Mutagenetix > Incidental Mutation

Incidental Mutation 'R0220:Kdm4d'

33791

Institutional Source

Beutler Lab

Gene Symbol

Kdm4d

Ensembl Gene

ENSMUSG00000053914

Gene Name

lysine (K)-specific demethylase 4D

Synonyms

Jmjd2d

MMRRC Submission

038469-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0220 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

14373844-14411778 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 14374418 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glutamic Acid at position 480 (V480E)

Ref Sequence

ENSEMBL: ENSMUSP00000061632 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000058796] [ENSMUST00000115647]

AlphaFold

Q3U2K5

Predicted Effect

probably benign
Transcript: ENSMUST00000058796
AA Change: V480E

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

SMART Domains

Protein: ENSMUSP00000061632
Gene: ENSMUSG00000053914
AA Change: V480E

Domain	Start	End	E-Value	Type
Pfam:JmjN	16	50	3.3e-15	PFAM
JmjC	143	309	2.3e-57	SMART
low complexity region	370	383	N/A	INTRINSIC
low complexity region	417	434	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000115647

SMART Domains

Protein: ENSMUSP00000111311
Gene: ENSMUSG00000053914

Domain	Start	End	E-Value	Type
Pfam:JmjN	16	50	1.1e-16	PFAM
JmjC	143	309	2.3e-57	SMART
low complexity region	370	383	N/A	INTRINSIC
low complexity region	417	434	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 96.9%
20x: 94.6%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele exhibit accumulation of histone 3 methylation in spermatids, a transient increase in testes size, wider tubules, occasional male germ cell apoptosis, and decreased body weight. However, fertility is normal. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	T	C	12: 71,195,194 (GRCm39)		probably null	Het
Abcc5	A	G	16: 20,187,852 (GRCm39)	V863A	probably benign	Het
Anxa6	A	C	11: 54,872,588 (GRCm39)		probably null	Het
Armc10	A	G	5: 21,866,582 (GRCm39)	K296R	probably benign	Het
Arpc2	T	A	1: 74,287,293 (GRCm39)	F38I	probably damaging	Het
Ass1	A	T	2: 31,404,831 (GRCm39)	N371Y	probably damaging	Het
Bcl6	T	A	16: 23,784,969 (GRCm39)	H677L	possibly damaging	Het
Bcl7a	G	A	5: 123,489,982 (GRCm39)	V49I	probably damaging	Het
Ccnj	T	C	19: 40,833,254 (GRCm39)	L144P	probably damaging	Het
Cdh8	G	T	8: 99,838,311 (GRCm39)	P510T	probably benign	Het
Cgnl1	C	A	9: 71,632,225 (GRCm39)	K375N	possibly damaging	Het
Cubn	C	A	2: 13,361,520 (GRCm39)	R1695L	probably damaging	Het
Cyp3a59	G	A	5: 146,035,080 (GRCm39)	V253I	probably benign	Het
Cyp4f13	A	G	17: 33,148,476 (GRCm39)	I208T	probably damaging	Het
Dennd4a	A	C	9: 64,759,727 (GRCm39)	E277D	probably damaging	Het
Depdc1a	G	A	3: 159,229,542 (GRCm39)	V625I	probably benign	Het
Dot1l	A	T	10: 80,621,692 (GRCm39)	D448V	probably damaging	Het
Efhc1	A	G	1: 21,037,582 (GRCm39)	D253G	probably damaging	Het
Eme1	T	A	11: 94,541,084 (GRCm39)	E246V	probably null	Het
Foxred1	A	G	9: 35,120,749 (GRCm39)	L128P	probably damaging	Het
Gm4787	G	T	12: 81,425,422 (GRCm39)	S245R	probably damaging	Het
Gm5141	T	A	13: 62,922,271 (GRCm39)	K299N	probably damaging	Het
Greb1	C	A	12: 16,732,287 (GRCm39)	R1558L	probably damaging	Het
Ip6k3	A	T	17: 27,364,203 (GRCm39)	F282I	probably damaging	Het
Kdm2a	T	C	19: 4,374,947 (GRCm39)	D288G	possibly damaging	Het
Kif26a	A	T	12: 112,123,824 (GRCm39)	Q143L	probably damaging	Het
Klhl41	G	A	2: 69,500,829 (GRCm39)	D97N	probably benign	Het
Krt34	C	T	11: 99,929,519 (GRCm39)		probably benign	Het
Lcn11	A	T	2: 25,667,843 (GRCm39)	H77L	probably benign	Het
Megf6	G	A	4: 154,342,672 (GRCm39)	R529H	probably damaging	Het
Mipol1	A	G	12: 57,503,936 (GRCm39)	E368G	probably damaging	Het
Mtus1	A	T	8: 41,447,609 (GRCm39)	M442K	probably damaging	Het
Naca	T	C	10: 127,879,255 (GRCm39)		probably benign	Het
Nbea	G	A	3: 55,912,724 (GRCm39)	T1021I	probably benign	Het
Nfib	A	T	4: 82,215,013 (GRCm39)	V530E	probably damaging	Het
Nptx1	A	G	11: 119,435,467 (GRCm39)	V283A	probably damaging	Het
Opn5	A	G	17: 42,907,495 (GRCm39)	V127A	probably benign	Het
Or4c126	G	T	2: 89,824,206 (GRCm39)	L156F	probably benign	Het
Or5h22	A	T	16: 58,895,095 (GRCm39)	M116K	probably damaging	Het
Pcgf6	A	G	19: 47,028,529 (GRCm39)	V291A	probably benign	Het
Pilrb2	C	A	5: 137,869,459 (GRCm39)	R47L	probably benign	Het
Prom2	A	C	2: 127,383,027 (GRCm39)	S72A	probably benign	Het
Sema3e	T	C	5: 14,214,167 (GRCm39)	F144S	possibly damaging	Het
Sephs1	A	G	2: 4,904,371 (GRCm39)	T250A	probably benign	Het
Smarcc2	A	T	10: 128,319,505 (GRCm39)	D798V	probably benign	Het
Taf5	T	C	19: 47,068,999 (GRCm39)	S563P	probably damaging	Het
Topaz1	A	G	9: 122,578,368 (GRCm39)	H426R	possibly damaging	Het
Tpgs1	T	A	10: 79,511,271 (GRCm39)	C138S	possibly damaging	Het
Traf1	A	T	2: 34,839,115 (GRCm39)	V70D	probably benign	Het
Ttn	T	C	2: 76,641,737 (GRCm39)	Y13453C	probably damaging	Het
Ubxn4	T	A	1: 128,183,931 (GRCm39)	V97D	possibly damaging	Het
Ugt1a8	A	T	1: 88,016,057 (GRCm39)	I157L	probably benign	Het
Vmn2r13	A	T	5: 109,304,332 (GRCm39)	C700S	probably damaging	Het
Wee1	A	T	7: 109,723,733 (GRCm39)	D216V	probably benign	Het
Zc3h4	T	C	7: 16,163,198 (GRCm39)	Y533H	unknown	Het
Zfp1005	A	T	2: 150,110,595 (GRCm39)	Q428H	unknown	Het
Zfp81	A	G	17: 33,555,698 (GRCm39)	I43T	possibly damaging	Het
Zfp963	A	T	8: 70,196,145 (GRCm39)	Y103N	probably benign	Het
Zfp963	A	T	8: 70,196,143 (GRCm39)	Y103*	probably null	Het
Zzef1	G	T	11: 72,756,792 (GRCm39)	D1126Y	probably damaging	Het

Other mutations in Kdm4d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01011:Kdm4d	APN	9	14,375,515 (GRCm39)	missense	probably benign	0.10
IGL01114:Kdm4d	APN	9	14,375,493 (GRCm39)	missense	probably damaging	1.00
IGL01609:Kdm4d	APN	9	14,375,714 (GRCm39)	missense	probably damaging	0.99
IGL02342:Kdm4d	APN	9	14,374,860 (GRCm39)	missense	probably damaging	0.99
IGL02513:Kdm4d	APN	9	14,375,850 (GRCm39)	missense	probably benign	0.00
IGL03276:Kdm4d	APN	9	14,375,838 (GRCm39)	missense	probably benign	0.04
IGL03379:Kdm4d	APN	9	14,375,139 (GRCm39)	missense	probably damaging	1.00
R0755:Kdm4d	UTSW	9	14,375,591 (GRCm39)	missense	probably damaging	0.99
R1195:Kdm4d	UTSW	9	14,374,395 (GRCm39)	missense	probably benign
R1195:Kdm4d	UTSW	9	14,374,395 (GRCm39)	missense	probably benign
R1195:Kdm4d	UTSW	9	14,374,395 (GRCm39)	missense	probably benign
R1455:Kdm4d	UTSW	9	14,375,691 (GRCm39)	missense	probably damaging	0.98
R1552:Kdm4d	UTSW	9	14,375,325 (GRCm39)	missense	probably damaging	1.00
R1692:Kdm4d	UTSW	9	14,375,807 (GRCm39)	missense	probably benign	0.43
R1871:Kdm4d	UTSW	9	14,375,679 (GRCm39)	missense	probably damaging	1.00
R1892:Kdm4d	UTSW	9	14,375,613 (GRCm39)	missense	probably benign	0.14
R4792:Kdm4d	UTSW	9	14,374,686 (GRCm39)	missense	probably benign
R5113:Kdm4d	UTSW	9	14,375,409 (GRCm39)	missense	probably damaging	1.00
R5211:Kdm4d	UTSW	9	14,374,400 (GRCm39)	missense	probably benign	0.04
R5352:Kdm4d	UTSW	9	14,375,654 (GRCm39)	missense	probably damaging	1.00
R6692:Kdm4d	UTSW	9	14,374,361 (GRCm39)	missense	probably benign
R7014:Kdm4d	UTSW	9	14,375,475 (GRCm39)	missense	probably damaging	0.99
R7198:Kdm4d	UTSW	9	14,375,316 (GRCm39)	missense	probably damaging	1.00
R7260:Kdm4d	UTSW	9	14,374,454 (GRCm39)	missense	probably benign	0.05
R8116:Kdm4d	UTSW	9	14,375,237 (GRCm39)	missense	probably damaging	1.00
R8134:Kdm4d	UTSW	9	14,374,532 (GRCm39)	missense	probably damaging	1.00
R8354:Kdm4d	UTSW	9	14,375,235 (GRCm39)	missense	possibly damaging	0.80
R9006:Kdm4d	UTSW	9	14,374,833 (GRCm39)	missense	probably benign	0.01
R9197:Kdm4d	UTSW	9	14,375,537 (GRCm39)	missense	probably damaging	1.00
R9298:Kdm4d	UTSW	9	14,375,336 (GRCm39)	missense	probably damaging	1.00
R9300:Kdm4d	UTSW	9	14,375,336 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGCCAATGTCCTGCAAACTCAGTC -3'
(R):5'- TCCAGGCAACCATCAGATGTGAAAG -3'

Sequencing Primer
(F):5'- CTCAGTCAAAACTATGAGGTAATGG -3'
(R):5'- GATGATGTCCAGAAGTCTGACTC -3'

Posted On

2013-05-09