Incidental Mutation 'R5098:Kdm1b'
| ID |
388146 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm1b
|
| Ensembl Gene |
ENSMUSG00000038080 |
| Gene Name |
lysine (K)-specific demethylase 1B |
| Synonyms |
4632428N09Rik, Aof1 |
| MMRRC Submission |
042687-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.557)
|
| Stock # |
R5098 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
47043499-47085279 bp(+) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 47062991 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 279
(Y279C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000038373
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
|
| AlphaFold |
Q8CIG3 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000037025
AA Change: Y279C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: Y279C
| 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 |
0.1949 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.0%
|
| Validation Efficiency |
100% (54/54) |
| 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: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930402H24Rik |
A |
G |
2: 130,798,181 (GRCm38) |
S128P |
probably damaging |
Het |
| Abca8b |
T |
C |
11: 109,957,118 (GRCm38) |
I784V |
probably benign |
Het |
| Agxt |
A |
G |
1: 93,137,307 (GRCm38) |
H146R |
probably benign |
Het |
| AI314180 |
T |
C |
4: 58,877,048 (GRCm38) |
D129G |
probably damaging |
Het |
| Art5 |
A |
G |
7: 102,097,970 (GRCm38) |
F201L |
probably damaging |
Het |
| Bcl2a1b |
T |
A |
9: 89,199,379 (GRCm38) |
M7K |
probably benign |
Het |
| Card10 |
G |
A |
15: 78,776,717 (GRCm38) |
A1030V |
probably benign |
Het |
| Ccdc66 |
G |
A |
14: 27,498,793 (GRCm38) |
T58M |
probably damaging |
Het |
| Cd72 |
C |
T |
4: 43,452,610 (GRCm38) |
G74R |
probably damaging |
Het |
| Cdc27 |
T |
C |
11: 104,507,287 (GRCm38) |
K749R |
probably damaging |
Het |
| Commd3 |
A |
T |
2: 18,674,177 (GRCm38) |
T102S |
possibly damaging |
Het |
| Cyp2f2 |
A |
G |
7: 27,129,879 (GRCm38) |
T270A |
possibly damaging |
Het |
| Dclre1b |
A |
G |
3: 103,809,136 (GRCm38) |
|
probably benign |
Het |
| Dennd1b |
T |
A |
1: 139,133,721 (GRCm38) |
D380E |
probably damaging |
Het |
| Dhx58 |
T |
C |
11: 100,695,173 (GRCm38) |
E674G |
probably benign |
Het |
| Exoc5 |
T |
C |
14: 49,048,847 (GRCm38) |
T108A |
possibly damaging |
Het |
| Fat4 |
T |
C |
3: 38,888,289 (GRCm38) |
S444P |
probably benign |
Het |
| Gm3327 |
A |
T |
14: 44,124,835 (GRCm38) |
I64F |
unknown |
Het |
| Gm4787 |
G |
C |
12: 81,377,830 (GRCm38) |
T518S |
probably benign |
Het |
| Gpr15 |
T |
A |
16: 58,718,527 (GRCm38) |
R66S |
probably damaging |
Het |
| Hmga1b |
T |
C |
11: 120,763,192 (GRCm38) |
S102P |
probably benign |
Het |
| Kat6b |
G |
A |
14: 21,619,015 (GRCm38) |
|
probably benign |
Het |
| Krtap9-3 |
C |
A |
11: 99,597,990 (GRCm38) |
C22F |
probably benign |
Het |
| Map3k14 |
T |
A |
11: 103,224,359 (GRCm38) |
D817V |
probably damaging |
Het |
| Mybpc1 |
T |
C |
10: 88,546,064 (GRCm38) |
D588G |
probably damaging |
Het |
| Olfr1 |
AGCGGTCGTAGGC |
AGC |
11: 73,395,654 (GRCm38) |
|
probably null |
Het |
| Olfr720 |
A |
G |
14: 14,175,683 (GRCm38) |
V133A |
probably benign |
Het |
| Olfr998 |
A |
G |
2: 85,590,632 (GRCm38) |
I31V |
probably benign |
Het |
| Pcdhb20 |
A |
G |
18: 37,504,805 (GRCm38) |
D128G |
probably damaging |
Het |
| Ppil6 |
A |
G |
10: 41,490,620 (GRCm38) |
E47G |
probably null |
Het |
| Rad17 |
A |
T |
13: 100,617,646 (GRCm38) |
*689K |
probably null |
Het |
| Scin |
A |
T |
12: 40,077,542 (GRCm38) |
Y416* |
probably null |
Het |
| Serf1 |
A |
G |
13: 100,109,067 (GRCm38) |
T18A |
probably benign |
Het |
| Sik2 |
T |
C |
9: 50,995,591 (GRCm38) |
|
probably benign |
Het |
| Slc39a8 |
C |
A |
3: 135,858,157 (GRCm38) |
N254K |
probably benign |
Het |
| Spint3 |
A |
G |
2: 164,569,901 (GRCm38) |
F63L |
probably damaging |
Het |
| Suox |
A |
T |
10: 128,671,158 (GRCm38) |
S334T |
probably damaging |
Het |
| Tas2r119 |
A |
G |
15: 32,178,082 (GRCm38) |
M265V |
probably benign |
Het |
| Tmem126b |
A |
G |
7: 90,469,642 (GRCm38) |
L146P |
probably damaging |
Het |
| Tmem8 |
A |
T |
17: 26,118,928 (GRCm38) |
N429Y |
probably damaging |
Het |
| Trpc3 |
G |
T |
3: 36,662,898 (GRCm38) |
D330E |
probably benign |
Het |
| Ugt2a2 |
T |
C |
5: 87,464,181 (GRCm38) |
E290G |
possibly damaging |
Het |
| Ugt2b37 |
T |
A |
5: 87,242,953 (GRCm38) |
T352S |
probably damaging |
Het |
| Vmn1r40 |
T |
C |
6: 89,714,948 (GRCm38) |
V249A |
probably damaging |
Het |
| Zc3h18 |
A |
G |
8: 122,386,869 (GRCm38) |
D200G |
probably damaging |
Het |
| Zfp652 |
T |
C |
11: 95,752,936 (GRCm38) |
V140A |
probably damaging |
Het |
|
| Other mutations in Kdm1b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00587:Kdm1b
|
APN |
13 |
47,068,540 (GRCm38) |
missense |
probably benign |
0.01 |
|
IGL00924:Kdm1b
|
APN |
13 |
47,068,480 (GRCm38) |
missense |
probably benign |
|
|
IGL01553:Kdm1b
|
APN |
13 |
47,080,548 (GRCm38) |
missense |
probably damaging |
0.96 |
|
IGL01663:Kdm1b
|
APN |
13 |
47,073,737 (GRCm38) |
missense |
probably damaging |
0.99 |
|
IGL02385:Kdm1b
|
APN |
13 |
47,068,506 (GRCm38) |
missense |
possibly damaging |
0.49 |
|
IGL02505:Kdm1b
|
APN |
13 |
47,060,855 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL02826:Kdm1b
|
APN |
13 |
47,080,467 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL03257:Kdm1b
|
APN |
13 |
47,049,266 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0052:Kdm1b
|
UTSW |
13 |
47,064,117 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0319:Kdm1b
|
UTSW |
13 |
47,053,719 (GRCm38) |
missense |
probably benign |
|
|
R0426:Kdm1b
|
UTSW |
13 |
47,064,244 (GRCm38) |
splice site |
probably benign |
|
|
R0599:Kdm1b
|
UTSW |
13 |
47,058,810 (GRCm38) |
missense |
possibly damaging |
0.47 |
|
R0764:Kdm1b
|
UTSW |
13 |
47,068,603 (GRCm38) |
missense |
possibly damaging |
0.70 |
|
R1163:Kdm1b
|
UTSW |
13 |
47,071,922 (GRCm38) |
missense |
probably benign |
0.02 |
|
R1543:Kdm1b
|
UTSW |
13 |
47,068,521 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R1584:Kdm1b
|
UTSW |
13 |
47,064,054 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1627:Kdm1b
|
UTSW |
13 |
47,064,231 (GRCm38) |
critical splice donor site |
probably null |
|
|
R1669:Kdm1b
|
UTSW |
13 |
47,068,548 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1758:Kdm1b
|
UTSW |
13 |
47,060,768 (GRCm38) |
missense |
probably benign |
0.00 |
|
R1860:Kdm1b
|
UTSW |
13 |
47,049,190 (GRCm38) |
missense |
probably benign |
0.03 |
|
R1907:Kdm1b
|
UTSW |
13 |
47,064,120 (GRCm38) |
missense |
probably benign |
0.00 |
|
R2225:Kdm1b
|
UTSW |
13 |
47,064,088 (GRCm38) |
frame shift |
probably null |
|
|
R2239:Kdm1b
|
UTSW |
13 |
47,073,755 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R2271:Kdm1b
|
UTSW |
13 |
47,064,088 (GRCm38) |
frame shift |
probably null |
|
|
R2302:Kdm1b
|
UTSW |
13 |
47,064,088 (GRCm38) |
frame shift |
probably null |
|
|
R2303:Kdm1b
|
UTSW |
13 |
47,064,088 (GRCm38) |
frame shift |
probably null |
|
|
R2380:Kdm1b
|
UTSW |
13 |
47,073,755 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R2442:Kdm1b
|
UTSW |
13 |
47,062,975 (GRCm38) |
missense |
probably benign |
0.32 |
|
R3022:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R3054:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R3545:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R3546:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R3548:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4094:Kdm1b
|
UTSW |
13 |
47,063,020 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4419:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4420:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4502:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4547:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4548:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4785:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4793:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4804:Kdm1b
|
UTSW |
13 |
47,063,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4882:Kdm1b
|
UTSW |
13 |
47,060,893 (GRCm38) |
missense |
probably benign |
|
|
R4906:Kdm1b
|
UTSW |
13 |
47,063,144 (GRCm38) |
critical splice donor site |
probably null |
|
|
R4965:Kdm1b
|
UTSW |
13 |
47,074,367 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R5039:Kdm1b
|
UTSW |
13 |
47,077,486 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5265:Kdm1b
|
UTSW |
13 |
47,062,969 (GRCm38) |
missense |
probably benign |
0.35 |
|
R5541:Kdm1b
|
UTSW |
13 |
47,079,196 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5814:Kdm1b
|
UTSW |
13 |
47,063,146 (GRCm38) |
splice site |
probably null |
|
|
R6046:Kdm1b
|
UTSW |
13 |
47,079,253 (GRCm38) |
missense |
possibly damaging |
0.92 |
|
R6798:Kdm1b
|
UTSW |
13 |
47,068,536 (GRCm38) |
missense |
probably benign |
0.00 |
|
R6903:Kdm1b
|
UTSW |
13 |
47,074,404 (GRCm38) |
missense |
probably benign |
0.00 |
|
R7831:Kdm1b
|
UTSW |
13 |
47,050,622 (GRCm38) |
missense |
probably benign |
0.17 |
|
R7973:Kdm1b
|
UTSW |
13 |
47,077,446 (GRCm38) |
missense |
probably benign |
0.00 |
|
R8181:Kdm1b
|
UTSW |
13 |
47,051,901 (GRCm38) |
critical splice donor site |
probably null |
|
|
R8248:Kdm1b
|
UTSW |
13 |
47,071,878 (GRCm38) |
intron |
probably benign |
|
|
R8821:Kdm1b
|
UTSW |
13 |
47,064,141 (GRCm38) |
missense |
possibly damaging |
0.94 |
|
R8831:Kdm1b
|
UTSW |
13 |
47,064,141 (GRCm38) |
missense |
possibly damaging |
0.94 |
|
R8842:Kdm1b
|
UTSW |
13 |
47,078,356 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8861:Kdm1b
|
UTSW |
13 |
47,064,106 (GRCm38) |
missense |
probably benign |
0.02 |
|
R8885:Kdm1b
|
UTSW |
13 |
47,053,708 (GRCm38) |
nonsense |
probably null |
|
|
R9038:Kdm1b
|
UTSW |
13 |
47,049,294 (GRCm38) |
missense |
probably benign |
0.07 |
|
R9132:Kdm1b
|
UTSW |
13 |
47,071,982 (GRCm38) |
missense |
probably benign |
0.05 |
|
R9268:Kdm1b
|
UTSW |
13 |
47,064,229 (GRCm38) |
missense |
probably benign |
0.00 |
|
R9616:Kdm1b
|
UTSW |
13 |
47,080,554 (GRCm38) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- AAAGTGCCAAAGGGTGTTTG -3'
(R):5'- GACTCTGCTCGTTAGTCACTG -3'
Sequencing Primer
(F):5'- TCCTAGAGATTGAACTGAGGCCATC -3'
(R):5'- GCTCGTTAGTCACTGGTGCC -3'
|
| Posted On |
2016-06-06 |
Incidental Mutation