Incidental Mutation 'R9038:Kdm1b'
| ID |
687554 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm1b
|
| Ensembl Gene |
ENSMUSG00000038080 |
| Gene Name |
lysine (K)-specific demethylase 1B |
| Synonyms |
Aof1, 4632428N09Rik |
| MMRRC Submission |
068866-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.504)
|
| Stock # |
R9038 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
13 |
| Chromosomal Location |
47196849-47238085 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 47202770 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Arginine
at position 68
(S68R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000038373
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
[ENSMUST00000143868]
[ENSMUST00000154802]
|
| AlphaFold |
Q8CIG3 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000037025
AA Change: S68R
PolyPhen 2
Score 0.068 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: S68R
| 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 benign
Transcript: ENSMUST00000143868
AA Change: S68R
PolyPhen 2
Score 0.068 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000117793
Gene: ENSMUSG00000038080
AA Change: S68R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:zf-CW
|
137 |
175 |
3.6e-13 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000154802
|
| SMART Domains |
Protein: ENSMUSP00000121827
Gene: ENSMUSG00000021376
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TPMT
|
19 |
182 |
2.9e-62 |
PFAM |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.8%
- 10x: 98.9%
- 20x: 95.4%
|
| 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: 69 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb5 |
A |
T |
12: 118,895,651 (GRCm39) |
C382S |
probably benign |
Het |
| Abcf2 |
A |
G |
5: 24,776,191 (GRCm39) |
V296A |
possibly damaging |
Het |
| Aco2 |
C |
G |
15: 81,756,620 (GRCm39) |
|
probably benign |
Het |
| Acvrl1 |
A |
G |
15: 101,039,011 (GRCm39) |
D436G |
possibly damaging |
Het |
| Adamts7 |
A |
G |
9: 90,056,692 (GRCm39) |
I254V |
|
Het |
| Arhgef18 |
A |
G |
8: 3,503,257 (GRCm39) |
I888V |
probably benign |
Het |
| Arhgef40 |
C |
A |
14: 52,235,072 (GRCm39) |
A1083D |
probably damaging |
Het |
| Arnt2 |
C |
A |
7: 83,954,059 (GRCm39) |
A275S |
probably benign |
Het |
| Brd10 |
A |
T |
19: 29,731,900 (GRCm39) |
Y371N |
possibly damaging |
Het |
| Brip1 |
C |
T |
11: 86,080,599 (GRCm39) |
V156I |
probably benign |
Het |
| Camk4 |
C |
A |
18: 33,291,953 (GRCm39) |
C204* |
probably null |
Het |
| Cenpe |
A |
G |
3: 134,923,797 (GRCm39) |
T161A |
probably benign |
Het |
| Chd2 |
G |
A |
7: 73,105,358 (GRCm39) |
H1256Y |
probably damaging |
Het |
| Chd9 |
G |
A |
8: 91,716,233 (GRCm39) |
V936I |
unknown |
Het |
| D6Ertd527e |
A |
G |
6: 87,089,233 (GRCm39) |
*465W |
probably null |
Het |
| Dcaf11 |
T |
A |
14: 55,803,114 (GRCm39) |
D309E |
probably damaging |
Het |
| Dtna |
A |
G |
18: 23,743,553 (GRCm39) |
N373S |
probably benign |
Het |
| Eif2b2 |
A |
G |
12: 85,266,897 (GRCm39) |
D104G |
probably benign |
Het |
| Fras1 |
A |
T |
5: 96,874,742 (GRCm39) |
T2302S |
probably benign |
Het |
| Gga1 |
A |
G |
15: 78,768,321 (GRCm39) |
K114E |
probably damaging |
Het |
| Gm12887 |
A |
G |
4: 121,473,616 (GRCm39) |
|
probably null |
Het |
| Gss |
A |
T |
2: 155,406,794 (GRCm39) |
I396N |
|
Het |
| H2-M5 |
T |
C |
17: 37,299,422 (GRCm39) |
I199M |
possibly damaging |
Het |
| Hjurp |
GT |
GTT |
1: 88,194,246 (GRCm39) |
|
probably null |
Het |
| Ift172 |
G |
T |
5: 31,441,399 (GRCm39) |
T245K |
possibly damaging |
Het |
| Ift70a2 |
G |
A |
2: 75,808,215 (GRCm39) |
T99I |
probably benign |
Het |
| Iqck |
A |
G |
7: 118,498,881 (GRCm39) |
D173G |
probably damaging |
Het |
| Itga11 |
A |
G |
9: 62,675,039 (GRCm39) |
N857S |
possibly damaging |
Het |
| Ly6c1 |
C |
A |
15: 74,917,300 (GRCm39) |
G116V |
probably damaging |
Het |
| Myo6 |
G |
T |
9: 80,162,285 (GRCm39) |
V341L |
unknown |
Het |
| Nfkbie |
C |
A |
17: 45,870,183 (GRCm39) |
A176E |
probably damaging |
Het |
| Nlrp2 |
C |
T |
7: 5,330,478 (GRCm39) |
M639I |
probably benign |
Het |
| Or10g3 |
T |
A |
14: 52,609,716 (GRCm39) |
S265C |
probably damaging |
Het |
| Or10j2 |
T |
A |
1: 173,098,147 (GRCm39) |
I135N |
possibly damaging |
Het |
| Or56a41 |
T |
C |
7: 104,740,433 (GRCm39) |
I138V |
probably benign |
Het |
| Or5w16 |
A |
G |
2: 87,577,125 (GRCm39) |
N195S |
probably damaging |
Het |
| Or6c215 |
T |
C |
10: 129,637,564 (GRCm39) |
T277A |
probably damaging |
Het |
| Or8k40 |
A |
T |
2: 86,584,354 (GRCm39) |
S243T |
probably damaging |
Het |
| Pak4 |
G |
A |
7: 28,264,263 (GRCm39) |
T213M |
probably damaging |
Het |
| Pan2 |
C |
T |
10: 128,153,810 (GRCm39) |
Q1003* |
probably null |
Het |
| Pde4c |
G |
C |
8: 71,179,550 (GRCm39) |
V34L |
probably benign |
Het |
| Pi4k2a |
G |
A |
19: 42,089,235 (GRCm39) |
V199M |
probably damaging |
Het |
| Platr25 |
T |
C |
13: 62,848,007 (GRCm39) |
E285G |
probably damaging |
Het |
| Polr3e |
T |
C |
7: 120,536,906 (GRCm39) |
V356A |
possibly damaging |
Het |
| Prcp |
A |
G |
7: 92,567,017 (GRCm39) |
D243G |
probably benign |
Het |
| Qsox2 |
T |
C |
2: 26,115,246 (GRCm39) |
T161A |
probably damaging |
Het |
| Rhoj |
A |
G |
12: 75,355,700 (GRCm39) |
T35A |
|
Het |
| Scn9a |
T |
A |
2: 66,325,147 (GRCm39) |
M1336L |
probably damaging |
Het |
| Sel1l2 |
G |
T |
2: 140,117,384 (GRCm39) |
N162K |
probably damaging |
Het |
| Slc15a3 |
T |
C |
19: 10,820,866 (GRCm39) |
L161P |
probably damaging |
Het |
| Slc4a11 |
G |
A |
2: 130,533,663 (GRCm39) |
A100V |
probably damaging |
Het |
| Sp1 |
A |
G |
15: 102,316,320 (GRCm39) |
S41G |
probably benign |
Het |
| Tbx15 |
A |
G |
3: 99,222,085 (GRCm39) |
M183V |
probably benign |
Het |
| Tfip11 |
A |
G |
5: 112,481,214 (GRCm39) |
T397A |
possibly damaging |
Het |
| Themis |
T |
C |
10: 28,657,749 (GRCm39) |
S259P |
probably damaging |
Het |
| Tm7sf2 |
T |
C |
19: 6,117,172 (GRCm39) |
Y77C |
probably damaging |
Het |
| Tnnt2 |
C |
A |
1: 135,774,484 (GRCm39) |
P81H |
possibly damaging |
Het |
| Trpc7 |
T |
C |
13: 57,035,886 (GRCm39) |
T16A |
probably benign |
Het |
| Ttn |
T |
A |
2: 76,745,056 (GRCm39) |
Y5331F |
possibly damaging |
Het |
| Virma |
A |
G |
4: 11,526,922 (GRCm39) |
Q1057R |
possibly damaging |
Het |
| Vmn2r118 |
A |
T |
17: 55,918,649 (GRCm39) |
F81Y |
probably damaging |
Het |
| Vmn2r88 |
T |
C |
14: 51,651,490 (GRCm39) |
V268A |
|
Het |
| Vmn2r93 |
T |
A |
17: 18,524,471 (GRCm39) |
M155K |
probably benign |
Het |
| Vps13b |
G |
T |
15: 35,875,931 (GRCm39) |
C2772F |
possibly damaging |
Het |
| Wdr90 |
T |
C |
17: 26,076,200 (GRCm39) |
N86D |
|
Het |
| Zbtb34 |
T |
C |
2: 33,301,248 (GRCm39) |
D431G |
probably damaging |
Het |
| Zc3h3 |
G |
A |
15: 75,711,237 (GRCm39) |
P408L |
probably benign |
Het |
| Zfp345 |
A |
G |
2: 150,313,864 (GRCm39) |
Y558H |
probably benign |
Het |
| Zfp583 |
G |
A |
7: 6,319,543 (GRCm39) |
P490S |
probably 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 |
|
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 |
|
|
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'- ATGTGACCTCAGCAGCAGAC -3'
(R):5'- TCTCTCCCACTAGGCTAGAAC -3'
Sequencing Primer
(F):5'- AGCAGACCTGTTGCCATC -3'
(R):5'- TAGGCTAGAACCAGCCACAGAATATG -3'
|
| Posted On |
2021-11-19 |
Incidental Mutation