Mutagenetix > Incidental Mutation

Incidental Mutation 'R1078:Kdm2b'

85726

Institutional Source

Beutler Lab

Gene Symbol

Kdm2b

Ensembl Gene

ENSMUSG00000029475

Gene Name

lysine (K)-specific demethylase 2B

Synonyms

Jhdm1b, Fbxl10, Cxxc2

MMRRC Submission

039164-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1078 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

122870665-122989823 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 122961541 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 118 (T118A)

Ref Sequence

ENSEMBL: ENSMUSP00000038229 (fasta)

Gene Model

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

AlphaFold

Q6P1G2

Predicted Effect

possibly damaging
Transcript: ENSMUST00000046073
AA Change: T118A

PolyPhen 2 Score 0.831 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000038229
Gene: ENSMUSG00000029475
AA Change: T118A

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 benign
Transcript: ENSMUST00000086200
AA Change: T112A

PolyPhen 2 Score 0.051 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000083376
Gene: ENSMUSG00000029475
AA Change: T112A

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 benign
Transcript: ENSMUST00000118027
AA Change: T118A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000114052
Gene: ENSMUSG00000029475
AA Change: T118A

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 benign
Transcript: ENSMUST00000121739
AA Change: T63A

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000114049
Gene: ENSMUSG00000029475
AA Change: T63A

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

silent
Transcript: ENSMUST00000127403

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134501

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150543

Predicted Effect

probably benign
Transcript: ENSMUST00000156474
AA Change: T112A

PolyPhen 2 Score 0.297 (Sensitivity: 0.91; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000118488
Gene: ENSMUSG00000029475
AA Change: T112A

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

Meta Mutation Damage Score

0.0831

Coding Region Coverage

1x: 99.7%
3x: 99.1%
10x: 97.4%
20x: 94.4%

Validation Efficiency

96% (53/55)

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610010F05Rik	A	C	11: 23,611,762	I358S	probably benign	Het
9130230L23Rik	T	C	5: 65,988,355	T138A	unknown	Het
Abi3bp	T	C	16: 56,654,081		probably null	Het
Alpk3	A	T	7: 81,078,600	M493L	probably benign	Het
Bace2	C	T	16: 97,356,860	A20V	unknown	Het
Bms1	T	C	6: 118,405,221	D452G	probably benign	Het
Ccdc187	T	C	2: 26,294,377	T3A	probably damaging	Het
Ctu2	T	C	8: 122,481,499	V95A	possibly damaging	Het
Cyp2a5	A	G	7: 26,835,541	K60E	probably benign	Het
Cyp4f13	T	C	17: 32,925,568	H318R	probably damaging	Het
Dlgap5	G	A	14: 47,399,566	T485M	probably damaging	Het
Dsp	C	T	13: 38,183,106		probably benign	Het
Ell2	T	C	13: 75,746,419		probably benign	Het
Eml2	A	T	7: 19,179,762	Y168F	probably benign	Het
Ep400	C	T	5: 110,735,522		probably benign	Het
Ercc4	C	A	16: 13,130,197	A336D	probably benign	Het
Fam189a2	T	A	19: 23,973,575	R547S	probably benign	Het
Fat4	T	C	3: 38,983,086	L3629S	probably benign	Het
Gabbr2	C	T	4: 46,664,833	R925H	probably damaging	Het
Gfi1b	A	T	2: 28,613,865	W108R	probably damaging	Het
Gtse1	C	T	15: 85,862,307	P108L	probably damaging	Het
Hfm1	A	T	5: 106,878,830	F140I	probably damaging	Het
Hyal2	T	A	9: 107,572,246	H400Q	probably benign	Het
Igfn1	A	G	1: 135,974,847	Y371H	probably damaging	Het
Iltifb	T	G	10: 118,290,151	*180C	probably null	Het
Lama5	A	T	2: 180,179,764		probably benign	Het
Lgr6	C	T	1: 134,994,010	A199T	probably damaging	Het
Lmo7	C	T	14: 101,920,474		probably benign	Het
Lrrc37a	G	T	11: 103,497,631	P2323T	unknown	Het
Lrrc38	A	G	4: 143,350,518	Y117C	probably benign	Het
Myo1e	T	C	9: 70,383,999	V1024A	probably benign	Het
Myrfl	T	C	10: 116,776,732	N904S	possibly damaging	Het
Olfr1015	T	C	2: 85,786,093	V194A	possibly damaging	Het
Olfr103	T	A	17: 37,337,026	I69F	probably damaging	Het
Olfr1297	T	C	2: 111,621,345	H243R	probably damaging	Het
Pld4	A	T	12: 112,763,442	I53F	probably benign	Het
Plekhg4	T	A	8: 105,381,677	C1117*	probably null	Het
Prss39	G	A	1: 34,502,086	E224K	probably benign	Het
Psme1	G	T	14: 55,580,650	G149V	probably damaging	Het
Soat2	T	A	15: 102,153,138		probably null	Het
Stab2	C	T	10: 86,907,133		probably null	Het
Tcf7l2	A	G	19: 55,743,195	T127A	probably benign	Het
Tcp1	T	C	17: 12,923,204		probably benign	Het
Thbs4	G	A	13: 92,762,926		probably benign	Het
Tmf1	T	C	6: 97,173,300	D482G	probably damaging	Het
Trim66	G	T	7: 109,472,319	P591H	probably damaging	Het
Umodl1	T	C	17: 30,959,373	S108P	probably benign	Het
Unc79	T	G	12: 103,074,853	M715R	probably benign	Het
Usp34	C	A	11: 23,433,175		probably benign	Het
Utrn	T	G	10: 12,455,566		probably null	Het
Zfp830	T	C	11: 82,765,339		probably null	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
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
R6526:Kdm2b	UTSW	5	122961469	missense	probably damaging	1.00
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
R8899:Kdm2b	UTSW	5	122987788	nonsense	probably null
R8997:Kdm2b	UTSW	5	122880173	missense	probably null	0.99
R9142:Kdm2b	UTSW	5	122989049	unclassified	probably benign
R9192:Kdm2b	UTSW	5	122932616	missense	probably benign	0.05
R9238:Kdm2b	UTSW	5	122871826	missense	probably damaging	0.98
R9455:Kdm2b	UTSW	5	122961474	missense	probably damaging	1.00
R9644:Kdm2b	UTSW	5	122982779	missense	probably damaging	0.98
R9731:Kdm2b	UTSW	5	122987760	missense	probably benign	0.03
Z1177:Kdm2b	UTSW	5	122880797	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- ATCCGTCATAAGCACACGGAGC -3'
(R):5'- ACAGTCACTGGCAGACTGGGAATAG -3'

Sequencing Primer
(F):5'- ATACCCTAAGGGATCAGTCTCGG -3'
(R):5'- TAGAGGTGACGCGAGTTGG -3'

Posted On

2013-11-18