Incidental Mutation 'R8821:Kdm1b'
| ID |
673068 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm1b
|
| Ensembl Gene |
ENSMUSG00000038080 |
| Gene Name |
lysine (K)-specific demethylase 1B |
| Synonyms |
Aof1, 4632428N09Rik |
| MMRRC Submission |
068654-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.504)
|
| Stock # |
R8821 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
47196849-47238085 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 47217617 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Isoleucine
at position 359
(L359I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000038373
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
|
| AlphaFold |
Q8CIG3 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000037025
AA Change: L359I
PolyPhen 2
Score 0.944 (Sensitivity: 0.80; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: L359I
| 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 |
probably damaging
Transcript: ENSMUST00000143518
AA Change: L75I
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000114999
Gene: ENSMUSG00000038080
AA Change: L75I
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
100% (74/74) |
| 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: 76 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A230072I06Rik |
A |
T |
8: 12,329,688 (GRCm39) |
I48L |
unknown |
Het |
| Abca8a |
A |
T |
11: 109,949,362 (GRCm39) |
I927K |
probably damaging |
Het |
| Abcc3 |
A |
C |
11: 94,241,787 (GRCm39) |
C1415G |
probably damaging |
Het |
| Abcf3 |
C |
T |
16: 20,369,214 (GRCm39) |
R205C |
probably damaging |
Het |
| Aldh3a1 |
A |
G |
11: 61,107,142 (GRCm39) |
Y282C |
probably damaging |
Het |
| Alyref |
CCCGCGCGGCGGCCTGCACTGCGCCGCCGCGGCCGCCCTGGGAGCCGGCCCTGCCGCG |
CCCGCG |
11: 120,489,023 (GRCm39) |
|
probably null |
Het |
| Arfgef3 |
A |
G |
10: 18,528,491 (GRCm39) |
S299P |
possibly damaging |
Het |
| Asic2 |
A |
T |
11: 81,858,726 (GRCm39) |
N95K |
probably damaging |
Het |
| Atp2c2 |
A |
G |
8: 120,476,033 (GRCm39) |
|
probably null |
Het |
| Btbd18 |
A |
G |
2: 84,497,601 (GRCm39) |
D413G |
probably damaging |
Het |
| C8b |
A |
G |
4: 104,647,874 (GRCm39) |
Y355C |
probably damaging |
Het |
| Carm1 |
A |
G |
9: 21,491,663 (GRCm39) |
E244G |
probably damaging |
Het |
| Castor2 |
T |
A |
5: 134,164,092 (GRCm39) |
V96E |
possibly damaging |
Het |
| Catsperg1 |
A |
T |
7: 28,904,361 (GRCm39) |
|
probably benign |
Het |
| Cish |
T |
A |
9: 107,177,671 (GRCm39) |
F116I |
probably damaging |
Het |
| Ckmt1 |
G |
A |
2: 121,191,302 (GRCm39) |
|
probably benign |
Het |
| Clasrp |
C |
T |
7: 19,320,362 (GRCm39) |
R432H |
unknown |
Het |
| Clstn1 |
G |
A |
4: 149,730,780 (GRCm39) |
R837Q |
probably benign |
Het |
| Col27a1 |
A |
G |
4: 63,143,148 (GRCm39) |
T279A |
probably benign |
Het |
| Cox10 |
A |
G |
11: 63,855,306 (GRCm39) |
F325S |
probably damaging |
Het |
| Cpne5 |
T |
C |
17: 29,430,668 (GRCm39) |
I81V |
probably benign |
Het |
| Ctps1 |
A |
T |
4: 120,424,507 (GRCm39) |
S36T |
possibly damaging |
Het |
| Dchs2 |
T |
C |
3: 83,192,670 (GRCm39) |
L1705P |
probably benign |
Het |
| Dcstamp |
A |
G |
15: 39,618,185 (GRCm39) |
H198R |
probably benign |
Het |
| Dhx58 |
T |
A |
11: 100,594,806 (GRCm39) |
K30M |
probably damaging |
Het |
| Dnah1 |
C |
T |
14: 31,018,455 (GRCm39) |
A1392T |
probably benign |
Het |
| Dnah14 |
C |
A |
1: 181,619,569 (GRCm39) |
Y3964* |
probably null |
Het |
| Dnah8 |
T |
C |
17: 31,013,712 (GRCm39) |
S3818P |
probably damaging |
Het |
| Dnmt3b |
T |
A |
2: 153,518,734 (GRCm39) |
N632K |
probably benign |
Het |
| Drc7 |
G |
A |
8: 95,788,845 (GRCm39) |
R301Q |
probably damaging |
Het |
| Dsg1a |
T |
C |
18: 20,453,365 (GRCm39) |
V21A |
probably damaging |
Het |
| Dtd1 |
T |
C |
2: 144,459,261 (GRCm39) |
L95P |
probably benign |
Het |
| Efhb |
A |
T |
17: 53,707,772 (GRCm39) |
|
probably benign |
Het |
| Fam186b |
T |
A |
15: 99,178,733 (GRCm39) |
M198L |
possibly damaging |
Het |
| Fam193a |
A |
G |
5: 34,616,374 (GRCm39) |
T850A |
probably benign |
Het |
| Fan1 |
G |
A |
7: 64,004,249 (GRCm39) |
P739L |
probably damaging |
Het |
| Flii |
A |
T |
11: 60,616,074 (GRCm39) |
N28K |
probably benign |
Het |
| Fmo3 |
T |
C |
1: 162,796,407 (GRCm39) |
Y55C |
probably damaging |
Het |
| Gfi1 |
G |
A |
5: 107,868,138 (GRCm39) |
R377C |
probably damaging |
Het |
| Gm9195 |
C |
T |
14: 72,717,536 (GRCm39) |
E266K |
possibly damaging |
Het |
| Hdac1-ps |
T |
A |
17: 78,799,969 (GRCm39) |
L320Q |
probably damaging |
Het |
| Helz |
A |
T |
11: 107,525,919 (GRCm39) |
M825L |
probably damaging |
Het |
| Hsd3b9 |
A |
T |
3: 98,354,047 (GRCm39) |
W151R |
probably benign |
Het |
| Ift80 |
G |
A |
3: 68,869,583 (GRCm39) |
A236V |
probably damaging |
Het |
| Il1rn |
A |
T |
2: 24,239,505 (GRCm39) |
T134S |
possibly damaging |
Het |
| Imp4 |
T |
C |
1: 34,483,445 (GRCm39) |
M257T |
probably benign |
Het |
| Impdh2 |
T |
C |
9: 108,441,957 (GRCm39) |
L377S |
probably damaging |
Het |
| Kcnrg |
T |
C |
14: 61,844,981 (GRCm39) |
V7A |
possibly damaging |
Het |
| Lima1 |
T |
A |
15: 99,704,306 (GRCm39) |
T288S |
probably benign |
Het |
| Lrrc37 |
A |
T |
11: 103,510,470 (GRCm39) |
D499E |
unknown |
Het |
| Lrrc4c |
A |
T |
2: 97,460,040 (GRCm39) |
D222V |
possibly damaging |
Het |
| Mybpc3 |
T |
A |
2: 90,948,524 (GRCm39) |
V4E |
probably null |
Het |
| Ncor1 |
A |
T |
11: 62,260,234 (GRCm39) |
D505E |
probably benign |
Het |
| Nell1 |
A |
G |
7: 50,476,097 (GRCm39) |
S579G |
probably damaging |
Het |
| Npc1 |
T |
A |
18: 12,333,877 (GRCm39) |
M735L |
probably benign |
Het |
| Or1j13 |
G |
A |
2: 36,369,794 (GRCm39) |
T116I |
possibly damaging |
Het |
| Or2at4 |
A |
G |
7: 99,384,893 (GRCm39) |
H181R |
possibly damaging |
Het |
| Or4a73 |
A |
G |
2: 89,420,880 (GRCm39) |
I193T |
probably damaging |
Het |
| Pcdhb12 |
A |
G |
18: 37,570,386 (GRCm39) |
M511V |
probably benign |
Het |
| Peli2 |
G |
A |
14: 48,490,130 (GRCm39) |
E201K |
possibly damaging |
Het |
| Phf3 |
T |
A |
1: 30,860,347 (GRCm39) |
K828* |
probably null |
Het |
| Pih1d1 |
A |
G |
7: 44,806,196 (GRCm39) |
D44G |
possibly damaging |
Het |
| Prag1 |
A |
T |
8: 36,613,891 (GRCm39) |
T1148S |
probably benign |
Het |
| Ptpn18 |
A |
T |
1: 34,511,271 (GRCm39) |
R338W |
probably null |
Het |
| Slc7a6os |
A |
T |
8: 106,937,189 (GRCm39) |
D90E |
probably benign |
Het |
| Sp7 |
T |
A |
15: 102,267,227 (GRCm39) |
H211L |
possibly damaging |
Het |
| Ssh3 |
A |
G |
19: 4,319,053 (GRCm39) |
V19A |
possibly damaging |
Het |
| Tcp11l2 |
A |
G |
10: 84,449,522 (GRCm39) |
I496V |
probably damaging |
Het |
| Tenm3 |
C |
T |
8: 48,729,417 (GRCm39) |
A1530T |
|
Het |
| Tmem232 |
A |
G |
17: 65,743,367 (GRCm39) |
L308P |
probably damaging |
Het |
| Tulp4 |
A |
G |
17: 6,189,409 (GRCm39) |
N77S |
probably damaging |
Het |
| Unc13d |
AATGCCTCCCATGCC |
AATGCCTCCCATGCCTCCCATGCC |
11: 115,958,998 (GRCm39) |
|
probably benign |
Het |
| Usp48 |
A |
T |
4: 137,341,080 (GRCm39) |
D360V |
probably damaging |
Het |
| Vmn2r84 |
G |
A |
10: 130,226,968 (GRCm39) |
A290V |
probably benign |
Het |
| Zfp1007 |
A |
T |
5: 109,824,174 (GRCm39) |
S425R |
probably benign |
Het |
| Zfp512b |
T |
C |
2: 181,228,525 (GRCm39) |
N738S |
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 |
|
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 |
|
|
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'- GACTAACTAGTTTGAGTGCTGGGA -3'
(R):5'- TCTGCAGTATCTGGTACCAGTA -3'
Sequencing Primer
(F):5'- TCCAGCCACATATGTAGCAGAGG -3'
(R):5'- GCAGTATCTGGTACCAGTATAGCAAC -3'
|
| Posted On |
2021-04-30 |
Incidental Mutation