Mutagenetix > Incidental Mutation

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

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1109 (G1)

Quality Score

219

Status

Validated

Chromosome

Chromosomal Location

56633062-56709870 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 56706430 bp (GRCm39)

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]

AlphaFold

Q91VY5

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
Abcd3	T	G	3: 121,573,245 (GRCm39)	E262D	probably damaging	Het
Abcg1	G	A	17: 31,330,210 (GRCm39)	A504T	probably benign	Het
Acot11	T	C	4: 106,606,545 (GRCm39)	T515A	probably benign	Het
Alg8	A	T	7: 97,032,891 (GRCm39)		probably null	Het
Arhgap44	T	A	11: 64,917,642 (GRCm39)	H375L	probably benign	Het
Aspm	A	T	1: 139,384,496 (GRCm39)	I98F	probably damaging	Het
Atp8b5	T	C	4: 43,305,719 (GRCm39)		probably benign	Het
Coa3	T	C	11: 101,169,611 (GRCm39)	K48R	probably damaging	Het
Col12a1	A	G	9: 79,607,005 (GRCm39)	S473P	probably damaging	Het
Dnmt1	A	T	9: 20,833,684 (GRCm39)	Y451N	probably damaging	Het
Dock5	A	G	14: 68,043,927 (GRCm39)	Y819H	possibly damaging	Het
Dtx1	G	A	5: 120,848,484 (GRCm39)		probably benign	Het
Dus2	T	A	8: 106,780,114 (GRCm39)	F479I	probably benign	Het
Elp1	T	C	4: 56,786,723 (GRCm39)	T407A	probably benign	Het
Esrp1	T	C	4: 11,365,205 (GRCm39)	E262G	probably damaging	Het
Exoc4	A	G	6: 33,418,951 (GRCm39)	Y466C	probably damaging	Het
Fasn	A	G	11: 120,703,150 (GRCm39)	F1625S	possibly damaging	Het
Fbxw25	A	T	9: 109,479,128 (GRCm39)	H374Q	probably benign	Het
Focad	T	C	4: 88,114,984 (GRCm39)		probably benign	Het
Gad2	G	T	2: 22,571,406 (GRCm39)	R448L	probably damaging	Het
Gad2	G	A	2: 22,580,171 (GRCm39)		probably benign	Het
Galnt16	G	T	12: 80,637,405 (GRCm39)	E377D	probably benign	Het
Gcc1	A	C	6: 28,419,166 (GRCm39)	L389R	probably damaging	Het
Ggct	A	T	6: 54,966,554 (GRCm39)		probably benign	Het
Gm7052	G	A	17: 22,259,133 (GRCm39)		probably benign	Het
Gps2	T	A	11: 69,806,507 (GRCm39)	H177Q	possibly damaging	Het
Heg1	T	A	16: 33,583,961 (GRCm39)	L1256Q	probably damaging	Het
Il36a	G	A	2: 24,106,602 (GRCm39)	G62E	probably damaging	Het
Il3ra	C	T	14: 14,349,317 (GRCm38)	R138W	probably damaging	Het
Itprid1	G	T	6: 55,945,245 (GRCm39)	K655N	probably damaging	Het
L3hypdh	A	G	12: 72,120,770 (GRCm39)	V327A	possibly damaging	Het
Lepr	G	T	4: 101,628,552 (GRCm39)	L552F	probably damaging	Het
Lpin3	T	C	2: 160,740,941 (GRCm39)	I449T	probably damaging	Het
Lrrn1	A	G	6: 107,544,225 (GRCm39)	K8E	probably benign	Het
Mex3a	G	T	3: 88,443,967 (GRCm39)	D348Y	possibly damaging	Het
Mindy2	G	A	9: 70,538,361 (GRCm39)	R325*	probably null	Het
Mkrn1	A	T	6: 39,376,268 (GRCm39)	M382K	probably damaging	Het
Mroh1	G	T	15: 76,330,709 (GRCm39)		probably benign	Het
Myo15a	T	A	11: 60,383,892 (GRCm39)	D1646E	probably damaging	Het
Neu2	A	G	1: 87,524,450 (GRCm39)	D145G	probably damaging	Het
Obi1	A	T	14: 104,717,200 (GRCm39)	L391*	probably null	Het
Or10ah1-ps1	A	T	5: 143,123,374 (GRCm39)	N216K	probably benign	Het
Or11g27	T	C	14: 50,771,159 (GRCm39)	S97P	possibly damaging	Het
Or2w3b	T	C	11: 58,623,742 (GRCm39)	Y83C	probably benign	Het
Plekhm2	T	A	4: 141,355,295 (GRCm39)	I938F	probably benign	Het
Pnma8a	A	T	7: 16,695,392 (GRCm39)	K416*	probably null	Het
Ppid	T	C	3: 79,506,168 (GRCm39)	S198P	probably benign	Het
Rabl6	G	T	2: 25,477,538 (GRCm39)	P304Q	probably damaging	Het
Rasal2	A	T	1: 157,005,208 (GRCm39)		probably benign	Het
Ripor1	G	T	8: 106,345,560 (GRCm39)		probably benign	Het
Rnf216	A	T	5: 143,054,124 (GRCm39)	L658Q	probably damaging	Het
Safb	T	A	17: 56,908,228 (GRCm39)		probably benign	Het
Sf3b5	T	C	10: 12,884,497 (GRCm39)	M44T	probably benign	Het
Slc26a9	A	T	1: 131,686,536 (GRCm39)	M419L	probably benign	Het
Slc38a8	T	C	8: 120,209,394 (GRCm39)	D393G	probably benign	Het
Slc6a3	A	G	13: 73,705,199 (GRCm39)	D230G	probably benign	Het
Smc1b	T	C	15: 84,997,016 (GRCm39)	T535A	probably damaging	Het
Smg7	G	C	1: 152,721,334 (GRCm39)	P626R	probably damaging	Het
Smu1	C	T	4: 40,755,722 (GRCm39)	V48M	probably benign	Het
Spag17	T	C	3: 99,934,667 (GRCm39)	Y650H	possibly damaging	Het
Spata1	C	T	3: 146,181,053 (GRCm39)	V302I	possibly damaging	Het
Sptb	G	A	12: 76,650,377 (GRCm39)	A1780V	probably damaging	Het
Srrm2	G	A	17: 24,038,591 (GRCm39)		probably benign	Het
Sspo	A	C	6: 48,474,377 (GRCm39)	N4933H	probably damaging	Het
Sult2a2	T	C	7: 13,468,798 (GRCm39)	I88T	probably benign	Het
Tgfa	G	T	6: 86,247,072 (GRCm39)		probably benign	Het
Thsd1	T	A	8: 22,733,708 (GRCm39)	C252S	possibly damaging	Het
Tmem102	T	A	11: 69,695,630 (GRCm39)	H114L	probably damaging	Het
Tnni3k	T	A	3: 154,498,414 (GRCm39)	K808N	possibly damaging	Het
Trpm7	G	T	2: 126,639,713 (GRCm39)	L1628M	probably benign	Het
Ttn	A	G	2: 76,561,081 (GRCm39)	Y29107H	probably damaging	Het
Upb1	T	C	10: 75,273,999 (GRCm39)	L342P	probably damaging	Het
Vmn2r120	T	C	17: 57,832,829 (GRCm39)	T117A	probably benign	Het
Vmn2r16	A	G	5: 109,487,652 (GRCm39)	D175G	probably damaging	Het
Vps35l	A	T	7: 118,374,552 (GRCm39)	I351F	probably damaging	Het
Zfhx4	T	G	3: 5,464,930 (GRCm39)	M1696R	possibly damaging	Het
Zfp746	A	G	6: 48,041,856 (GRCm39)	V289A	possibly damaging	Het
Zfyve26	A	C	12: 79,318,901 (GRCm39)	F1146V	probably damaging	Het

Other mutations in Kdm4b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01293:Kdm4b	APN	17	56,660,019 (GRCm39)	missense	probably benign	0.28
IGL01408:Kdm4b	APN	17	56,660,518 (GRCm39)	splice site	probably benign
IGL01610:Kdm4b	APN	17	56,660,522 (GRCm39)	splice site	probably benign
IGL01936:Kdm4b	APN	17	56,704,355 (GRCm39)	missense	probably damaging	1.00
IGL01964:Kdm4b	APN	17	56,696,256 (GRCm39)	splice site	probably null
IGL02151:Kdm4b	APN	17	56,703,234 (GRCm39)	missense	probably benign	0.05
IGL02596:Kdm4b	APN	17	56,706,706 (GRCm39)	missense	probably benign	0.14
IGL02975:Kdm4b	APN	17	56,682,996 (GRCm39)	splice site	probably null
IGL03172:Kdm4b	APN	17	56,708,649 (GRCm39)	missense	probably damaging	0.98
Coelestinum	UTSW	17	56,660,091 (GRCm39)	missense	probably benign	0.31
mistflower	UTSW	17	56,696,564 (GRCm39)	missense	possibly damaging	0.65
R0193:Kdm4b	UTSW	17	56,700,952 (GRCm39)	missense	probably benign	0.04
R0311:Kdm4b	UTSW	17	56,693,200 (GRCm39)	missense	probably benign	0.42
R0331:Kdm4b	UTSW	17	56,693,289 (GRCm39)	splice site	probably benign
R1499:Kdm4b	UTSW	17	56,707,025 (GRCm39)	missense	probably damaging	1.00
R1895:Kdm4b	UTSW	17	56,704,340 (GRCm39)	missense	probably damaging	1.00
R1985:Kdm4b	UTSW	17	56,708,302 (GRCm39)	missense	probably damaging	1.00
R2087:Kdm4b	UTSW	17	56,696,564 (GRCm39)	missense	possibly damaging	0.65
R2185:Kdm4b	UTSW	17	56,700,750 (GRCm39)	missense	probably benign	0.00
R2904:Kdm4b	UTSW	17	56,662,884 (GRCm39)	missense	probably benign	0.03
R3792:Kdm4b	UTSW	17	56,662,944 (GRCm39)	missense	probably damaging	1.00
R3897:Kdm4b	UTSW	17	56,703,955 (GRCm39)	missense	probably damaging	1.00
R4661:Kdm4b	UTSW	17	56,706,459 (GRCm39)	missense	probably damaging	1.00
R4685:Kdm4b	UTSW	17	56,708,675 (GRCm39)	missense	probably benign	0.06
R4716:Kdm4b	UTSW	17	56,693,178 (GRCm39)	missense	probably benign	0.10
R4790:Kdm4b	UTSW	17	56,708,618 (GRCm39)	missense	probably damaging	0.97
R4864:Kdm4b	UTSW	17	56,660,091 (GRCm39)	missense	probably benign	0.31
R5700:Kdm4b	UTSW	17	56,658,700 (GRCm39)	missense	possibly damaging	0.93
R5963:Kdm4b	UTSW	17	56,706,732 (GRCm39)	missense	probably damaging	1.00
R6003:Kdm4b	UTSW	17	56,703,916 (GRCm39)	missense	probably damaging	1.00
R6029:Kdm4b	UTSW	17	56,703,576 (GRCm39)	missense	probably damaging	0.98
R6769:Kdm4b	UTSW	17	56,658,754 (GRCm39)	missense	possibly damaging	0.54
R6771:Kdm4b	UTSW	17	56,658,754 (GRCm39)	missense	possibly damaging	0.54
R6927:Kdm4b	UTSW	17	56,706,435 (GRCm39)	missense	probably damaging	1.00
R7041:Kdm4b	UTSW	17	56,703,592 (GRCm39)	missense	probably damaging	0.96
R7230:Kdm4b	UTSW	17	56,676,155 (GRCm39)	missense	probably damaging	1.00
R7275:Kdm4b	UTSW	17	56,703,333 (GRCm39)	missense	probably damaging	0.99
R7454:Kdm4b	UTSW	17	56,696,639 (GRCm39)	missense	probably benign	0.00
R7455:Kdm4b	UTSW	17	56,703,657 (GRCm39)	missense	probably damaging	0.98
R7457:Kdm4b	UTSW	17	56,703,319 (GRCm39)	missense	probably damaging	1.00
R8171:Kdm4b	UTSW	17	56,696,534 (GRCm39)	missense	probably damaging	0.99
R8367:Kdm4b	UTSW	17	56,662,875 (GRCm39)	missense	probably damaging	1.00
R8524:Kdm4b	UTSW	17	56,706,384 (GRCm39)	missense	probably damaging	1.00
R8810:Kdm4b	UTSW	17	56,706,771 (GRCm39)	missense	probably damaging	1.00
R9260:Kdm4b	UTSW	17	56,701,775 (GRCm39)	missense	probably benign
R9459:Kdm4b	UTSW	17	56,706,509 (GRCm39)	missense	probably benign	0.15
R9466:Kdm4b	UTSW	17	56,696,548 (GRCm39)	missense	probably benign	0.04
R9559:Kdm4b	UTSW	17	56,693,228 (GRCm39)	missense	probably damaging	1.00
X0024:Kdm4b	UTSW	17	56,708,278 (GRCm39)	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