Incidental Mutation 'R5598:Kdm6b'
| ID |
437934 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm6b
|
| Ensembl Gene |
ENSMUSG00000018476 |
| Gene Name |
KDM1 lysine (K)-specific demethylase 6B |
| Synonyms |
Jmjd3 |
| MMRRC Submission |
043150-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5598 (G1)
|
| Quality Score |
120 |
|
Status
|
Not validated
|
| Chromosome |
11 |
| Chromosomal Location |
69289334-69304501 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 69296900 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Threonine
at position 456
(A456T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000091620
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000094077]
|
| AlphaFold |
Q5NCY0 |
| PDB Structure |
The free structure of the mouse C-terminal domain of KDM6B [X-RAY DIFFRACTION]
free KDM6B structure [X-RAY DIFFRACTION]
the crystal structure of KDM6B bound with H3K27me3 peptide [X-RAY DIFFRACTION]
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000094077
AA Change: A456T
PolyPhen 2
Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000091620
Gene: ENSMUSG00000018476
AA Change: A456T
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
29 |
43 |
N/A |
INTRINSIC |
|
low complexity region
|
54 |
71 |
N/A |
INTRINSIC |
|
SCOP:d1elwa_
|
91 |
152 |
9e-5 |
SMART |
|
low complexity region
|
214 |
227 |
N/A |
INTRINSIC |
|
low complexity region
|
239 |
270 |
N/A |
INTRINSIC |
|
low complexity region
|
312 |
329 |
N/A |
INTRINSIC |
|
low complexity region
|
333 |
345 |
N/A |
INTRINSIC |
|
low complexity region
|
389 |
415 |
N/A |
INTRINSIC |
|
low complexity region
|
461 |
487 |
N/A |
INTRINSIC |
|
low complexity region
|
515 |
524 |
N/A |
INTRINSIC |
|
low complexity region
|
544 |
577 |
N/A |
INTRINSIC |
|
low complexity region
|
585 |
615 |
N/A |
INTRINSIC |
|
low complexity region
|
643 |
650 |
N/A |
INTRINSIC |
|
low complexity region
|
711 |
719 |
N/A |
INTRINSIC |
|
low complexity region
|
743 |
766 |
N/A |
INTRINSIC |
|
low complexity region
|
771 |
811 |
N/A |
INTRINSIC |
|
low complexity region
|
840 |
879 |
N/A |
INTRINSIC |
|
low complexity region
|
890 |
909 |
N/A |
INTRINSIC |
|
low complexity region
|
950 |
989 |
N/A |
INTRINSIC |
|
low complexity region
|
993 |
1011 |
N/A |
INTRINSIC |
|
low complexity region
|
1044 |
1068 |
N/A |
INTRINSIC |
|
low complexity region
|
1284 |
1317 |
N/A |
INTRINSIC |
|
JmjC
|
1337 |
1500 |
1.61e-47 |
SMART |
|
Blast:JmjC
|
1536 |
1600 |
1e-18 |
BLAST |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129924
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156562
|
| Meta Mutation Damage Score |
0.0632 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.2%
- 20x: 94.8%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a lysine-specific demethylase that specifically demethylates di- or tri-methylated lysine 27 of histone H3 (H3K27me2 or H3K27me3). H3K27 trimethylation is a repressive epigenetic mark controlling chromatin organization and gene silencing. This protein can also demethylate non-histone proteins such as retinoblastoma protein. Through its demethylation actvity this gene influences cellular differentiation and development, tumorigenesis, inflammatory diseases, and neurodegenerative diseases. This protein has two classical nuclear localization signals at its N-terminus. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]
PHENOTYPE: Mice homozygous for a null allele show perinatal death, thick alveolar septum, and absence of air space in the lungs. Mice homozygous for a different null allele die neonatally displaying abnormal lung development, dwarfism, kyphosis, short limbs, and a severe delay in endochondral ossification. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adnp |
T |
C |
2: 168,025,645 (GRCm39) |
D550G |
probably damaging |
Het |
| Ano6 |
A |
G |
15: 95,839,228 (GRCm39) |
T457A |
probably damaging |
Het |
| Ano8 |
A |
G |
8: 71,935,221 (GRCm39) |
V359A |
probably damaging |
Het |
| Aqp2 |
G |
T |
15: 99,476,993 (GRCm39) |
|
probably benign |
Het |
| Atp13a5 |
C |
T |
16: 29,075,829 (GRCm39) |
|
probably benign |
Het |
| Carmil3 |
ACCCCC |
ACCCCCCCCCCCC |
14: 55,741,456 (GRCm39) |
|
probably null |
Het |
| Ccr1l1 |
A |
G |
9: 123,778,030 (GRCm39) |
V139A |
probably benign |
Het |
| Cecr2 |
A |
G |
6: 120,708,407 (GRCm39) |
|
probably null |
Het |
| Celsr2 |
A |
G |
3: 108,310,119 (GRCm39) |
V1537A |
possibly damaging |
Het |
| Chd6 |
T |
A |
2: 160,856,032 (GRCm39) |
K741N |
probably damaging |
Het |
| Chrna1 |
T |
A |
2: 73,397,075 (GRCm39) |
T405S |
probably benign |
Het |
| Cish |
T |
C |
9: 107,174,227 (GRCm39) |
V5A |
possibly damaging |
Het |
| Cmss1 |
C |
A |
16: 57,131,649 (GRCm39) |
C159F |
probably damaging |
Het |
| Col1a2 |
A |
G |
6: 4,516,916 (GRCm39) |
|
probably benign |
Het |
| Cradd |
G |
T |
10: 95,011,666 (GRCm39) |
S158* |
probably null |
Het |
| Dmxl1 |
G |
A |
18: 49,997,545 (GRCm39) |
A578T |
probably benign |
Het |
| Drd2 |
A |
G |
9: 49,318,315 (GRCm39) |
N419S |
possibly damaging |
Het |
| E4f1 |
T |
C |
17: 24,666,103 (GRCm39) |
T232A |
probably damaging |
Het |
| Fat2 |
T |
A |
11: 55,171,956 (GRCm39) |
E2919V |
probably damaging |
Het |
| Gc |
T |
C |
5: 89,586,309 (GRCm39) |
|
probably null |
Het |
| Gprc5c |
G |
T |
11: 114,755,093 (GRCm39) |
V257L |
possibly damaging |
Het |
| Hsd11b2 |
G |
A |
8: 106,249,143 (GRCm39) |
V173I |
probably benign |
Het |
| Kif18b |
G |
A |
11: 102,799,015 (GRCm39) |
P729S |
possibly damaging |
Het |
| Lgi1 |
A |
G |
19: 38,294,629 (GRCm39) |
D467G |
possibly damaging |
Het |
| Loxl1 |
A |
G |
9: 58,219,650 (GRCm39) |
Y174H |
possibly damaging |
Het |
| Mtus1 |
A |
T |
8: 41,475,592 (GRCm39) |
I824N |
probably damaging |
Het |
| Myrf |
C |
T |
19: 10,192,654 (GRCm39) |
E622K |
probably benign |
Het |
| Ncam1 |
A |
G |
9: 49,457,051 (GRCm39) |
Y416H |
probably damaging |
Het |
| Nceh1 |
A |
G |
3: 27,280,248 (GRCm39) |
T132A |
probably benign |
Het |
| Nhlrc4 |
G |
A |
17: 26,162,466 (GRCm39) |
P94S |
probably damaging |
Het |
| Or2v1 |
C |
G |
11: 49,025,941 (GRCm39) |
D307E |
probably benign |
Het |
| Or52s1b |
A |
T |
7: 102,822,841 (GRCm39) |
M1K |
probably null |
Het |
| Or8b1 |
A |
T |
9: 38,399,821 (GRCm39) |
R165S |
possibly damaging |
Het |
| Pcdhac2 |
A |
G |
18: 37,277,476 (GRCm39) |
Y152C |
probably damaging |
Het |
| Pdia3 |
C |
A |
2: 121,244,611 (GRCm39) |
T8K |
possibly damaging |
Het |
| Pogz |
T |
A |
3: 94,771,820 (GRCm39) |
V304E |
probably damaging |
Het |
| Snrnp200 |
A |
G |
2: 127,068,007 (GRCm39) |
S835G |
possibly damaging |
Het |
| Susd4 |
T |
C |
1: 182,719,635 (GRCm39) |
S417P |
probably benign |
Het |
| Thsd7b |
G |
A |
1: 129,523,578 (GRCm39) |
R127H |
probably damaging |
Het |
| Tmco4 |
A |
G |
4: 138,781,216 (GRCm39) |
D460G |
probably damaging |
Het |
| Ttll9 |
T |
A |
2: 152,826,234 (GRCm39) |
M148K |
probably damaging |
Het |
| Ubn2 |
G |
A |
6: 38,467,323 (GRCm39) |
C677Y |
probably benign |
Het |
| Vmn2r98 |
T |
C |
17: 19,301,161 (GRCm39) |
I721T |
probably benign |
Het |
| Wdfy4 |
C |
A |
14: 32,855,454 (GRCm39) |
C720F |
probably damaging |
Het |
| Zzef1 |
G |
A |
11: 72,807,347 (GRCm39) |
D2742N |
probably damaging |
Het |
|
| Other mutations in Kdm6b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00484:Kdm6b
|
APN |
11 |
69,297,132 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
IGL02271:Kdm6b
|
APN |
11 |
69,296,893 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
beine
|
UTSW |
11 |
69,294,418 (GRCm39) |
missense |
unknown |
|
|
Gaudy
|
UTSW |
11 |
69,291,032 (GRCm39) |
missense |
unknown |
|
|
Hypocrisy
|
UTSW |
11 |
69,292,977 (GRCm39) |
nonsense |
probably null |
|
|
Knochen
|
UTSW |
11 |
69,290,881 (GRCm39) |
unclassified |
probably benign |
|
|
Ostentatious
|
UTSW |
11 |
69,294,424 (GRCm39) |
missense |
unknown |
|
|
Piquant
|
UTSW |
11 |
69,294,620 (GRCm39) |
missense |
unknown |
|
|
preen
|
UTSW |
11 |
69,292,919 (GRCm39) |
missense |
unknown |
|
|
Tart
|
UTSW |
11 |
69,297,192 (GRCm39) |
missense |
probably damaging |
1.00 |
|
BB007:Kdm6b
|
UTSW |
11 |
69,290,778 (GRCm39) |
missense |
unknown |
|
|
BB017:Kdm6b
|
UTSW |
11 |
69,290,778 (GRCm39) |
missense |
unknown |
|
|
PIT4458001:Kdm6b
|
UTSW |
11 |
69,290,778 (GRCm39) |
missense |
unknown |
|
|
R0455:Kdm6b
|
UTSW |
11 |
69,297,822 (GRCm39) |
nonsense |
probably null |
|
|
R0645:Kdm6b
|
UTSW |
11 |
69,295,844 (GRCm39) |
missense |
unknown |
|
|
R1659:Kdm6b
|
UTSW |
11 |
69,298,414 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R1855:Kdm6b
|
UTSW |
11 |
69,298,112 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1962:Kdm6b
|
UTSW |
11 |
69,292,191 (GRCm39) |
unclassified |
probably benign |
|
|
R1993:Kdm6b
|
UTSW |
11 |
69,297,129 (GRCm39) |
missense |
probably null |
0.85 |
|
R2029:Kdm6b
|
UTSW |
11 |
69,294,418 (GRCm39) |
missense |
unknown |
|
|
R2181:Kdm6b
|
UTSW |
11 |
69,291,952 (GRCm39) |
nonsense |
probably null |
|
|
R2215:Kdm6b
|
UTSW |
11 |
69,295,870 (GRCm39) |
missense |
unknown |
|
|
R2904:Kdm6b
|
UTSW |
11 |
69,296,611 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R2992:Kdm6b
|
UTSW |
11 |
69,297,133 (GRCm39) |
small deletion |
probably benign |
|
|
R3236:Kdm6b
|
UTSW |
11 |
69,297,192 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3950:Kdm6b
|
UTSW |
11 |
69,296,441 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4027:Kdm6b
|
UTSW |
11 |
69,297,094 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R4830:Kdm6b
|
UTSW |
11 |
69,294,620 (GRCm39) |
missense |
unknown |
|
|
R4996:Kdm6b
|
UTSW |
11 |
69,296,557 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5034:Kdm6b
|
UTSW |
11 |
69,292,736 (GRCm39) |
splice site |
probably benign |
|
|
R5140:Kdm6b
|
UTSW |
11 |
69,290,881 (GRCm39) |
unclassified |
probably benign |
|
|
R5160:Kdm6b
|
UTSW |
11 |
69,291,594 (GRCm39) |
unclassified |
probably benign |
|
|
R5240:Kdm6b
|
UTSW |
11 |
69,292,730 (GRCm39) |
splice site |
probably benign |
|
|
R5273:Kdm6b
|
UTSW |
11 |
69,295,027 (GRCm39) |
missense |
unknown |
|
|
R5386:Kdm6b
|
UTSW |
11 |
69,291,636 (GRCm39) |
unclassified |
probably benign |
|
|
R5597:Kdm6b
|
UTSW |
11 |
69,296,900 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R5812:Kdm6b
|
UTSW |
11 |
69,296,755 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5976:Kdm6b
|
UTSW |
11 |
69,294,614 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6000:Kdm6b
|
UTSW |
11 |
69,294,424 (GRCm39) |
missense |
unknown |
|
|
R6145:Kdm6b
|
UTSW |
11 |
69,295,852 (GRCm39) |
missense |
unknown |
|
|
R6191:Kdm6b
|
UTSW |
11 |
69,297,584 (GRCm39) |
missense |
probably benign |
0.01 |
|
R6256:Kdm6b
|
UTSW |
11 |
69,297,555 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6304:Kdm6b
|
UTSW |
11 |
69,295,084 (GRCm39) |
missense |
unknown |
|
|
R6917:Kdm6b
|
UTSW |
11 |
69,297,419 (GRCm39) |
missense |
probably benign |
0.04 |
|
R6939:Kdm6b
|
UTSW |
11 |
69,297,588 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7356:Kdm6b
|
UTSW |
11 |
69,292,991 (GRCm39) |
nonsense |
probably null |
|
|
R7644:Kdm6b
|
UTSW |
11 |
69,291,032 (GRCm39) |
missense |
unknown |
|
|
R7673:Kdm6b
|
UTSW |
11 |
69,296,568 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7698:Kdm6b
|
UTSW |
11 |
69,296,807 (GRCm39) |
missense |
probably benign |
0.14 |
|
R7776:Kdm6b
|
UTSW |
11 |
69,296,960 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R7930:Kdm6b
|
UTSW |
11 |
69,290,778 (GRCm39) |
missense |
unknown |
|
|
R8383:Kdm6b
|
UTSW |
11 |
69,296,876 (GRCm39) |
missense |
probably benign |
|
|
R8725:Kdm6b
|
UTSW |
11 |
69,292,919 (GRCm39) |
missense |
unknown |
|
|
R8727:Kdm6b
|
UTSW |
11 |
69,292,919 (GRCm39) |
missense |
unknown |
|
|
R8813:Kdm6b
|
UTSW |
11 |
69,297,658 (GRCm39) |
small insertion |
probably benign |
|
|
R8813:Kdm6b
|
UTSW |
11 |
69,297,655 (GRCm39) |
small insertion |
probably benign |
|
|
R8851:Kdm6b
|
UTSW |
11 |
69,291,993 (GRCm39) |
missense |
unknown |
|
|
R9074:Kdm6b
|
UTSW |
11 |
69,292,977 (GRCm39) |
nonsense |
probably null |
|
|
R9130:Kdm6b
|
UTSW |
11 |
69,295,424 (GRCm39) |
missense |
unknown |
|
|
R9179:Kdm6b
|
UTSW |
11 |
69,297,521 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9535:Kdm6b
|
UTSW |
11 |
69,297,276 (GRCm39) |
nonsense |
probably null |
|
|
Z1177:Kdm6b
|
UTSW |
11 |
69,294,692 (GRCm39) |
missense |
unknown |
|
|
| Predicted Primers |
PCR Primer
(F):5'- CTGAGTGCCCACAGAAAAGC -3'
(R):5'- ATGACATTGGGCTGAAGGTG -3'
Sequencing Primer
(F):5'- CCAAGAAGCCATCACGGTGG -3'
(R):5'- CTGAAGGTGGGTGACATTGTC -3'
|
| Posted On |
2016-10-26 |
Incidental Mutation