Mutagenetix > Incidental Mutations

Incidental Mutation 'R1109:Kdm4b'

98694

Institutional Source

Beutler Lab

Gene Symbol

Kdm4b

Ensembl Gene

ENSMUSG00000024201

Gene Name

lysine (K)-specific demethylase 4B

Synonyms

Jmjd2b, 4732474L06Rik

MMRRC Submission

039182-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1109 (G1)

Quality Score

219

Status

Validated

Chromosome

Chromosomal Location

56326062-56402870 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 56399430 bp

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 848 (I848N)

Ref Sequence

ENSEMBL: ENSMUSP00000084045 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025036] [ENSMUST00000086835]

Predicted Effect

probably damaging
Transcript: ENSMUST00000025036
AA Change: I855N

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000025036
Gene: ENSMUSG00000024201
AA Change: I855N

Domain	Start	End	E-Value	Type
JmjN	14	56	5.88e-17	SMART
low complexity region	61	68	N/A	INTRINSIC
JmjC	143	309	1.19e-59	SMART
low complexity region	349	361	N/A	INTRINSIC
low complexity region	380	399	N/A	INTRINSIC
low complexity region	443	449	N/A	INTRINSIC
low complexity region	481	495	N/A	INTRINSIC
low complexity region	511	537	N/A	INTRINSIC
PHD	719	777	2.5e-5	SMART
PHD	839	895	7.07e-5	SMART
TUDOR	905	962	1.68e-9	SMART
TUDOR	963	1019	7.94e-11	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000086835
AA Change: I848N

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000084045
Gene: ENSMUSG00000024201
AA Change: I848N

Domain	Start	End	E-Value	Type
JmjN	14	56	5.88e-17	SMART
low complexity region	61	68	N/A	INTRINSIC
JmjC	143	309	1.19e-59	SMART
low complexity region	349	361	N/A	INTRINSIC
low complexity region	380	399	N/A	INTRINSIC
low complexity region	443	449	N/A	INTRINSIC
low complexity region	481	495	N/A	INTRINSIC
low complexity region	511	537	N/A	INTRINSIC
PHD	712	770	2.5e-5	SMART
PHD	832	888	7.07e-5	SMART
TUDOR	898	954	2.31e-12	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000141507
AA Change: I312N

SMART Domains

Protein: ENSMUSP00000116789
Gene: ENSMUSG00000024201
AA Change: I312N

Domain	Start	End	E-Value	Type
PHD	177	235	2.5e-5	SMART
PHD	297	353	7.07e-5	SMART
TUDOR	363	420	1.68e-9	SMART
TUDOR	421	477	7.94e-11	SMART

Meta Mutation Damage Score

0.8520

Coding Region Coverage

1x: 98.9%
3x: 98.0%
10x: 95.3%
20x: 88.9%

Validation Efficiency

100% (80/80)

MGI Phenotype

PHENOTYPE: Mice homozygous for a targeted allele lacking demethylase activity exhibit no gross abnormalities. Mice homozygous for a conditional allele activated in mammary gland epithelial cells exhibit delayed mammary gland development with reduced branching. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9030624J02Rik	A	T	7: 118,775,329	I351F	probably damaging	Het
Abcd3	T	G	3: 121,779,596	E262D	probably damaging	Het
Abcg1	G	A	17: 31,111,236	A504T	probably benign	Het
Acot11	T	C	4: 106,749,348	T515A	probably benign	Het
Alg8	A	T	7: 97,383,684		probably null	Het
Arhgap44	T	A	11: 65,026,816	H375L	probably benign	Het
Aspm	A	T	1: 139,456,758	I98F	probably damaging	Het
Atp8b5	T	C	4: 43,305,719		probably benign	Het
Ccdc129	G	T	6: 55,968,260	K655N	probably damaging	Het
Coa3	T	C	11: 101,278,785	K48R	probably damaging	Het
Col12a1	A	G	9: 79,699,723	S473P	probably damaging	Het
Dnmt1	A	T	9: 20,922,388	Y451N	probably damaging	Het
Dock5	A	G	14: 67,806,478	Y819H	possibly damaging	Het
Dtx1	G	A	5: 120,710,419		probably benign	Het
Dus2	T	A	8: 106,053,482	F479I	probably benign	Het
Esrp1	T	C	4: 11,365,205	E262G	probably damaging	Het
Exoc4	A	G	6: 33,442,016	Y466C	probably damaging	Het
Fasn	A	G	11: 120,812,324	F1625S	possibly damaging	Het
Fbxw25	A	T	9: 109,650,060	H374Q	probably benign	Het
Focad	T	C	4: 88,196,747		probably benign	Het
Gad2	G	T	2: 22,681,394	R448L	probably damaging	Het
Gad2	G	A	2: 22,690,159		probably benign	Het
Galnt16	G	T	12: 80,590,631	E377D	probably benign	Het
Gcc1	A	C	6: 28,419,167	L389R	probably damaging	Het
Ggct	A	T	6: 54,989,569		probably benign	Het
Gm7052	G	A	17: 22,040,152		probably benign	Het
Gps2	T	A	11: 69,915,681	H177Q	possibly damaging	Het
Heg1	T	A	16: 33,763,591	L1256Q	probably damaging	Het
Ikbkap	T	C	4: 56,786,723	T407A	probably benign	Het
Il1f6	G	A	2: 24,216,590	G62E	probably damaging	Het
Il3ra	C	T	14: 14,349,317	R138W	probably damaging	Het
L3hypdh	A	G	12: 72,073,996	V327A	possibly damaging	Het
Lepr	G	T	4: 101,771,355	L552F	probably damaging	Het
Lpin3	T	C	2: 160,899,021	I449T	probably damaging	Het
Lrrn1	A	G	6: 107,567,264	K8E	probably benign	Het
Mex3a	G	T	3: 88,536,660	D348Y	possibly damaging	Het
Mindy2	G	A	9: 70,631,079	R325*	probably null	Het
Mkrn1	A	T	6: 39,399,334	M382K	probably damaging	Het
Mroh1	G	T	15: 76,446,509		probably benign	Het
Myo15	T	A	11: 60,493,066	D1646E	probably damaging	Het
Neu2	A	G	1: 87,596,728	D145G	probably damaging	Het
Olfr317	T	C	11: 58,732,916	Y83C	probably benign	Het
Olfr718-ps1	A	T	5: 143,137,619	N216K	probably benign	Het
Olfr743	T	C	14: 50,533,702	S97P	possibly damaging	Het
Plekhm2	T	A	4: 141,627,984	I938F	probably benign	Het
Pnmal1	A	T	7: 16,961,467	K416*	probably null	Het
Ppid	T	C	3: 79,598,861	S198P	probably benign	Het
Rabl6	G	T	2: 25,587,526	P304Q	probably damaging	Het
Rasal2	A	T	1: 157,177,638		probably benign	Het
Ripor1	G	T	8: 105,618,928		probably benign	Het
Rnf216	A	T	5: 143,068,369	L658Q	probably damaging	Het
Rnf219	A	T	14: 104,479,764	L391*	probably null	Het
Safb	T	A	17: 56,601,228		probably benign	Het
Sf3b5	T	C	10: 13,008,753	M44T	probably benign	Het
Slc26a9	A	T	1: 131,758,798	M419L	probably benign	Het
Slc38a8	T	C	8: 119,482,655	D393G	probably benign	Het
Slc6a3	A	G	13: 73,557,080	D230G	probably benign	Het
Smc1b	T	C	15: 85,112,815	T535A	probably damaging	Het
Smg7	G	C	1: 152,845,583	P626R	probably damaging	Het
Smu1	C	T	4: 40,755,722	V48M	probably benign	Het
Spag17	T	C	3: 100,027,351	Y650H	possibly damaging	Het
Spata1	C	T	3: 146,475,298	V302I	possibly damaging	Het
Sptb	G	A	12: 76,603,603	A1780V	probably damaging	Het
Srrm2	G	A	17: 23,819,617		probably benign	Het
Sspo	A	C	6: 48,497,443	N4933H	probably damaging	Het
Sult2a2	T	C	7: 13,734,873	I88T	probably benign	Het
Tgfa	G	T	6: 86,270,090		probably benign	Het
Thsd1	T	A	8: 22,243,692	C252S	possibly damaging	Het
Tmem102	T	A	11: 69,804,804	H114L	probably damaging	Het
Tnni3k	T	A	3: 154,792,777	K808N	possibly damaging	Het
Trpm7	G	T	2: 126,797,793	L1628M	probably benign	Het
Ttn	A	G	2: 76,730,737	Y29107H	probably damaging	Het
Upb1	T	C	10: 75,438,165	L342P	probably damaging	Het
Vmn2r120	T	C	17: 57,525,829	T117A	probably benign	Het
Vmn2r16	A	G	5: 109,339,786	D175G	probably damaging	Het
Zfhx4	T	G	3: 5,399,870	M1696R	possibly damaging	Het
Zfp746	A	G	6: 48,064,922	V289A	possibly damaging	Het
Zfyve26	A	C	12: 79,272,127	F1146V	probably damaging	Het

Other mutations in Kdm4b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01293:Kdm4b	APN	17	56353019	missense	probably benign	0.28
IGL01408:Kdm4b	APN	17	56353518	splice site	probably benign
IGL01610:Kdm4b	APN	17	56353522	splice site	probably benign
IGL01936:Kdm4b	APN	17	56397355	missense	probably damaging	1.00
IGL01964:Kdm4b	APN	17	56389256	splice site	probably null
IGL02151:Kdm4b	APN	17	56396234	missense	probably benign	0.05
IGL02596:Kdm4b	APN	17	56399706	missense	probably benign	0.14
IGL02975:Kdm4b	APN	17	56375996	splice site	probably null
IGL03172:Kdm4b	APN	17	56401649	missense	probably damaging	0.98
Coelestinum	UTSW	17	56353091	missense	probably benign	0.31
mistflower	UTSW	17	56389564	missense	possibly damaging	0.65
R0193:Kdm4b	UTSW	17	56393952	missense	probably benign	0.04
R0311:Kdm4b	UTSW	17	56386200	missense	probably benign	0.42
R0331:Kdm4b	UTSW	17	56386289	splice site	probably benign
R1499:Kdm4b	UTSW	17	56400025	missense	probably damaging	1.00
R1895:Kdm4b	UTSW	17	56397340	missense	probably damaging	1.00
R1985:Kdm4b	UTSW	17	56401302	missense	probably damaging	1.00
R2087:Kdm4b	UTSW	17	56389564	missense	possibly damaging	0.65
R2185:Kdm4b	UTSW	17	56393750	missense	probably benign	0.00
R2904:Kdm4b	UTSW	17	56355884	missense	probably benign	0.03
R3792:Kdm4b	UTSW	17	56355944	missense	probably damaging	1.00
R3897:Kdm4b	UTSW	17	56396955	missense	probably damaging	1.00
R4661:Kdm4b	UTSW	17	56399459	missense	probably damaging	1.00
R4685:Kdm4b	UTSW	17	56401675	missense	probably benign	0.06
R4716:Kdm4b	UTSW	17	56386178	missense	probably benign	0.10
R4790:Kdm4b	UTSW	17	56401618	missense	probably damaging	0.97
R4864:Kdm4b	UTSW	17	56353091	missense	probably benign	0.31
R5700:Kdm4b	UTSW	17	56351700	missense	possibly damaging	0.93
R5963:Kdm4b	UTSW	17	56399732	missense	probably damaging	1.00
R6003:Kdm4b	UTSW	17	56396916	missense	probably damaging	1.00
R6029:Kdm4b	UTSW	17	56396576	missense	probably damaging	0.98
R6769:Kdm4b	UTSW	17	56351754	missense	possibly damaging	0.54
R6771:Kdm4b	UTSW	17	56351754	missense	possibly damaging	0.54
R6927:Kdm4b	UTSW	17	56399435	missense	probably damaging	1.00
R7041:Kdm4b	UTSW	17	56396592	missense	probably damaging	0.96
R7230:Kdm4b	UTSW	17	56369155	missense	probably damaging	1.00
R7275:Kdm4b	UTSW	17	56396333	missense	probably damaging	0.99
R7454:Kdm4b	UTSW	17	56389639	missense	probably benign	0.00
R7455:Kdm4b	UTSW	17	56396657	missense	probably damaging	0.98
R7457:Kdm4b	UTSW	17	56396319	missense	probably damaging	1.00
X0024:Kdm4b	UTSW	17	56401278	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATCAAGCTCCAGTCGTGTCCTGTC -3'
(R):5'- GCCATCGTCAAAGTTGACCTCGTAG -3'

Sequencing Primer
(F):5'- AGTCGTGTCCTGTCCAGTC -3'
(R):5'- CGATAGTAGAGCCCATTGCG -3'

Posted On

2014-01-05