Incidental Mutation 'IGL01970:Kdm5b'
ID |
182534 |
Institutional Source |
Australian Phenomics Network
(link to record)
|
Gene Symbol |
Kdm5b
|
Ensembl Gene |
ENSMUSG00000042207 |
Gene Name |
lysine (K)-specific demethylase 5B |
Synonyms |
Jarid1b, Plu1, Rb-Bp2, 2210016I17Rik, 2010009J12Rik, PLU-1, D1Ertd202e |
Accession Numbers |
|
Is this an essential gene? |
Possibly non essential
(E-score: 0.329)
|
Stock # |
IGL01970
|
Quality Score |
|
Status
|
|
Chromosome |
1 |
Chromosomal Location |
134560171-134635285 bp(+) (GRCm38) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 134600727 bp (GRCm38)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Threonine
at position 391
(S391T)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000107817
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000047714]
[ENSMUST00000112198]
|
AlphaFold |
Q80Y84 |
PDB Structure |
Solution structure of the ARID domain of Jarid1b protein [SOLUTION NMR]
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000047714
AA Change: S391T
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000038138 Gene: ENSMUSG00000042207 AA Change: S391T
Domain | Start | End | E-Value | Type |
low complexity region
|
7 |
30 |
N/A |
INTRINSIC |
JmjN
|
31 |
72 |
2.87e-20 |
SMART |
ARID
|
94 |
183 |
7.39e-32 |
SMART |
BRIGHT
|
98 |
188 |
1.51e-35 |
SMART |
low complexity region
|
228 |
239 |
N/A |
INTRINSIC |
PHD
|
311 |
357 |
6.15e-14 |
SMART |
JmjC
|
453 |
619 |
2.33e-67 |
SMART |
Pfam:zf-C5HC2
|
692 |
744 |
2.2e-17 |
PFAM |
Pfam:PLU-1
|
757 |
1088 |
5.6e-92 |
PFAM |
low complexity region
|
1097 |
1109 |
N/A |
INTRINSIC |
PHD
|
1178 |
1222 |
6.2e-10 |
SMART |
low complexity region
|
1225 |
1236 |
N/A |
INTRINSIC |
low complexity region
|
1406 |
1417 |
N/A |
INTRINSIC |
low complexity region
|
1470 |
1484 |
N/A |
INTRINSIC |
PHD
|
1486 |
1536 |
1.18e-6 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000112197
|
SMART Domains |
Protein: ENSMUSP00000107816 Gene: ENSMUSG00000042207
Domain | Start | End | E-Value | Type |
low complexity region
|
7 |
30 |
N/A |
INTRINSIC |
JmjN
|
31 |
72 |
2.87e-20 |
SMART |
ARID
|
94 |
183 |
7.39e-32 |
SMART |
BRIGHT
|
98 |
188 |
1.51e-35 |
SMART |
low complexity region
|
225 |
236 |
N/A |
INTRINSIC |
PHD
|
308 |
354 |
6.15e-14 |
SMART |
JmjC
|
450 |
595 |
2.6e-24 |
SMART |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000112198
AA Change: S391T
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000107817 Gene: ENSMUSG00000042207 AA Change: S391T
Domain | Start | End | E-Value | Type |
low complexity region
|
7 |
30 |
N/A |
INTRINSIC |
JmjN
|
31 |
72 |
2.87e-20 |
SMART |
ARID
|
94 |
183 |
7.39e-32 |
SMART |
BRIGHT
|
98 |
188 |
1.51e-35 |
SMART |
low complexity region
|
228 |
239 |
N/A |
INTRINSIC |
PHD
|
311 |
357 |
6.15e-14 |
SMART |
JmjC
|
453 |
619 |
2.33e-67 |
SMART |
Pfam:zf-C5HC2
|
692 |
745 |
6.7e-21 |
PFAM |
Pfam:PLU-1
|
756 |
1088 |
6e-94 |
PFAM |
low complexity region
|
1097 |
1109 |
N/A |
INTRINSIC |
PHD
|
1178 |
1222 |
6.2e-10 |
SMART |
low complexity region
|
1225 |
1236 |
N/A |
INTRINSIC |
low complexity region
|
1406 |
1417 |
N/A |
INTRINSIC |
low complexity region
|
1470 |
1484 |
N/A |
INTRINSIC |
|
Coding Region Coverage |
|
Validation Efficiency |
|
MGI Phenotype |
FUNCTION: This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Homozygous mutant mice display decreased body weight, decreased female fertility, lower uterine weight, and a delay in mammary development. Knockout of this gene has also been associated with embryonic lethality. [provided by RefSeq, Dec 2016] PHENOTYPE: Mice homozygous for a gene trapped allele exhibit decreased body weight, background-sensitive premature mortality, decreased female fertility, delayed mammary gland development, decreased serum estradiol levels, and reduced mammary epithelial cell proliferation in early puberty. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 25 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Cdk9 |
T |
C |
2: 32,708,051 |
H280R |
possibly damaging |
Het |
Cenpt |
C |
T |
8: 105,845,116 |
R461H |
probably damaging |
Het |
Cpa4 |
A |
G |
6: 30,579,646 |
T151A |
probably benign |
Het |
Glrb |
A |
G |
3: 80,861,925 |
I165T |
possibly damaging |
Het |
Gm17305 |
A |
T |
11: 69,364,820 |
|
probably benign |
Het |
Klrg2 |
T |
C |
6: 38,636,448 |
K207E |
probably damaging |
Het |
Krt1 |
T |
C |
15: 101,846,864 |
I487V |
possibly damaging |
Het |
Krt27 |
A |
G |
11: 99,348,721 |
L311P |
probably damaging |
Het |
Leng9 |
T |
C |
7: 4,148,327 |
Y450C |
probably damaging |
Het |
Oacyl |
A |
T |
18: 65,749,714 |
I627F |
possibly damaging |
Het |
Perm1 |
G |
T |
4: 156,217,661 |
G221W |
probably damaging |
Het |
Rft1 |
C |
T |
14: 30,690,535 |
L518F |
probably benign |
Het |
Sdk1 |
A |
T |
5: 142,085,682 |
Q1209L |
possibly damaging |
Het |
Selenbp1 |
A |
G |
3: 94,937,002 |
S57G |
probably benign |
Het |
Sema5a |
T |
C |
15: 32,686,646 |
M968T |
probably benign |
Het |
Slc16a3 |
G |
A |
11: 120,957,038 |
V351M |
probably damaging |
Het |
Sorbs2 |
G |
A |
8: 45,745,803 |
V73I |
probably damaging |
Het |
Specc1l |
T |
A |
10: 75,245,761 |
D347E |
probably damaging |
Het |
Tas2r116 |
A |
C |
6: 132,855,669 |
T78P |
probably benign |
Het |
Tpm3 |
A |
G |
3: 90,089,828 |
E224G |
probably damaging |
Het |
Trnau1ap |
T |
C |
4: 132,313,987 |
|
probably benign |
Het |
Vmn2r17 |
T |
A |
5: 109,427,947 |
M228K |
probably damaging |
Het |
Vnn1 |
T |
C |
10: 23,897,402 |
I109T |
probably benign |
Het |
Wee1 |
C |
A |
7: 110,139,250 |
H523Q |
probably damaging |
Het |
Xpr1 |
T |
C |
1: 155,290,234 |
N524S |
probably benign |
Het |
|
Other mutations in Kdm5b |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00230:Kdm5b
|
APN |
1 |
134620955 |
missense |
probably damaging |
1.00 |
IGL01458:Kdm5b
|
APN |
1 |
134621986 |
missense |
possibly damaging |
0.53 |
IGL01567:Kdm5b
|
APN |
1 |
134602540 |
missense |
probably damaging |
1.00 |
IGL01625:Kdm5b
|
APN |
1 |
134617968 |
missense |
possibly damaging |
0.74 |
IGL02183:Kdm5b
|
APN |
1 |
134624931 |
missense |
probably benign |
0.09 |
IGL02592:Kdm5b
|
APN |
1 |
134624853 |
missense |
probably damaging |
0.99 |
IGL02695:Kdm5b
|
APN |
1 |
134604485 |
missense |
possibly damaging |
0.94 |
IGL02697:Kdm5b
|
APN |
1 |
134588773 |
splice site |
probably benign |
|
IGL03036:Kdm5b
|
APN |
1 |
134608937 |
missense |
probably damaging |
1.00 |
IGL03056:Kdm5b
|
APN |
1 |
134587979 |
missense |
probably damaging |
0.99 |
IGL03206:Kdm5b
|
APN |
1 |
134627317 |
missense |
probably benign |
|
IGL03342:Kdm5b
|
APN |
1 |
134602576 |
missense |
probably benign |
0.00 |
IGL03388:Kdm5b
|
APN |
1 |
134627322 |
missense |
probably benign |
|
amaryllis
|
UTSW |
1 |
134609061 |
critical splice donor site |
probably null |
|
PIT4486001:Kdm5b
|
UTSW |
1 |
134628685 |
missense |
probably damaging |
1.00 |
R0233:Kdm5b
|
UTSW |
1 |
134604634 |
splice site |
probably benign |
|
R0334:Kdm5b
|
UTSW |
1 |
134604522 |
missense |
probably damaging |
0.99 |
R0504:Kdm5b
|
UTSW |
1 |
134621023 |
critical splice donor site |
probably null |
|
R0505:Kdm5b
|
UTSW |
1 |
134602571 |
missense |
probably damaging |
0.96 |
R0521:Kdm5b
|
UTSW |
1 |
134618033 |
missense |
possibly damaging |
0.65 |
R1004:Kdm5b
|
UTSW |
1 |
134588904 |
missense |
possibly damaging |
0.71 |
R1087:Kdm5b
|
UTSW |
1 |
134600637 |
missense |
probably damaging |
1.00 |
R1126:Kdm5b
|
UTSW |
1 |
134613991 |
missense |
possibly damaging |
0.90 |
R1221:Kdm5b
|
UTSW |
1 |
134599091 |
missense |
probably damaging |
0.98 |
R1230:Kdm5b
|
UTSW |
1 |
134613254 |
missense |
probably damaging |
1.00 |
R1345:Kdm5b
|
UTSW |
1 |
134630550 |
missense |
possibly damaging |
0.94 |
R1482:Kdm5b
|
UTSW |
1 |
134624897 |
missense |
probably damaging |
1.00 |
R1582:Kdm5b
|
UTSW |
1 |
134624853 |
missense |
probably damaging |
0.99 |
R1653:Kdm5b
|
UTSW |
1 |
134602481 |
missense |
probably damaging |
1.00 |
R1693:Kdm5b
|
UTSW |
1 |
134597576 |
splice site |
probably benign |
|
R1721:Kdm5b
|
UTSW |
1 |
134613181 |
splice site |
probably benign |
|
R1741:Kdm5b
|
UTSW |
1 |
134618017 |
missense |
possibly damaging |
0.82 |
R1762:Kdm5b
|
UTSW |
1 |
134604467 |
nonsense |
probably null |
|
R1820:Kdm5b
|
UTSW |
1 |
134597670 |
missense |
possibly damaging |
0.87 |
R1872:Kdm5b
|
UTSW |
1 |
134624994 |
missense |
probably damaging |
1.00 |
R1966:Kdm5b
|
UTSW |
1 |
134613873 |
splice site |
probably null |
|
R2056:Kdm5b
|
UTSW |
1 |
134613214 |
missense |
probably benign |
0.05 |
R2059:Kdm5b
|
UTSW |
1 |
134613214 |
missense |
probably benign |
0.05 |
R2405:Kdm5b
|
UTSW |
1 |
134609016 |
missense |
probably damaging |
0.97 |
R3417:Kdm5b
|
UTSW |
1 |
134587977 |
missense |
probably damaging |
1.00 |
R3771:Kdm5b
|
UTSW |
1 |
134613345 |
missense |
probably damaging |
1.00 |
R3783:Kdm5b
|
UTSW |
1 |
134630542 |
missense |
probably benign |
|
R3803:Kdm5b
|
UTSW |
1 |
134615941 |
missense |
probably benign |
0.07 |
R3980:Kdm5b
|
UTSW |
1 |
134619670 |
missense |
probably benign |
0.11 |
R3983:Kdm5b
|
UTSW |
1 |
134631304 |
missense |
possibly damaging |
0.91 |
R4013:Kdm5b
|
UTSW |
1 |
134627329 |
missense |
possibly damaging |
0.86 |
R4162:Kdm5b
|
UTSW |
1 |
134625161 |
missense |
probably benign |
0.01 |
R4701:Kdm5b
|
UTSW |
1 |
134606012 |
intron |
probably benign |
|
R4791:Kdm5b
|
UTSW |
1 |
134630800 |
missense |
possibly damaging |
0.82 |
R4836:Kdm5b
|
UTSW |
1 |
134593315 |
splice site |
probably null |
|
R4924:Kdm5b
|
UTSW |
1 |
134631351 |
missense |
probably benign |
0.00 |
R5135:Kdm5b
|
UTSW |
1 |
134588746 |
intron |
probably benign |
|
R5248:Kdm5b
|
UTSW |
1 |
134620997 |
missense |
probably benign |
0.11 |
R5290:Kdm5b
|
UTSW |
1 |
134622099 |
splice site |
probably null |
|
R5358:Kdm5b
|
UTSW |
1 |
134607694 |
nonsense |
probably null |
|
R5388:Kdm5b
|
UTSW |
1 |
134608897 |
nonsense |
probably null |
|
R5396:Kdm5b
|
UTSW |
1 |
134622098 |
splice site |
probably null |
|
R5397:Kdm5b
|
UTSW |
1 |
134622098 |
splice site |
probably null |
|
R5398:Kdm5b
|
UTSW |
1 |
134622098 |
splice site |
probably null |
|
R5399:Kdm5b
|
UTSW |
1 |
134622098 |
splice site |
probably null |
|
R5529:Kdm5b
|
UTSW |
1 |
134588003 |
missense |
probably damaging |
1.00 |
R5540:Kdm5b
|
UTSW |
1 |
134631241 |
missense |
probably damaging |
0.98 |
R5661:Kdm5b
|
UTSW |
1 |
134599073 |
missense |
probably benign |
0.01 |
R5663:Kdm5b
|
UTSW |
1 |
134630635 |
missense |
probably benign |
|
R5822:Kdm5b
|
UTSW |
1 |
134588773 |
splice site |
probably benign |
|
R6226:Kdm5b
|
UTSW |
1 |
134608878 |
missense |
probably damaging |
0.99 |
R6368:Kdm5b
|
UTSW |
1 |
134599207 |
missense |
probably damaging |
1.00 |
R6681:Kdm5b
|
UTSW |
1 |
134613269 |
missense |
possibly damaging |
0.90 |
R6715:Kdm5b
|
UTSW |
1 |
134609061 |
critical splice donor site |
probably null |
|
R7132:Kdm5b
|
UTSW |
1 |
134599106 |
missense |
probably damaging |
1.00 |
R7202:Kdm5b
|
UTSW |
1 |
134624759 |
missense |
probably benign |
|
R7258:Kdm5b
|
UTSW |
1 |
134621021 |
missense |
probably damaging |
1.00 |
R7335:Kdm5b
|
UTSW |
1 |
134560439 |
missense |
probably damaging |
1.00 |
R7420:Kdm5b
|
UTSW |
1 |
134604497 |
missense |
probably benign |
0.14 |
R7426:Kdm5b
|
UTSW |
1 |
134595833 |
missense |
probably benign |
0.02 |
R7452:Kdm5b
|
UTSW |
1 |
134624948 |
missense |
probably damaging |
1.00 |
R7595:Kdm5b
|
UTSW |
1 |
134608966 |
missense |
probably benign |
0.00 |
R7612:Kdm5b
|
UTSW |
1 |
134624918 |
nonsense |
probably null |
|
R7704:Kdm5b
|
UTSW |
1 |
134587931 |
missense |
probably damaging |
1.00 |
R7846:Kdm5b
|
UTSW |
1 |
134617840 |
missense |
probably damaging |
1.00 |
R8115:Kdm5b
|
UTSW |
1 |
134619673 |
missense |
possibly damaging |
0.83 |
R8146:Kdm5b
|
UTSW |
1 |
134625126 |
missense |
probably benign |
0.05 |
R8160:Kdm5b
|
UTSW |
1 |
134613919 |
missense |
probably damaging |
1.00 |
R8527:Kdm5b
|
UTSW |
1 |
134605774 |
missense |
possibly damaging |
0.78 |
R8542:Kdm5b
|
UTSW |
1 |
134605774 |
missense |
possibly damaging |
0.78 |
R8930:Kdm5b
|
UTSW |
1 |
134616272 |
missense |
probably damaging |
1.00 |
R8932:Kdm5b
|
UTSW |
1 |
134616272 |
missense |
probably damaging |
1.00 |
R8950:Kdm5b
|
UTSW |
1 |
134613926 |
missense |
possibly damaging |
0.84 |
R9089:Kdm5b
|
UTSW |
1 |
134607768 |
missense |
probably damaging |
0.98 |
R9109:Kdm5b
|
UTSW |
1 |
134600755 |
critical splice donor site |
probably null |
|
R9133:Kdm5b
|
UTSW |
1 |
134602585 |
missense |
probably benign |
|
R9298:Kdm5b
|
UTSW |
1 |
134600755 |
critical splice donor site |
probably null |
|
R9423:Kdm5b
|
UTSW |
1 |
134587967 |
missense |
possibly damaging |
0.85 |
X0063:Kdm5b
|
UTSW |
1 |
134588876 |
missense |
probably benign |
0.07 |
Z1176:Kdm5b
|
UTSW |
1 |
134625035 |
missense |
probably damaging |
1.00 |
Z1177:Kdm5b
|
UTSW |
1 |
134595798 |
frame shift |
probably null |
|
|
Posted On |
2014-05-07 |