Mutagenetix > Incidental Mutation

Incidental Mutation 'R5265:Kdm2b'

401644

Institutional Source

Beutler Lab

Gene Symbol

Kdm2b

Ensembl Gene

ENSMUSG00000029475

Gene Name

lysine (K)-specific demethylase 2B

Synonyms

Jhdm1b, Fbxl10, Cxxc2

MMRRC Submission

042833-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5265 (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 122878588 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 1161 (T1161A)

Ref Sequence

ENSEMBL: ENSMUSP00000114052 (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: T666A

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

SMART Domains

Protein: ENSMUSP00000031435
Gene: ENSMUSG00000029475
AA Change: T666A

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: T1199A

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000038229
Gene: ENSMUSG00000029475
AA Change: T1199A

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

possibly damaging
Transcript: ENSMUST00000086200
AA Change: T1193A

PolyPhen 2 Score 0.805 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000083376
Gene: ENSMUSG00000029475
AA Change: T1193A

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: T1161A

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

SMART Domains

Protein: ENSMUSP00000114052
Gene: ENSMUSG00000029475
AA Change: T1161A

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

possibly damaging
Transcript: ENSMUST00000121739
AA Change: T1144A

PolyPhen 2 Score 0.882 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000114049
Gene: ENSMUSG00000029475
AA Change: T1144A

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

noncoding transcript
Transcript: ENSMUST00000129998

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132419

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139674

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173355

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174357

Meta Mutation Damage Score

0.8454

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.7%

Validation Efficiency

100% (59/59)

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: 56 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017B05Rik	A	G	9: 57,258,894	W66R	probably damaging	Het
Adamts3	A	G	5: 89,861,552	V84A	possibly damaging	Het
Caap1	C	A	4: 94,501,228	E290*	probably null	Het
Cant1	G	A	11: 118,408,050	R296C	probably damaging	Het
Ccdc114	T	A	7: 45,947,435	D395E	probably damaging	Het
Cdh5	A	T	8: 104,142,739	H699L	probably benign	Het
Cfdp1	T	C	8: 111,830,985	T175A	probably benign	Het
Col4a4	C	T	1: 82,493,591	G681E	unknown	Het
Comtd1	G	A	14: 21,848,793	T27I	probably benign	Het
Copg1	T	A	6: 87,892,270	V155D	probably damaging	Het
Dag1	A	G	9: 108,207,699	Y748H	possibly damaging	Het
Dmwd	T	A	7: 19,080,281	N285K	possibly damaging	Het
Dsp	A	G	13: 38,195,183	E1968G	possibly damaging	Het
Ednra	A	G	8: 77,667,375	I364T	probably damaging	Het
Elovl3	C	A	19: 46,134,681	T232K	probably damaging	Het
Ercc3	T	A	18: 32,254,243	I503N	probably damaging	Het
Ercc6	C	A	14: 32,569,623	A1008D	probably benign	Het
Gm10563	TTTC	TTTCATTC	4: 155,614,496		probably null	Het
H2-DMb2	G	T	17: 34,148,562	V117F	probably damaging	Het
Helt	A	T	8: 46,292,433	W138R	probably damaging	Het
Itga11	A	T	9: 62,737,412	H215L	probably benign	Het
Kcnn1	T	A	8: 70,854,653	I156F	probably benign	Het
Kdm1b	A	G	13: 47,062,969	N272D	probably benign	Het
Lin54	A	G	5: 100,485,519	L102P	probably damaging	Het
Mlh1	A	C	9: 111,271,523	M1R	probably null	Het
Naip2	G	A	13: 100,152,560	L1165F	probably damaging	Het
Nfkbiz	A	G	16: 55,819,641	S118P	probably damaging	Het
Nkx3-2	T	A	5: 41,761,848	M266L	probably benign	Het
Npr1	T	C	3: 90,457,002	E771G	probably benign	Het
Obox8	C	T	7: 14,332,029	R188H	probably benign	Het
Olfr187	A	T	16: 59,036,143	V198D	possibly damaging	Het
Olfr497	T	A	7: 108,423,402	V277E	possibly damaging	Het
Palm3	T	C	8: 84,021,530		probably null	Het
Palmd	A	T	3: 116,923,849	V333D	possibly damaging	Het
Pikfyve	A	G	1: 65,267,829	E1747G	possibly damaging	Het
Polr3a	T	C	14: 24,454,941	I1084V	possibly damaging	Het
Ranbp3l	T	A	15: 9,007,203	F127I	probably benign	Het
Rsl1d1	A	G	16: 11,201,384	F97L	possibly damaging	Het
Scaper	A	G	9: 55,864,546	V362A	probably benign	Het
Scg5	A	T	2: 113,776,865	L192*	probably null	Het
Slc34a2	T	C	5: 53,061,434	I198T	probably damaging	Het
Slc45a3	T	A	1: 131,978,194	D318E	possibly damaging	Het
Sorl1	A	G	9: 42,106,516	M105T	possibly damaging	Het
St3gal5	T	A	6: 72,149,131	I320N	probably damaging	Het
Stx17	A	G	4: 48,183,470		probably benign	Het
Syt5	C	T	7: 4,541,075		probably null	Het
Thrap3	A	G	4: 126,167,640	S774P	probably damaging	Het
Tnc	A	T	4: 63,993,206	M1376K	probably benign	Het
Tnks1bp1	T	A	2: 85,062,754	D1008E	probably benign	Het
Trav7-1	G	T	14: 52,655,304	A105S	probably damaging	Het
Vmn1r28	T	A	6: 58,265,964	V264D	probably damaging	Het
Vmn1r44	T	C	6: 89,893,839	V46A	probably benign	Het
Vmn2r10	A	G	5: 108,995,720	I788T	probably damaging	Het
Vmn2r78	T	A	7: 86,920,124	I75N	probably damaging	Het
Zfp821	T	C	8: 109,724,359	M328T	probably damaging	Het
Zfp995	G	A	17: 21,880,623	P210L	possibly 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
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'- AACCGCTGTAACCAGATACTG -3'
(R):5'- CTGATGTGGAAGCTTCTAAGGATG -3'

Sequencing Primer
(F):5'- AGATACTGGGGCCCACCTC -3'
(R):5'- AAGCTTCTAAGGATGAGATTCTGGC -3'

Posted On

2016-07-06