Incidental Mutation 'R9132:Kdm1b'
| ID |
693731 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm1b
|
| Ensembl Gene |
ENSMUSG00000038080 |
| Gene Name |
lysine (K)-specific demethylase 1B |
| Synonyms |
Aof1, 4632428N09Rik |
| MMRRC Submission |
068929-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.504)
|
| Stock # |
R9132 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
47196849-47238085 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 47225458 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Asparagine
at position 547
(S547N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000038373
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
|
| AlphaFold |
Q8CIG3 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000037025
AA Change: S547N
PolyPhen 2
Score 0.047 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: S547N
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.6%
|
| Validation Efficiency |
97% (65/67) |
| 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: 65 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| AC133488.1 |
A |
T |
16: 18,440,075 (GRCm39) |
V363E |
probably benign |
Het |
| Adamts16 |
A |
G |
13: 70,901,408 (GRCm39) |
S890P |
probably benign |
Het |
| Amd1 |
A |
G |
10: 40,169,158 (GRCm39) |
|
probably null |
Het |
| Apcs |
A |
G |
1: 172,722,061 (GRCm39) |
I95T |
probably damaging |
Het |
| Arhgap18 |
A |
G |
10: 26,730,886 (GRCm39) |
D188G |
probably benign |
Het |
| Arhgap42 |
C |
T |
9: 9,011,419 (GRCm39) |
V456M |
probably damaging |
Het |
| Atp2a2 |
T |
C |
5: 122,599,633 (GRCm39) |
Y586C |
probably damaging |
Het |
| Cbr1 |
G |
C |
16: 93,406,794 (GRCm39) |
G170A |
probably benign |
Het |
| Cdh23 |
T |
A |
10: 60,270,283 (GRCm39) |
|
probably benign |
Het |
| Cfap53 |
T |
A |
18: 74,416,272 (GRCm39) |
Y2N |
probably damaging |
Het |
| Clcn3 |
A |
G |
8: 61,382,136 (GRCm39) |
I511T |
probably damaging |
Het |
| Col28a1 |
T |
A |
6: 8,014,993 (GRCm39) |
D804V |
probably damaging |
Het |
| Csmd2 |
A |
G |
4: 128,443,007 (GRCm39) |
T3253A |
|
Het |
| Csta3 |
G |
A |
16: 36,038,069 (GRCm39) |
V69I |
probably benign |
Het |
| Cyp2c40 |
A |
T |
19: 39,762,317 (GRCm39) |
D443E |
probably damaging |
Het |
| Cyp7b1 |
A |
G |
3: 18,151,476 (GRCm39) |
C246R |
probably benign |
Het |
| Dmxl1 |
C |
G |
18: 50,072,639 (GRCm39) |
N2744K |
probably damaging |
Het |
| Dnai4 |
A |
G |
4: 102,916,930 (GRCm39) |
M592T |
probably damaging |
Het |
| Dpyd |
T |
A |
3: 118,710,897 (GRCm39) |
I435N |
probably damaging |
Het |
| Fat2 |
A |
T |
11: 55,189,436 (GRCm39) |
L1194Q |
possibly damaging |
Het |
| Firrm |
A |
G |
1: 163,814,514 (GRCm39) |
I143T |
probably damaging |
Het |
| Gabrg1 |
A |
T |
5: 70,939,622 (GRCm39) |
I170N |
possibly damaging |
Het |
| Gon4l |
C |
T |
3: 88,815,484 (GRCm39) |
P2016S |
probably benign |
Het |
| Hax1 |
T |
C |
3: 89,903,127 (GRCm39) |
R251G |
probably damaging |
Het |
| Hbq1b |
A |
T |
11: 32,237,228 (GRCm39) |
K41* |
probably null |
Het |
| Ido2 |
G |
A |
8: 25,023,933 (GRCm39) |
P302S |
probably damaging |
Het |
| Igf2bp2 |
G |
A |
16: 21,900,502 (GRCm39) |
T213I |
probably damaging |
Het |
| Itga2 |
A |
T |
13: 115,014,298 (GRCm39) |
L210* |
probably null |
Het |
| Ltbp2 |
G |
A |
12: 84,837,864 (GRCm39) |
P1192L |
probably benign |
Het |
| Lyz2 |
A |
T |
10: 117,116,562 (GRCm39) |
C95* |
probably null |
Het |
| Mafa |
A |
T |
15: 75,619,048 (GRCm39) |
S242T |
possibly damaging |
Het |
| Mapk1 |
T |
C |
16: 16,856,300 (GRCm39) |
|
probably null |
Het |
| Mta1 |
T |
A |
12: 113,100,025 (GRCm39) |
V645E |
probably damaging |
Het |
| Muc5ac |
T |
C |
7: 141,363,529 (GRCm39) |
I2280T |
unknown |
Het |
| Naa35 |
T |
C |
13: 59,772,341 (GRCm39) |
I438T |
possibly damaging |
Het |
| Necab2 |
T |
C |
8: 120,189,303 (GRCm39) |
Y158H |
probably damaging |
Het |
| Nphp3 |
T |
A |
9: 103,897,980 (GRCm39) |
L523Q |
probably damaging |
Het |
| Ogdh |
A |
T |
11: 6,290,488 (GRCm39) |
I369F |
probably benign |
Het |
| Pglyrp4 |
C |
T |
3: 90,635,238 (GRCm39) |
Q28* |
probably null |
Het |
| Pla2g4a |
C |
T |
1: 149,747,230 (GRCm39) |
V319I |
probably benign |
Het |
| Plk3 |
ACACTCAC |
ACAC |
4: 116,989,090 (GRCm39) |
|
probably benign |
Het |
| Prdm6 |
C |
A |
18: 53,598,019 (GRCm39) |
A127D |
unknown |
Het |
| Prop1 |
T |
G |
11: 50,843,037 (GRCm39) |
E50A |
|
Het |
| Ripk1 |
A |
G |
13: 34,212,184 (GRCm39) |
N498S |
probably benign |
Het |
| Rnf213 |
A |
G |
11: 119,374,742 (GRCm39) |
N5069S |
|
Het |
| Saa3 |
T |
C |
7: 46,362,121 (GRCm39) |
D41G |
probably damaging |
Het |
| Setd2 |
T |
C |
9: 110,374,385 (GRCm39) |
|
probably null |
Het |
| Shbg |
G |
A |
11: 69,506,430 (GRCm39) |
L327F |
probably benign |
Het |
| Slc12a5 |
G |
A |
2: 164,835,876 (GRCm39) |
|
probably benign |
Het |
| Slc1a4 |
C |
T |
11: 20,258,527 (GRCm39) |
G304D |
probably damaging |
Het |
| Slf1 |
T |
C |
13: 77,249,073 (GRCm39) |
K372E |
probably benign |
Het |
| Smad2 |
T |
A |
18: 76,395,573 (GRCm39) |
I4N |
possibly damaging |
Het |
| Smad6 |
A |
C |
9: 63,914,870 (GRCm39) |
S300A |
probably benign |
Het |
| Spata31h1 |
T |
C |
10: 82,127,896 (GRCm39) |
T1705A |
possibly damaging |
Het |
| Spem2 |
T |
A |
11: 69,707,414 (GRCm39) |
|
probably benign |
Het |
| Syde1 |
T |
C |
10: 78,425,340 (GRCm39) |
S224G |
probably benign |
Het |
| Tacc1 |
A |
T |
8: 25,672,151 (GRCm39) |
V359E |
possibly damaging |
Het |
| Tex15 |
T |
G |
8: 34,067,554 (GRCm39) |
V2328G |
possibly damaging |
Het |
| Tmem43 |
A |
C |
6: 91,459,291 (GRCm39) |
D254A |
probably benign |
Het |
| Trav6d-3 |
T |
A |
14: 52,964,210 (GRCm39) |
Y58N |
possibly damaging |
Het |
| Trrap |
A |
G |
5: 144,726,362 (GRCm39) |
E437G |
probably benign |
Het |
| Wars1 |
A |
G |
12: 108,827,199 (GRCm39) |
F474L |
probably benign |
Het |
| Zfp169 |
T |
C |
13: 48,644,557 (GRCm39) |
E190G |
unknown |
Het |
| Zfp541 |
T |
A |
7: 15,816,966 (GRCm39) |
V918D |
probably benign |
Het |
| Zfp747 |
T |
C |
7: 126,974,922 (GRCm39) |
D26G |
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 |
|
|
R9038:Kdm1b
|
UTSW |
13 |
47,202,770 (GRCm39) |
missense |
probably benign |
0.07 |
|
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'- TCTGTTGGGGAAAGCAGCAG -3'
(R):5'- TGGGCAACAGAACCTTTCTTC -3'
Sequencing Primer
(F):5'- GGATCAAGAACCAGACAGGAGTTTC -3'
(R):5'- TTGGCACTGAGATCACACG -3'
|
| Posted On |
2022-01-20 |
Incidental Mutation