Incidental Mutation 'R6798:Kdm1b'
ID |
533136 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Kdm1b
|
Ensembl Gene |
ENSMUSG00000038080 |
Gene Name |
lysine (K)-specific demethylase 1B |
Synonyms |
Aof1, 4632428N09Rik |
MMRRC Submission |
044911-MU
|
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.504)
|
Stock # |
R6798 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
13 |
Chromosomal Location |
47196849-47238085 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 47222012 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Alanine
at position 484
(T484A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000038373
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
|
AlphaFold |
Q8CIG3 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000037025
AA Change: T484A
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
SMART Domains |
Protein: ENSMUSP00000038373 Gene: ENSMUSG00000038080 AA Change: T484A
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: 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 |
0.0661 |
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.3%
- 20x: 95.4%
|
Validation Efficiency |
97% (73/75) |
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: 74 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abcb1a |
T |
C |
5: 8,782,364 (GRCm39) |
Y916H |
probably damaging |
Het |
Adam11 |
A |
G |
11: 102,667,834 (GRCm39) |
I740V |
probably damaging |
Het |
Adam22 |
A |
T |
5: 8,210,784 (GRCm39) |
D161E |
probably damaging |
Het |
Agap3 |
A |
G |
5: 24,703,280 (GRCm39) |
|
probably null |
Het |
Ank2 |
T |
C |
3: 126,737,913 (GRCm39) |
|
probably benign |
Het |
Aspm |
T |
A |
1: 139,396,423 (GRCm39) |
H867Q |
possibly damaging |
Het |
Aurkaip1 |
T |
C |
4: 155,917,196 (GRCm39) |
|
probably null |
Het |
BC048507 |
A |
C |
13: 68,011,683 (GRCm39) |
D20A |
probably benign |
Het |
Cacna1a |
G |
A |
8: 85,338,231 (GRCm39) |
A1704T |
probably damaging |
Het |
Cep152 |
A |
C |
2: 125,408,447 (GRCm39) |
|
probably null |
Het |
Cep19 |
T |
C |
16: 31,922,867 (GRCm39) |
|
probably null |
Het |
Cfhr4 |
T |
C |
1: 139,625,859 (GRCm39) |
T813A |
probably benign |
Het |
Chd9 |
A |
T |
8: 91,778,182 (GRCm39) |
E2731V |
possibly damaging |
Het |
Chrd |
T |
C |
16: 20,553,056 (GRCm39) |
L139P |
probably damaging |
Het |
Cit |
A |
G |
5: 116,064,585 (GRCm39) |
E489G |
possibly damaging |
Het |
Clcn7 |
A |
G |
17: 25,378,734 (GRCm39) |
N720D |
probably damaging |
Het |
Col6a3 |
T |
C |
1: 90,722,731 (GRCm39) |
|
probably null |
Het |
Dchs2 |
T |
A |
3: 83,255,593 (GRCm39) |
Y2430N |
probably damaging |
Het |
Dpy30 |
A |
G |
17: 74,614,751 (GRCm39) |
I64T |
probably damaging |
Het |
Eif2b3 |
G |
T |
4: 116,923,655 (GRCm39) |
W290L |
probably benign |
Het |
Epha6 |
T |
G |
16: 60,425,427 (GRCm39) |
E62A |
possibly damaging |
Het |
Epha6 |
C |
T |
16: 60,425,428 (GRCm39) |
E62K |
possibly damaging |
Het |
Epha8 |
C |
T |
4: 136,672,980 (GRCm39) |
R268Q |
probably benign |
Het |
Fbxw17 |
C |
A |
13: 50,587,300 (GRCm39) |
|
probably null |
Het |
Fndc8 |
C |
T |
11: 82,783,217 (GRCm39) |
T66I |
probably benign |
Het |
Frmpd1 |
A |
G |
4: 45,284,850 (GRCm39) |
T1224A |
probably benign |
Het |
Gcm2 |
T |
C |
13: 41,259,361 (GRCm39) |
D36G |
probably damaging |
Het |
Glt28d2 |
T |
C |
3: 85,779,296 (GRCm39) |
D59G |
probably benign |
Het |
Gorasp1 |
T |
C |
9: 119,758,663 (GRCm39) |
D243G |
probably benign |
Het |
Gtsf1l |
T |
C |
2: 162,929,391 (GRCm39) |
K31E |
probably benign |
Het |
Heatr5a |
A |
G |
12: 51,928,048 (GRCm39) |
V1816A |
probably benign |
Het |
Il10ra |
T |
C |
9: 45,167,730 (GRCm39) |
K274E |
probably damaging |
Het |
Il1rl2 |
T |
C |
1: 40,404,400 (GRCm39) |
I507T |
probably damaging |
Het |
Jak3 |
T |
G |
8: 72,133,615 (GRCm39) |
F408V |
probably damaging |
Het |
Lama5 |
G |
A |
2: 179,833,455 (GRCm39) |
P1519L |
probably damaging |
Het |
Map9 |
T |
G |
3: 82,287,471 (GRCm39) |
L31W |
probably damaging |
Het |
Mical2 |
T |
C |
7: 111,975,266 (GRCm39) |
|
probably benign |
Het |
Mt1 |
A |
G |
8: 94,906,516 (GRCm39) |
|
probably benign |
Het |
Myo18b |
T |
C |
5: 112,909,252 (GRCm39) |
I1964V |
probably damaging |
Het |
Nalf1 |
G |
A |
8: 9,820,205 (GRCm39) |
Q272* |
probably null |
Het |
Nod1 |
A |
T |
6: 54,921,596 (GRCm39) |
C241S |
probably damaging |
Het |
Nrxn1 |
T |
A |
17: 90,937,378 (GRCm39) |
D685V |
probably damaging |
Het |
Oog1 |
A |
T |
12: 87,655,609 (GRCm39) |
|
probably null |
Het |
Or11a4 |
T |
G |
17: 37,536,697 (GRCm39) |
L227R |
probably damaging |
Het |
Or2ag13 |
T |
C |
7: 106,313,402 (GRCm39) |
Y162C |
probably damaging |
Het |
Or4k2 |
A |
G |
14: 50,424,584 (GRCm39) |
V30A |
probably benign |
Het |
Or56b1b |
T |
A |
7: 108,164,967 (GRCm39) |
K12* |
probably null |
Het |
P4htm |
T |
A |
9: 108,460,117 (GRCm39) |
N219I |
possibly damaging |
Het |
Pcif1 |
T |
C |
2: 164,727,711 (GRCm39) |
L168P |
possibly damaging |
Het |
Pde4dip |
A |
G |
3: 97,795,850 (GRCm39) |
V46A |
probably benign |
Het |
Pias1 |
T |
C |
9: 62,799,451 (GRCm39) |
T480A |
probably benign |
Het |
Prkd2 |
A |
T |
7: 16,583,128 (GRCm39) |
K297* |
probably null |
Het |
Prl7d1 |
T |
A |
13: 27,893,380 (GRCm39) |
|
probably null |
Het |
Pxdc1 |
G |
T |
13: 34,836,408 (GRCm39) |
A4E |
possibly damaging |
Het |
Rcor1 |
A |
G |
12: 111,006,320 (GRCm39) |
|
probably benign |
Het |
Rev3l |
A |
T |
10: 39,730,759 (GRCm39) |
D2761V |
probably damaging |
Het |
Scgb1b7 |
A |
G |
7: 31,412,406 (GRCm39) |
T61A |
probably damaging |
Het |
Sec14l2 |
A |
G |
11: 4,061,213 (GRCm39) |
Y83H |
probably damaging |
Het |
Setd4 |
C |
A |
16: 93,386,841 (GRCm39) |
V286F |
probably damaging |
Het |
Slc22a29 |
A |
G |
19: 8,137,968 (GRCm39) |
S536P |
probably benign |
Het |
Snx25 |
T |
C |
8: 46,486,810 (GRCm39) |
H977R |
probably damaging |
Het |
Spint5 |
T |
A |
2: 164,559,060 (GRCm39) |
C95* |
probably null |
Het |
Sprr5 |
G |
C |
3: 92,440,243 (GRCm39) |
C65W |
unknown |
Het |
Srgap1 |
T |
C |
10: 121,761,809 (GRCm39) |
D113G |
probably damaging |
Het |
Stxbp2 |
T |
A |
8: 3,691,180 (GRCm39) |
S476T |
probably benign |
Het |
Tg |
A |
G |
15: 66,550,688 (GRCm39) |
T273A |
probably damaging |
Het |
Tnc |
C |
T |
4: 63,883,841 (GRCm39) |
R1868H |
probably benign |
Het |
Trappc10 |
A |
G |
10: 78,024,665 (GRCm39) |
Y1155H |
probably benign |
Het |
Trpm2 |
T |
A |
10: 77,750,574 (GRCm39) |
N1341Y |
probably damaging |
Het |
Vmn2r111 |
T |
C |
17: 22,778,032 (GRCm39) |
N549S |
possibly damaging |
Het |
Zfand1 |
T |
G |
3: 10,411,236 (GRCm39) |
K67T |
probably benign |
Het |
Zfand4 |
A |
C |
6: 116,305,214 (GRCm39) |
K214Q |
probably benign |
Het |
Zfp653 |
A |
T |
9: 21,968,668 (GRCm39) |
V465E |
probably damaging |
Het |
Zswim8 |
A |
G |
14: 20,766,060 (GRCm39) |
Y782C |
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 |
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'- ATTGGCCGGAAGCTGTTGTC -3'
(R):5'- CTGCAGAGTTCAGCCAAAGG -3'
Sequencing Primer
(F):5'- GAGTTATTAGCGTCATCATGAGAGC -3'
(R):5'- GGATGCATGTAAGGACCGGC -3'
|
Posted On |
2018-08-29 |