Mutagenetix > Incidental Mutation

Incidental Mutation 'R8411:Kdm2b'

652670

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

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8411 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

122870665-122989823 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 122880176 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Histidine at position 1067 (R1067H)

Ref Sequence

ENSEMBL: ENSMUSP00000038229 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031435] [ENSMUST00000046073] [ENSMUST00000086200] [ENSMUST00000118027] [ENSMUST00000121739] [ENSMUST00000127403] [ENSMUST00000152872]

AlphaFold

Q6P1G2

Predicted Effect

probably damaging
Transcript: ENSMUST00000031435
AA Change: R534H

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

SMART Domains

Protein: ENSMUSP00000031435
Gene: ENSMUSG00000029475
AA Change: R534H

Domain	Start	End	E-Value	Type
Pfam:zf-CXXC	45	91	1.6e-17	PFAM
PHD	101	163	8.58e-4	SMART
low complexity region	259	290	N/A	INTRINSIC
low complexity region	370	380	N/A	INTRINSIC
low complexity region	457	473	N/A	INTRINSIC
low complexity region	485	499	N/A	INTRINSIC
FBOX	505	545	1.69e-2	SMART
LRR	588	610	1.31e2	SMART
LRR	612	637	2.9e2	SMART
LRR	652	676	2.04e2	SMART
LRR	677	702	1.1e1	SMART
LRR	732	757	3.91e1	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000046073
AA Change: R1067H

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000038229
Gene: ENSMUSG00000029475
AA Change: R1067H

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: R1061H

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

SMART Domains

Protein: ENSMUSP00000083376
Gene: ENSMUSG00000029475
AA Change: R1061H

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: R1029H

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

SMART Domains

Protein: ENSMUSP00000114052
Gene: ENSMUSG00000029475
AA Change: R1029H

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: R1012H

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000114049
Gene: ENSMUSG00000029475
AA Change: R1012H

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

probably benign
Transcript: ENSMUST00000127403

Predicted Effect

probably benign
Transcript: ENSMUST00000152872

SMART Domains

Protein: ENSMUSP00000119746
Gene: ENSMUSG00000029475

Domain	Start	End	E-Value	Type
PHD	25	87	8.58e-4	SMART
low complexity region	243	253	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2900026A02Rik	A	G	5: 113,137,722	S89P	probably benign	Het
Aatf	A	T	11: 84,470,676	M367K	probably benign	Het
Adam18	A	T	8: 24,652,127	I211N	probably damaging	Het
Angpt1	T	C	15: 42,427,034	Y478C	probably damaging	Het
Apba2	A	T	7: 64,736,926	I434F	probably damaging	Het
Arfgef1	T	A	1: 10,216,534	K50N	probably benign	Het
Arfgef2	A	T	2: 166,873,983	Q1397H	probably benign	Het
Ascc2	G	A	11: 4,647,208	R129Q	probably damaging	Het
Atxn1	A	G	13: 45,566,556	V621A	probably benign	Het
Catsperz	A	T	19: 6,922,562	L192M	probably benign	Het
Cd5	G	A	19: 10,720,221	P465S	probably damaging	Het
Cfap57	C	T	4: 118,614,931	V84I	probably benign	Het
Cfap61	A	G	2: 145,947,183	E94G	probably benign	Het
Chd1	A	G	17: 15,762,449	H1392R	probably damaging	Het
Csnk1a1	A	G	18: 61,555,817	I23V	probably benign	Het
Ctnnd2	C	T	15: 30,647,033	R292C	probably benign	Het
Dcaf6	T	A	1: 165,388,675	H453L	probably benign	Het
Dnah3	C	A	7: 120,011,030	D1728Y	probably damaging	Het
Dtx3	T	C	10: 127,192,824	K179E	possibly damaging	Het
Fam3b	T	A	16: 97,481,853	Y74F	probably benign	Het
Gm5464	T	C	14: 66,869,106	L64P	unknown	Het
Gm5624	T	G	14: 44,561,890	N70T		Het
Kcnh7	T	A	2: 62,764,608	H706L	probably damaging	Het
Klhl28	A	T	12: 64,950,090	H492Q	probably damaging	Het
Loxl3	T	A	6: 83,050,624	C716S	probably damaging	Het
Ltbp2	A	G	12: 84,786,413	Y1474H	probably damaging	Het
Mcm3	C	T	1: 20,816,756	V142I	probably benign	Het
Mmp24	G	T	2: 155,814,015	V458L	probably benign	Het
Mpl	C	A	4: 118,446,109	S502I		Het
Nfatc1	A	T	18: 80,667,042	V503D	probably damaging	Het
Nim1k	A	G	13: 119,714,271	I133T	possibly damaging	Het
Nr1d2	T	C	14: 18,215,031	Y327C	probably damaging	Het
Olfr1214	T	C	2: 88,988,065	T46A	probably benign	Het
Oma1	C	T	4: 103,328,916	R360*	probably null	Het
Oog2	T	A	4: 144,194,173	W59R	probably damaging	Het
Pcdh10	A	G	3: 45,379,539	E96G	probably damaging	Het
Pcna	T	A	2: 132,251,930	T98S	probably benign	Het
Pcnx3	C	T	19: 5,679,590	C899Y	possibly damaging	Het
Phf11d	T	C	14: 59,356,434	N97S	probably benign	Het
Plekhg4	G	A	8: 105,377,329	W431*	probably null	Het
Plk4	A	G	3: 40,813,466	T815A	probably benign	Het
Pnma2	C	T	14: 66,916,313	T62I	possibly damaging	Het
Ppp1r9a	C	T	6: 5,057,568	R548W	probably damaging	Het
Ptx3	A	G	3: 66,224,780	S241G	probably benign	Het
Repin1	G	T	6: 48,597,345	E403*	probably null	Het
Rplp0	A	T	5: 115,560,764	K26N	probably damaging	Het
Sec62	A	C	3: 30,818,782	E338A	unknown	Het
Sema6a	T	C	18: 47,248,955	M842V	probably benign	Het
Serpina3j	T	C	12: 104,314,784	V72A	probably benign	Het
Siglecf	T	C	7: 43,351,944	F112S	probably damaging	Het
Slc29a4	A	G	5: 142,720,125	N455D	probably damaging	Het
Slc6a11	T	A	6: 114,131,437	F54Y	probably benign	Het
Spag6	G	A	2: 18,710,583	V80M	probably damaging	Het
Spic	T	C	10: 88,678,636	E34G	possibly damaging	Het
Tecpr2	A	G	12: 110,931,720	K469E	possibly damaging	Het
Them7	T	A	2: 105,297,845	L57Q	probably benign	Het
Tlr3	G	A	8: 45,396,941	A897V	probably damaging	Het
Tnp2	A	G	16: 10,788,508	C32R	possibly damaging	Het
Trpm6	A	T	19: 18,853,968	Q1399L	probably benign	Het
Ttn	C	A	2: 76,846,671	E11074*	probably null	Het
Ubash3b	G	A	9: 41,043,485	A243V	probably benign	Het
Vash1	G	A	12: 86,680,178	R64Q	possibly damaging	Het
Vmn1r167	T	A	7: 23,505,556	M12L	possibly damaging	Het
Vmn2r111	T	A	17: 22,548,581	H645L	probably benign	Het
Vmn2r75	A	T	7: 86,148,514	I697K	probably damaging	Het
Vmn2r87	A	G	10: 130,472,257	I704T	probably damaging	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
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
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'- ACTCAGCTTAAACTAGAATGCTGG -3'
(R):5'- CACCCAAGTGCATCCAGATG -3'

Sequencing Primer
(F):5'- CGGCTGTAATTAGTCAATATGGGCAC -3'
(R):5'- ATGGAGCGTCACGTGATC -3'

Posted On

2020-10-20