Incidental Mutation 'R1543:Kdm1b'
| ID |
171947 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm1b
|
| Ensembl Gene |
ENSMUSG00000038080 |
| Gene Name |
lysine (K)-specific demethylase 1B |
| Synonyms |
Aof1, 4632428N09Rik |
| MMRRC Submission |
039582-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.406)
|
| Stock # |
R1543 (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 47221997 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Tryptophan
at position 479
(R479W)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000038373
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
|
| AlphaFold |
Q8CIG3 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000037025
AA Change: R479W
PolyPhen 2
Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: R479W
| 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 |
0.6467 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.1%
- 10x: 95.7%
- 20x: 90.2%
|
| Validation Efficiency |
95% (77/81) |
| 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: 77 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1810009J06Rik |
G |
A |
6: 40,945,138 (GRCm39) |
V206I |
probably damaging |
Het |
| Abca8b |
A |
C |
11: 109,865,500 (GRCm39) |
M319R |
probably damaging |
Het |
| Abcc6 |
T |
C |
7: 45,665,928 (GRCm39) |
R231G |
probably benign |
Het |
| Acadm |
A |
G |
3: 153,635,209 (GRCm39) |
Y302H |
probably damaging |
Het |
| Acox3 |
C |
A |
5: 35,760,352 (GRCm39) |
R423S |
probably damaging |
Het |
| Adam7 |
T |
A |
14: 68,759,371 (GRCm39) |
|
probably benign |
Het |
| Adgrb3 |
A |
C |
1: 25,527,169 (GRCm39) |
M589R |
probably benign |
Het |
| Adgrl2 |
A |
C |
3: 148,564,909 (GRCm39) |
F224V |
probably damaging |
Het |
| Adm2 |
G |
C |
15: 89,208,282 (GRCm39) |
G74A |
probably damaging |
Het |
| Aen |
T |
A |
7: 78,552,370 (GRCm39) |
V15E |
probably damaging |
Het |
| Ankzf1 |
T |
A |
1: 75,169,160 (GRCm39) |
V22D |
possibly damaging |
Het |
| Arap2 |
T |
A |
5: 62,763,498 (GRCm39) |
K1549* |
probably null |
Het |
| Arhgef11 |
G |
A |
3: 87,620,324 (GRCm39) |
R430H |
probably benign |
Het |
| Asb17 |
T |
G |
3: 153,550,148 (GRCm39) |
L60W |
probably damaging |
Het |
| BC035044 |
T |
C |
6: 128,867,948 (GRCm39) |
|
probably benign |
Het |
| Bltp2 |
A |
G |
11: 78,166,000 (GRCm39) |
T1422A |
probably benign |
Het |
| Cacna2d1 |
A |
T |
5: 16,471,716 (GRCm39) |
M254L |
possibly damaging |
Het |
| Celf6 |
T |
C |
9: 59,511,160 (GRCm39) |
|
probably benign |
Het |
| Cemip2 |
G |
T |
19: 21,789,937 (GRCm39) |
A668S |
probably benign |
Het |
| Coro2b |
C |
T |
9: 62,333,123 (GRCm39) |
V120I |
probably benign |
Het |
| Cyp20a1 |
C |
A |
1: 60,415,353 (GRCm39) |
|
probably benign |
Het |
| Cyp2c67 |
C |
A |
19: 39,631,708 (GRCm39) |
|
probably benign |
Het |
| Dclk3 |
A |
G |
9: 111,297,122 (GRCm39) |
H222R |
probably benign |
Het |
| Deaf1 |
A |
G |
7: 140,904,060 (GRCm39) |
S109P |
possibly damaging |
Het |
| Dlg5 |
T |
A |
14: 24,194,516 (GRCm39) |
D1675V |
probably damaging |
Het |
| Dsg2 |
T |
A |
18: 20,727,268 (GRCm39) |
V605E |
probably benign |
Het |
| Dync2i1 |
T |
C |
12: 116,195,404 (GRCm39) |
|
probably benign |
Het |
| Frem2 |
A |
T |
3: 53,479,876 (GRCm39) |
I1939N |
possibly damaging |
Het |
| Fsip2 |
A |
T |
2: 82,811,931 (GRCm39) |
Y2750F |
possibly damaging |
Het |
| Gpr39 |
T |
A |
1: 125,800,161 (GRCm39) |
I304N |
probably damaging |
Het |
| Hdac7 |
G |
A |
15: 97,707,410 (GRCm39) |
|
probably benign |
Het |
| Hipk1 |
T |
C |
3: 103,685,480 (GRCm39) |
H45R |
probably benign |
Het |
| Hyal2 |
T |
C |
9: 107,447,386 (GRCm39) |
L13P |
probably damaging |
Het |
| Lilrb4b |
A |
G |
10: 51,357,517 (GRCm39) |
T118A |
probably damaging |
Het |
| Lin7a |
C |
A |
10: 107,247,930 (GRCm39) |
F78L |
possibly damaging |
Het |
| Lpin3 |
A |
G |
2: 160,737,310 (GRCm39) |
D119G |
possibly damaging |
Het |
| Lrp2 |
G |
A |
2: 69,331,074 (GRCm39) |
R1661C |
probably damaging |
Het |
| Lrrc45 |
A |
G |
11: 120,610,844 (GRCm39) |
K527E |
probably benign |
Het |
| Map10 |
C |
T |
8: 126,397,611 (GRCm39) |
P335S |
probably benign |
Het |
| Mast3 |
A |
G |
8: 71,244,955 (GRCm39) |
S2P |
possibly damaging |
Het |
| Mbtps1 |
A |
G |
8: 120,268,808 (GRCm39) |
|
probably benign |
Het |
| Mms22l |
T |
A |
4: 24,591,084 (GRCm39) |
N1018K |
probably benign |
Het |
| Nckipsd |
C |
A |
9: 108,689,571 (GRCm39) |
A244D |
possibly damaging |
Het |
| Nt5el |
A |
T |
13: 105,248,877 (GRCm39) |
R364* |
probably null |
Het |
| Or12k5 |
C |
A |
2: 36,895,139 (GRCm39) |
L162F |
probably damaging |
Het |
| Or1j1 |
A |
T |
2: 36,703,069 (GRCm39) |
F12I |
probably damaging |
Het |
| Or4k44 |
A |
G |
2: 111,368,142 (GRCm39) |
V164A |
probably benign |
Het |
| Or52j3 |
T |
A |
7: 102,836,421 (GRCm39) |
F204L |
probably benign |
Het |
| Or8b12c |
T |
A |
9: 37,715,243 (GRCm39) |
I12N |
possibly damaging |
Het |
| Pcx |
A |
T |
19: 4,652,251 (GRCm39) |
D112V |
probably damaging |
Het |
| Phf14 |
G |
A |
6: 11,987,682 (GRCm39) |
|
probably null |
Het |
| Pkd1l1 |
A |
G |
11: 8,851,200 (GRCm39) |
I744T |
probably damaging |
Het |
| Ppip5k2 |
A |
G |
1: 97,668,607 (GRCm39) |
L560P |
probably damaging |
Het |
| Psmd14 |
A |
T |
2: 61,615,874 (GRCm39) |
M248L |
probably benign |
Het |
| Ryr1 |
T |
G |
7: 28,782,962 (GRCm39) |
E1884A |
possibly damaging |
Het |
| Scn4b |
T |
A |
9: 45,061,727 (GRCm39) |
S204R |
probably damaging |
Het |
| Slc12a1 |
A |
T |
2: 125,026,777 (GRCm39) |
M471L |
possibly damaging |
Het |
| Slc17a5 |
A |
G |
9: 78,468,082 (GRCm39) |
V236A |
probably benign |
Het |
| Sobp |
T |
C |
10: 42,897,720 (GRCm39) |
T622A |
probably damaging |
Het |
| Spata31d1a |
G |
T |
13: 59,850,056 (GRCm39) |
R691S |
probably benign |
Het |
| Speg |
A |
G |
1: 75,398,595 (GRCm39) |
E2014G |
probably damaging |
Het |
| Steap4 |
A |
G |
5: 8,025,902 (GRCm39) |
|
probably benign |
Het |
| Tas2r144 |
G |
A |
6: 42,192,537 (GRCm39) |
M92I |
probably benign |
Het |
| Tbc1d5 |
T |
C |
17: 51,242,560 (GRCm39) |
Q179R |
probably benign |
Het |
| Tcf25 |
T |
C |
8: 124,115,326 (GRCm39) |
Y188H |
probably benign |
Het |
| Tmem200a |
G |
A |
10: 25,954,518 (GRCm39) |
|
probably benign |
Het |
| Trappc9 |
G |
A |
15: 72,897,816 (GRCm39) |
R377W |
probably damaging |
Het |
| Tssk5 |
T |
C |
15: 76,256,409 (GRCm39) |
T337A |
probably benign |
Het |
| Ttc23 |
T |
C |
7: 67,328,743 (GRCm39) |
V228A |
probably benign |
Het |
| Tulp1 |
A |
T |
17: 28,581,645 (GRCm39) |
|
probably benign |
Het |
| Uqcc3 |
A |
G |
19: 8,858,117 (GRCm39) |
F25L |
probably damaging |
Het |
| Vmn2r1 |
G |
A |
3: 63,996,994 (GRCm39) |
G217S |
probably damaging |
Het |
| Vmn2r120 |
C |
T |
17: 57,829,374 (GRCm39) |
E508K |
probably benign |
Het |
| Wdfy3 |
C |
A |
5: 101,991,947 (GRCm39) |
V3451L |
probably benign |
Het |
| Wdr19 |
G |
A |
5: 65,382,033 (GRCm39) |
V418I |
probably benign |
Het |
| Xirp2 |
C |
T |
2: 67,338,383 (GRCm39) |
T208I |
probably benign |
Het |
| Xpnpep1 |
A |
G |
19: 52,980,107 (GRCm39) |
V639A |
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 |
|
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 |
|
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'- GGAAGCTGTTGTCGCCTTATCTCC -3'
(R):5'- CCTGCCCACCTCTGAGAAAATCTG -3'
Sequencing Primer
(F):5'- AAAGCCTTGGTTTTGAGTTATTAGC -3'
(R):5'- AGTTCAGCCAAAGGGATGC -3'
|
| Posted On |
2014-04-13 |
Incidental Mutation