (GRCm39) |
T175A |
probably benign |
Het |
Col4a4 |
C |
T |
1: 82,471,312 (GRCm39) |
G681E |
unknown |
Het |
Comtd1 |
G |
A |
14: 21,898,861 (GRCm39) |
T27I |
probably benign |
Het |
Copg1 |
T |
A |
6: 87,869,252 (GRCm39) |
V155D |
probably damaging |
Het |
Dag1 |
A |
G |
9: 108,084,898 (GRCm39) |
Y748H |
possibly damaging |
Het |
Dmwd |
T |
A |
7: 18,814,206 (GRCm39) |
N285K |
possibly damaging |
Het |
Dsp |
A |
G |
13: 38,379,159 (GRCm39) |
E1968G |
possibly damaging |
Het |
Ednra |
A |
G |
8: 78,394,004 (GRCm39) |
I364T |
probably damaging |
Het |
Elovl3 |
C |
A |
19: 46,123,120 (GRCm39) |
T232K |
probably damaging |
Het |
Ercc3 |
T |
A |
18: 32,387,296 (GRCm39) |
I503N |
probably damaging |
Het |
Ercc6 |
C |
A |
14: 32,291,580 (GRCm39) |
A1008D |
probably benign |
Het |
Gm10563 |
TTTC |
TTTCATTC |
4: 155,698,953 (GRCm39) |
|
probably null |
Het |
H2-DMb2 |
G |
T |
17: 34,367,536 (GRCm39) |
V117F |
probably damaging |
Het |
Helt |
A |
T |
8: 46,745,470 (GRCm39) |
W138R |
probably damaging |
Het |
Itga11 |
A |
T |
9: 62,644,694 (GRCm39) |
H215L |
probably benign |
Het |
Kcnn1 |
T |
A |
8: 71,307,297 (GRCm39) |
I156F |
probably benign |
Het |
Kdm2b |
T |
C |
5: 123,016,651 (GRCm39) |
T1161A |
probably damaging |
Het |
Lin54 |
A |
G |
5: 100,633,378 (GRCm39) |
L102P |
probably damaging |
Het |
Mlh1 |
A |
C |
9: 111,100,591 (GRCm39) |
M1R |
probably null |
Het |
Naip2 |
G |
A |
13: 100,289,068 (GRCm39) |
L1165F |
probably damaging |
Het |
Nfkbiz |
A |
G |
16: 55,640,004 (GRCm39) |
S118P |
probably damaging |
Het |
Nkx3-2 |
T |
A |
5: 41,919,191 (GRCm39) |
M266L |
probably benign |
Het |
Npr1 |
T |
C |
3: 90,364,309 (GRCm39) |
E771G |
probably benign |
Het |
Obox8 |
C |
T |
7: 14,065,954 (GRCm39) |
R188H |
probably benign |
Het |
Odad1 |
T |
A |
7: 45,596,859 (GRCm39) |
D395E |
probably damaging |
Het |
Or5h19 |
A |
T |
16: 58,856,506 (GRCm39) |
V198D |
possibly damaging |
Het |
Or5p72 |
T |
A |
7: 108,022,609 (GRCm39) |
V277E |
possibly damaging |
Het |
Palm3 |
T |
C |
8: 84,748,159 (GRCm39) |
|
probably null |
Het |
Palmd |
A |
T |
3: 116,717,498 (GRCm39) |
V333D |
possibly damaging |
Het |
Pikfyve |
A |
G |
1: 65,306,988 (GRCm39) |
E1747G |
possibly damaging |
Het |
Polr3a |
T |
C |
14: 24,505,009 (GRCm39) |
I1084V |
possibly damaging |
Het |
Ranbp3l |
T |
A |
15: 9,037,077 (GRCm39) |
F127I |
probably benign |
Het |
Rsl1d1 |
A |
G |
16: 11,019,248 (GRCm39) |
F97L |
possibly damaging |
Het |
Scaper |
A |
G |
9: 55,771,830 (GRCm39) |
V362A |
probably benign |
Het |
Scg5 |
A |
T |
2: 113,607,210 (GRCm39) |
L192* |
probably null |
Het |
Slc34a2 |
T |
C |
5: 53,218,776 (GRCm39) |
I198T |
probably damaging |
Het |
Slc45a3 |
T |
A |
1: 131,905,932 (GRCm39) |
D318E |
possibly damaging |
Het |
Sorl1 |
A |
G |
9: 42,017,812 (GRCm39) |
M105T |
possibly damaging |
Het |
St3gal5 |
T |
A |
6: 72,126,115 (GRCm39) |
I320N |
probably damaging |
Het |
Stx17 |
A |
G |
4: 48,183,470 (GRCm39) |
|
probably benign |
Het |
Syt5 |
C |
T |
7: 4,544,074 (GRCm39) |
|
probably null |
Het |
Thrap3 |
A |
G |
4: 126,061,433 (GRCm39) |
S774P |
probably damaging |
Het |
Tnc |
A |
T |
4: 63,911,443 (GRCm39) |
M1376K |
probably benign |
Het |
Tnks1bp1 |
T |
A |
2: 84,893,098 (GRCm39) |
D1008E |
probably benign |
Het |
Trav7-1 |
G |
T |
14: 52,892,761 (GRCm39) |
A105S |
probably damaging |
Het |
Vmn1r28 |
T |
A |
6: 58,242,949 (GRCm39) |
V264D |
probably damaging |
Het |
Vmn1r44 |
T |
C |
6: 89,870,821 (GRCm39) |
V46A |
probably benign |
Het |
Vmn2r10 |
A |
G |
5: 109,143,586 (GRCm39) |
I788T |
probably damaging |
Het |
Vmn2r78 |
T |
A |
7: 86,569,332 (GRCm39) |
I75N |
probably damaging |
Het |
Zfp821 |
T |
C |
8: 110,450,991 (GRCm39) |
M328T |
probably damaging |
Het |
Zfp995 |
G |
A |
17: 22,099,604 (GRCm39) |
P210L |
possibly 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 |
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 |
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'- AAAGTGCCAAAGGGTGTTTG -3'
(R):5'- TTGTGTACCACAGTGCGAG -3'
Sequencing Primer
(F):5'- TCCTAGAGATTGAACTGAGGCCATC -3'
(R):5'- CACAGTGCGAGGATGAGGTTTC -3'
|
Posted On |
2016-07-06 |