Mutagenetix > Incidental Mutations

Incidental Mutation 'R6526:Kdm2b'

521831

Institutional Source

Beutler Lab

Gene Symbol

Kdm2b

Ensembl Gene

ENSMUSG00000029475

Gene Name

lysine (K)-specific demethylase 2B

Synonyms

Jhdm1b, Fbxl10, Cxxc2

MMRRC Submission

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R6526 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

122870665-122989823 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 122961469 bp

Zygosity

Heterozygous

Amino Acid Change

Valine to Phenylalanine at position 136 (V136F)

Ref Sequence

ENSEMBL: ENSMUSP00000118488 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000046073] [ENSMUST00000086200] [ENSMUST00000118027] [ENSMUST00000121739] [ENSMUST00000127403] [ENSMUST00000156474]

Predicted Effect

probably damaging
Transcript: ENSMUST00000046073
AA Change: V142F

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000038229
Gene: ENSMUSG00000029475
AA Change: V142F

Domain	Start	End	E-Value	Type
Blast:JmjC	23	101	4e-41	BLAST
JmjC	147	315	3.61e-41	SMART
low complexity region	380	401	N/A	INTRINSIC
low complexity region	406	424	N/A	INTRINSIC
PDB:2YU2\|A	472	546	1e-17	PDB
Pfam:zf-CXXC	578	624	3e-17	PFAM
PHD	634	696	8.58e-4	SMART
low complexity region	792	823	N/A	INTRINSIC
low complexity region	903	913	N/A	INTRINSIC
low complexity region	990	1006	N/A	INTRINSIC
low complexity region	1018	1032	N/A	INTRINSIC
FBOX	1038	1078	1.69e-2	SMART
LRR	1121	1143	1.31e2	SMART
LRR	1145	1170	2.9e2	SMART
LRR	1185	1209	2.04e2	SMART
LRR	1210	1235	1.1e1	SMART
LRR	1265	1290	3.91e1	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000086200
AA Change: V136F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000083376
Gene: ENSMUSG00000029475
AA Change: V136F

Domain	Start	End	E-Value	Type
Blast:JmjC	17	95	4e-41	BLAST
JmjC	141	309	3.61e-41	SMART
low complexity region	374	395	N/A	INTRINSIC
low complexity region	400	418	N/A	INTRINSIC
PDB:2YU2\|A	466	540	1e-17	PDB
Pfam:zf-CXXC	572	618	2.1e-17	PFAM
PHD	628	690	8.58e-4	SMART
low complexity region	786	817	N/A	INTRINSIC
low complexity region	897	907	N/A	INTRINSIC
low complexity region	984	1000	N/A	INTRINSIC
low complexity region	1012	1026	N/A	INTRINSIC
FBOX	1032	1072	1.69e-2	SMART
LRR	1115	1137	1.31e2	SMART
LRR	1139	1164	2.9e2	SMART
LRR	1179	1203	2.04e2	SMART
LRR	1204	1229	1.1e1	SMART
LRR	1259	1284	3.91e1	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000118027
AA Change: V142F

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000114052
Gene: ENSMUSG00000029475
AA Change: V142F

Domain	Start	End	E-Value	Type
Blast:JmjC	23	101	4e-41	BLAST
JmjC	147	315	3.61e-41	SMART
low complexity region	380	401	N/A	INTRINSIC
low complexity region	406	424	N/A	INTRINSIC
PDB:2YU2\|A	472	546	9e-18	PDB
Pfam:zf-CXXC	578	624	2.1e-17	PFAM
PHD	634	696	8.58e-4	SMART
low complexity region	865	875	N/A	INTRINSIC
low complexity region	952	968	N/A	INTRINSIC
low complexity region	980	994	N/A	INTRINSIC
FBOX	1000	1040	1.69e-2	SMART
LRR	1083	1105	1.31e2	SMART
LRR	1107	1132	2.9e2	SMART
LRR	1147	1171	2.04e2	SMART
LRR	1172	1197	1.1e1	SMART
LRR	1227	1252	3.91e1	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000121739
AA Change: V87F

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000114049
Gene: ENSMUSG00000029475
AA Change: V87F

Domain	Start	End	E-Value	Type
Blast:JmjC	1	46	2e-19	BLAST
JmjC	92	260	3.61e-41	SMART
low complexity region	325	346	N/A	INTRINSIC
low complexity region	351	369	N/A	INTRINSIC
PDB:2YU2\|A	417	491	1e-17	PDB
Pfam:zf-CXXC	523	569	5.4e-17	PFAM
PHD	579	641	8.58e-4	SMART
low complexity region	737	768	N/A	INTRINSIC
low complexity region	848	858	N/A	INTRINSIC
low complexity region	935	951	N/A	INTRINSIC
low complexity region	963	977	N/A	INTRINSIC
FBOX	983	1023	1.69e-2	SMART
LRR	1066	1088	1.31e2	SMART
LRR	1090	1115	2.9e2	SMART
LRR	1130	1154	2.04e2	SMART
LRR	1155	1180	1.1e1	SMART
LRR	1210	1235	3.91e1	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123479

Predicted Effect

probably benign
Transcript: ENSMUST00000127403

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134501

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150543

Predicted Effect

probably damaging
Transcript: ENSMUST00000156474
AA Change: V136F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000118488
Gene: ENSMUSG00000029475
AA Change: V136F

Domain	Start	End	E-Value	Type
Blast:JmjC	17	95	3e-42	BLAST
JmjC	141	309	3.61e-41	SMART
low complexity region	374	395	N/A	INTRINSIC
low complexity region	400	418	N/A	INTRINSIC
PDB:2YU2\|A	466	512	1e-8	PDB

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.4%
20x: 91.5%

Validation Efficiency

100% (72/72)

MGI Phenotype

FUNCTION: The protein encoded by this gene is a H3K36-specific histone demethylase, which contains an N-terminal jumonji C domain, a CxxC zinc finger domain, a plant homeodomain finger, an F-box, and eight leucine-rich repeats. Amongst its demonstrated functions, this protein plays roles in the suppression of premature cellular senescence, leukemia maintenance and development, maintenance of mouse embryonic stem cell pluripotency, and induced pluripotent stem cell generation. Mice homozygous for a targeted deletion of the zinc finger domain display embryonic lethality with development ceasing at approximately 7 to 8 days post coitum, demonstrating an essential role in early development. A pseudogene of this gene is found on chromosome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
PHENOTYPE: Mice homozygous for a targeted allele that does not express the long form protein exhibit exencephaly, fetal and postnatal lethality, coloboma, curly tail, oligozoospermia, increased apoptosis, and increased neuronal precursor proliferation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aamp	A	G	1: 74,284,172		probably null	Het
Abcc3	C	T	11: 94,359,372	G975D	probably benign	Het
Abhd13	G	A	8: 9,987,777	G125S	probably damaging	Het
Ache	T	A	5: 137,290,644	L204Q	probably damaging	Het
Acnat2	A	G	4: 49,383,497	S19P	probably benign	Het
Adprh	A	G	16: 38,447,276	Y216H	probably benign	Het
Anapc1	T	A	2: 128,672,135	K429*	probably null	Het
Anxa13	T	C	15: 58,344,957		noncoding transcript	Het
Aprt	A	C	8: 122,576,816	L6W	probably damaging	Het
Arhgef15	T	C	11: 68,949,994	T569A	probably damaging	Het
Atp11a	T	C	8: 12,864,999	L1139P	probably benign	Het
Atp2b4	A	G	1: 133,711,729	S1136P	probably damaging	Het
B9d1	T	A	11: 61,509,097	Y90*	probably null	Het
Btla	G	A	16: 45,239,094	A54T	probably damaging	Het
Cd63	T	C	10: 128,911,489	V35A	probably benign	Het
Chek2	T	C	5: 110,848,690	F173L	probably damaging	Het
Cntnap3	T	A	13: 64,781,888	N499I	possibly damaging	Het
Cog4	T	C	8: 110,881,786	L738P	probably damaging	Het
Cops6	T	C	5: 138,163,900		probably null	Het
Cpeb1	T	A	7: 81,361,669	I175F	probably benign	Het
Cyp3a16	C	T	5: 145,455,895	D174N	probably benign	Het
Dnah6	T	G	6: 73,074,704	I2984L	probably benign	Het
Dock10	A	T	1: 80,586,351	I540N	probably damaging	Het
Elf5	A	G	2: 103,439,233	Y53C	probably damaging	Het
Elmod2	T	C	8: 83,319,457	T164A	probably damaging	Het
Epn3	A	G	11: 94,494,932		probably null	Het
Fam151a	A	T	4: 106,734,004	I15F	possibly damaging	Het
Gm11115	T	A	5: 88,154,050		probably null	Het
Gm13103	A	G	4: 143,852,814	D323G	probably damaging	Het
Golga3	T	A	5: 110,204,895	I884N	probably damaging	Het
Gria2	A	T	3: 80,692,469	F703I	probably damaging	Het
Gtf2h3	C	T	5: 124,584,297	T121I	probably benign	Het
Gtpbp2	A	T	17: 46,164,111		probably null	Het
Herc2	T	C	7: 56,157,330	S2419P	probably damaging	Het
Ikbkap	T	C	4: 56,798,812		probably null	Het
Inpp5d	T	C	1: 87,676,250		probably benign	Het
Klra2	T	A	6: 131,221,876	D234V	probably benign	Het
Lct	A	T	1: 128,300,478	S1093T	probably benign	Het
March9	A	G	10: 127,056,689	L310P	probably benign	Het
Morc1	G	T	16: 48,587,124	E668*	probably null	Het
Mum1	A	G	10: 80,232,279	T86A	probably benign	Het
Nbas	A	T	12: 13,405,425	L1213F	probably damaging	Het
Neto1	A	G	18: 86,498,748	T397A	possibly damaging	Het
Oit3	A	G	10: 59,429,640	C268R	probably damaging	Het
Olfr476	A	G	7: 107,967,462	T22A	probably benign	Het
Pcx	T	C	19: 4,604,495	F312L	probably benign	Het
Pitx2	T	C	3: 129,214,783		probably null	Het
Pkhd1l1	G	A	15: 44,498,089		probably null	Het
Polr1a	C	A	6: 71,929,443	D414E	possibly damaging	Het
Prkch	T	C	12: 73,702,775	Y381H	probably damaging	Het
Ptger3	T	A	3: 157,567,502	V162E	probably damaging	Het
Ptgr2	T	G	12: 84,313,952	M332R	probably damaging	Het
Ptprq	G	T	10: 107,542,653	S2009*	probably null	Het
Rangrf	C	T	11: 68,973,688	G11R	probably damaging	Het
Rbl2	A	T	8: 91,096,839	Q465L	probably benign	Het
Rhbdd1	A	T	1: 82,340,659	M88L	probably benign	Het
Setd2	G	A	9: 110,532,717	M13I	probably benign	Het
Sirpb1a	T	C	3: 15,379,020	Y384C	probably damaging	Het
Slc13a1	C	T	6: 24,097,612	G439S	probably damaging	Het
Slc41a1	T	A	1: 131,841,149	I239N	probably damaging	Het
Slit2	T	A	5: 48,304,167	C1502S	probably damaging	Het
Slit3	G	A	11: 35,661,292	E888K	probably benign	Het
Srrm3	G	T	5: 135,835,234	R62L	probably damaging	Het
Synm	A	G	7: 67,735,583	V777A	possibly damaging	Het
Trmt13	T	A	3: 116,592,215	N31I	probably damaging	Het
Trpm8	G	A	1: 88,361,998	E893K	probably damaging	Het
Uqcc1	A	G	2: 155,851,423	F197S	probably damaging	Het
Vmn1r67	T	A	7: 10,447,671	N287K	probably benign	Het
Vmn2r44	A	T	7: 8,378,099	M265K	probably benign	Het
Wwc1	C	T	11: 35,853,437	E853K	probably benign	Het
Xdh	C	A	17: 73,900,551	C937F	probably damaging	Het
Zfp846	T	A	9: 20,593,871	N342K	probably benign	Het

Other mutations in Kdm2b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00578:Kdm2b	APN	5	122961567	missense	probably damaging	1.00
IGL02061:Kdm2b	APN	5	122883341	missense	probably damaging	1.00
IGL02142:Kdm2b	APN	5	122947835	missense	probably damaging	0.99
IGL02143:Kdm2b	APN	5	122947835	missense	probably damaging	0.99
IGL02147:Kdm2b	APN	5	122947835	missense	probably damaging	0.99
IGL02294:Kdm2b	APN	5	122961474	missense	probably damaging	1.00
IGL02309:Kdm2b	APN	5	122947820	missense	probably damaging	0.99
IGL03039:Kdm2b	APN	5	122881671	missense	probably benign	0.06
IGL03134:Kdm2b	UTSW	5	122932674	missense	probably damaging	1.00
PIT4520001:Kdm2b	UTSW	5	122941047	missense	probably damaging	1.00
R0008:Kdm2b	UTSW	5	122881743	missense	probably benign	0.08
R0592:Kdm2b	UTSW	5	122961134	splice site	probably benign
R0894:Kdm2b	UTSW	5	122984460	critical splice donor site	probably null
R1078:Kdm2b	UTSW	5	122961541	missense	possibly damaging	0.83
R1387:Kdm2b	UTSW	5	122880268	missense	probably damaging	1.00
R1441:Kdm2b	UTSW	5	122932880	missense	probably benign	0.25
R1550:Kdm2b	UTSW	5	122881057	missense	probably damaging	1.00
R1795:Kdm2b	UTSW	5	122984460	critical splice donor site	probably null
R2060:Kdm2b	UTSW	5	122883365	missense	probably damaging	1.00
R2161:Kdm2b	UTSW	5	122880699	missense	probably damaging	1.00
R2259:Kdm2b	UTSW	5	122882416	missense	probably damaging	1.00
R3843:Kdm2b	UTSW	5	122934793	missense	probably damaging	0.98
R3844:Kdm2b	UTSW	5	122934793	missense	probably damaging	0.98
R3859:Kdm2b	UTSW	5	122880227	missense	probably damaging	1.00
R4506:Kdm2b	UTSW	5	122888625	missense	possibly damaging	0.58
R4680:Kdm2b	UTSW	5	122934786	missense	probably damaging	0.99
R4786:Kdm2b	UTSW	5	122880854	critical splice acceptor site	probably null
R4894:Kdm2b	UTSW	5	122940967	nonsense	probably null
R5265:Kdm2b	UTSW	5	122878588	missense	probably damaging	1.00
R5522:Kdm2b	UTSW	5	122949162	missense	probably damaging	1.00
R5746:Kdm2b	UTSW	5	122879364	missense	probably damaging	1.00
R5813:Kdm2b	UTSW	5	122871868	missense	probably benign	0.37
R5920:Kdm2b	UTSW	5	122880296	missense	probably damaging	1.00
R5961:Kdm2b	UTSW	5	122932661	missense	probably benign	0.37
R6029:Kdm2b	UTSW	5	122879587	missense	probably damaging	1.00
R6280:Kdm2b	UTSW	5	122878624	missense	probably damaging	1.00
R6303:Kdm2b	UTSW	5	122881744	missense	probably benign	0.34
R6304:Kdm2b	UTSW	5	122881744	missense	probably benign	0.34
R6383:Kdm2b	UTSW	5	122934778	missense	probably damaging	1.00
R6432:Kdm2b	UTSW	5	122880191	missense	probably damaging	1.00
R6513:Kdm2b	UTSW	5	122880239	missense	probably damaging	0.99
R7213:Kdm2b	UTSW	5	122921469	missense	probably damaging	0.99
R7226:Kdm2b	UTSW	5	122921449	missense	possibly damaging	0.60
R7292:Kdm2b	UTSW	5	122880791	missense	probably damaging	0.98
R7893:Kdm2b	UTSW	5	122947739	missense	probably benign	0.12
R8021:Kdm2b	UTSW	5	122932919	missense	probably damaging	0.99
R8038:Kdm2b	UTSW	5	122960895	intron	probably benign
R8162:Kdm2b	UTSW	5	122934793	missense	probably damaging	0.98
R8397:Kdm2b	UTSW	5	122880516	missense	probably benign	0.03
R8411:Kdm2b	UTSW	5	122880176	missense	probably damaging	1.00
Z1177:Kdm2b	UTSW	5	122880797	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- GCATCAGATCCAACTCTGCC -3'
(R):5'- AGCTCTGTAGGAGAAGCAGTTG -3'

Sequencing Primer
(F):5'- TAAGGGATCAGTCTCGGCCAC -3'
(R):5'- CTCCCTCGTGGCGTCTG -3'

Posted On

2018-06-06