Incidental Mutation 'R4094:Kdm1b'
| ID |
317820 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm1b
|
| Ensembl Gene |
ENSMUSG00000038080 |
| Gene Name |
lysine (K)-specific demethylase 1B |
| Synonyms |
Aof1, 4632428N09Rik |
| MMRRC Submission |
041628-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.406)
|
| Stock # |
R4094 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
13 |
| Chromosomal Location |
47196849-47238085 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 47216496 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Arginine
at position 289
(C289R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000038373
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
|
| AlphaFold |
Q8CIG3 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000037025
AA Change: C289R
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: C289R
| 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 |
unknown
Transcript: ENSMUST00000143518
AA Change: C5R
|
| SMART Domains |
Protein: ENSMUSP00000114999
Gene: ENSMUSG00000038080
AA Change: C5R
| 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: 99.2%
- 3x: 98.6%
- 10x: 97.5%
- 20x: 95.8%
|
| 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: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca6 |
A |
G |
11: 110,071,192 (GRCm39) |
C1500R |
probably damaging |
Het |
| Amz1 |
A |
T |
5: 140,737,921 (GRCm39) |
M93L |
probably damaging |
Het |
| Asb18 |
A |
T |
1: 89,942,147 (GRCm39) |
N51K |
probably damaging |
Het |
| Bcl11b |
G |
T |
12: 107,883,094 (GRCm39) |
P335Q |
probably damaging |
Het |
| Bsn |
A |
C |
9: 107,991,069 (GRCm39) |
V1561G |
probably damaging |
Het |
| Cadm2 |
A |
T |
16: 66,679,685 (GRCm39) |
N49K |
probably damaging |
Het |
| Cct8 |
T |
G |
16: 87,284,516 (GRCm39) |
I283L |
possibly damaging |
Het |
| Cdc25b |
A |
G |
2: 131,031,037 (GRCm39) |
M121V |
probably benign |
Het |
| Cpne4 |
A |
G |
9: 104,563,734 (GRCm39) |
D37G |
probably damaging |
Het |
| Cym |
A |
G |
3: 107,121,582 (GRCm39) |
S237P |
probably benign |
Het |
| Dhx35 |
T |
A |
2: 158,684,276 (GRCm39) |
I517N |
probably damaging |
Het |
| Ehf |
T |
C |
2: 103,121,095 (GRCm39) |
|
probably benign |
Het |
| Erp29 |
A |
G |
5: 121,590,345 (GRCm39) |
|
probably benign |
Het |
| Fgd6 |
C |
A |
10: 93,879,296 (GRCm39) |
P50Q |
probably damaging |
Het |
| Fhip1b |
T |
C |
7: 105,037,425 (GRCm39) |
D386G |
probably damaging |
Het |
| Foxn3 |
G |
T |
12: 99,162,700 (GRCm39) |
D400E |
probably damaging |
Het |
| Frmd4a |
A |
G |
2: 4,615,843 (GRCm39) |
Y1031C |
probably damaging |
Het |
| Gna13 |
T |
A |
11: 109,287,242 (GRCm39) |
I355N |
probably damaging |
Het |
| Hgs |
T |
A |
11: 120,359,859 (GRCm39) |
L21* |
probably null |
Het |
| Htr2a |
G |
A |
14: 74,943,789 (GRCm39) |
M456I |
probably benign |
Het |
| Itga2 |
T |
C |
13: 115,007,161 (GRCm39) |
D389G |
probably benign |
Het |
| Kdm4c |
T |
A |
4: 74,229,915 (GRCm39) |
D237E |
probably benign |
Het |
| Lilrb4b |
A |
T |
10: 51,357,506 (GRCm39) |
E114V |
probably damaging |
Het |
| Loxl1 |
G |
A |
9: 58,219,739 (GRCm39) |
T144I |
probably damaging |
Het |
| Macf1 |
C |
T |
4: 123,353,062 (GRCm39) |
R1784Q |
probably benign |
Het |
| Maml2 |
G |
A |
9: 13,531,449 (GRCm39) |
S221N |
probably benign |
Het |
| Map3k1 |
A |
G |
13: 111,892,696 (GRCm39) |
M853T |
possibly damaging |
Het |
| Micu3 |
T |
G |
8: 40,788,929 (GRCm39) |
S147A |
probably null |
Het |
| Nccrp1 |
T |
C |
7: 28,243,651 (GRCm39) |
Y261C |
possibly damaging |
Het |
| Or51aa5 |
T |
A |
7: 103,167,244 (GRCm39) |
I116F |
possibly damaging |
Het |
| Or5m5 |
A |
G |
2: 85,814,562 (GRCm39) |
Y126C |
probably damaging |
Het |
| Or8k18 |
T |
C |
2: 86,085,674 (GRCm39) |
D121G |
probably damaging |
Het |
| Or8s10 |
T |
C |
15: 98,335,563 (GRCm39) |
L71P |
probably damaging |
Het |
| Pclo |
C |
A |
5: 14,905,659 (GRCm39) |
T4963N |
unknown |
Het |
| Pdxk |
T |
C |
10: 78,300,644 (GRCm39) |
H13R |
probably damaging |
Het |
| Plcg1 |
A |
G |
2: 160,589,761 (GRCm39) |
E95G |
probably damaging |
Het |
| Ppargc1a |
T |
C |
5: 51,647,406 (GRCm39) |
N276S |
possibly damaging |
Het |
| Prr12 |
A |
G |
7: 44,697,371 (GRCm39) |
L848P |
unknown |
Het |
| Ptcd2 |
A |
G |
13: 99,468,957 (GRCm39) |
I202T |
probably damaging |
Het |
| Rab27a |
A |
C |
9: 72,982,826 (GRCm39) |
I44L |
probably damaging |
Het |
| Rbfox2 |
A |
T |
15: 77,016,925 (GRCm39) |
S82T |
probably damaging |
Het |
| Rsbn1 |
T |
A |
3: 103,835,974 (GRCm39) |
F337L |
probably damaging |
Het |
| Samd8 |
T |
C |
14: 21,843,113 (GRCm39) |
I414T |
probably damaging |
Het |
| Sema3e |
A |
G |
5: 14,283,704 (GRCm39) |
I478V |
probably benign |
Het |
| Sfswap |
A |
G |
5: 129,637,805 (GRCm39) |
S821G |
possibly damaging |
Het |
| Slc2a3 |
A |
T |
6: 122,712,527 (GRCm39) |
I239N |
probably benign |
Het |
| Spc25 |
G |
A |
2: 69,032,975 (GRCm39) |
S50L |
probably damaging |
Het |
| St8sia4 |
A |
T |
1: 95,555,411 (GRCm39) |
S206R |
possibly damaging |
Het |
| Syngr3 |
G |
A |
17: 24,908,817 (GRCm39) |
|
probably benign |
Het |
| Tigd4 |
A |
G |
3: 84,501,947 (GRCm39) |
D288G |
probably damaging |
Het |
| Trim34b |
A |
G |
7: 103,983,795 (GRCm39) |
M251V |
probably benign |
Het |
| Ttll5 |
A |
T |
12: 86,003,376 (GRCm39) |
R214* |
probably null |
Het |
| Ttn |
T |
C |
2: 76,730,860 (GRCm39) |
|
probably benign |
Het |
| Vmp1 |
A |
G |
11: 86,534,406 (GRCm39) |
I167T |
probably benign |
Het |
| Zfp64 |
T |
C |
2: 168,767,855 (GRCm39) |
T586A |
probably benign |
Het |
| Zfp943 |
T |
A |
17: 22,211,963 (GRCm39) |
C350S |
probably damaging |
Het |
| Zscan4f |
A |
T |
7: 11,135,185 (GRCm39) |
N197I |
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 |
|
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'- AAAGTGCCAAAGGGTGTTTG -3'
(R):5'- CTGCTCGTTAGTCACTGGTG -3'
Sequencing Primer
(F):5'- TCCTAGAGATTGAACTGAGGCCATC -3'
(R):5'- GTTAGTCACTGGTGCCCTC -3'
|
| Posted On |
2015-05-15 |
Incidental Mutation