Mutagenetix > Incidental Mutation

Incidental Mutation 'R5113:Kdm4d'

394021

Institutional Source

Beutler Lab

Gene Symbol

Kdm4d

Ensembl Gene

ENSMUSG00000053914

Gene Name

lysine (K)-specific demethylase 4D

Synonyms

Jmjd2d

MMRRC Submission

042701-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5113 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

14462548-14500482 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 14464113 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 150 (N150D)

Ref Sequence

ENSEMBL: ENSMUSP00000061632 (fasta)

Gene Model

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

AlphaFold

Q3U2K5

Predicted Effect

probably damaging
Transcript: ENSMUST00000058796
AA Change: N150D

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

SMART Domains

Protein: ENSMUSP00000061632
Gene: ENSMUSG00000053914
AA Change: N150D

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 damaging
Transcript: ENSMUST00000115647
AA Change: N150D

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000111311
Gene: ENSMUSG00000053914
AA Change: N150D

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: 99.1%
3x: 98.4%
10x: 96.4%
20x: 92.6%

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alox12e	A	G	11: 70,315,995	V622A	possibly damaging	Het
Ankef1	A	G	2: 136,552,441	N590S	probably benign	Het
Anks6	C	T	4: 47,030,795	G601S	probably damaging	Het
Ano3	A	T	2: 110,661,480	N867K	possibly damaging	Het
Ash1l	T	C	3: 89,066,275	V2547A	probably damaging	Het
Ccpg1os	T	A	9: 72,979,893	R111*	probably null	Het
Chil5	A	T	3: 106,017,978	V209E	possibly damaging	Het
Cltc	A	T	11: 86,722,321	C459S	probably damaging	Het
Col6a4	T	A	9: 106,066,960	D1105V	possibly damaging	Het
Cyp2c66	A	G	19: 39,163,438	D199G	probably benign	Het
Cyp4f18	A	G	8: 71,989,058		probably null	Het
Cysrt1	A	T	2: 25,239,351	C50S	possibly damaging	Het
Dapk1	A	G	13: 60,721,778	K278R	probably benign	Het
Eefsec	C	A	6: 88,281,575	S512I	probably damaging	Het
Emilin1	T	C	5: 30,920,620	F908L	possibly damaging	Het
Eml1	T	C	12: 108,537,337	V731A	possibly damaging	Het
Erc2	T	C	14: 27,652,872	S16P	probably benign	Het
Gfpt2	A	G	11: 49,823,799	R342G	probably damaging	Het
Gpr142	A	T	11: 114,804,317	Q36L	probably benign	Het
Grik5	A	G	7: 25,015,527	S681P	probably damaging	Het
Hecw1	A	T	13: 14,346,029	S208T	possibly damaging	Het
Hmgcr	G	A	13: 96,656,732	A464V	probably benign	Het
Igkv2-109	A	G	6: 68,303,085	T97A	possibly damaging	Het
Ino80	G	T	2: 119,431,945	Q687K	probably damaging	Het
Klf4	A	G	4: 55,530,481	I210T	possibly damaging	Het
Klkb1	C	A	8: 45,270,697	Q560H	probably benign	Het
Lce1a2	A	T	3: 92,669,135	V40E	unknown	Het
Maob	T	C	X: 16,716,423	T400A	probably benign	Het
Mipol1	C	T	12: 57,496,499	T393I	probably benign	Het
Mst1	A	G	9: 108,082,247	D244G	probably damaging	Het
Nexn	G	A	3: 152,243,888	R258C	probably damaging	Het
Olfr1353	A	G	10: 78,970,203	I185V	probably benign	Het
Olfr748	A	C	14: 50,710,914	I195L	probably benign	Het
Olfr777	A	G	10: 129,268,666	I219T	probably damaging	Het
Olfr975	T	C	9: 39,949,925	N282S	probably damaging	Het
Optc	T	C	1: 133,900,977		probably benign	Het
Pabpc2	C	A	18: 39,775,383	P567Q	probably benign	Het
Ppm1j	A	G	3: 104,784,674	H324R	possibly damaging	Het
Reg3g	A	T	6: 78,466,561		probably null	Het
Sipa1l1	C	T	12: 82,440,908	A1652V	probably benign	Het
Ski	T	C	4: 155,159,392	T554A	probably benign	Het
Slfn5	G	A	11: 82,961,696	V883M	probably benign	Het
Stradb	T	C	1: 58,991,174		probably benign	Het
Tex19.1	A	G	11: 121,147,799	T328A	probably benign	Het
Tpsab1	T	C	17: 25,345,399	N27S	possibly damaging	Het
Ttn	A	T	2: 76,811,243	L5176Q	possibly damaging	Het
Ttn	A	T	2: 76,812,900	L13225Q	probably damaging	Het
Vmn1r28	A	G	6: 58,265,858	T229A	probably benign	Het
Wapl	A	G	14: 34,724,754	K600E	probably damaging	Het
Zfp217	T	C	2: 170,114,058		probably null	Het

Other mutations in Kdm4d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01011:Kdm4d	APN	9	14464219	missense	probably benign	0.10
IGL01114:Kdm4d	APN	9	14464197	missense	probably damaging	1.00
IGL01609:Kdm4d	APN	9	14464418	missense	probably damaging	0.99
IGL02342:Kdm4d	APN	9	14463564	missense	probably damaging	0.99
IGL02513:Kdm4d	APN	9	14464554	missense	probably benign	0.00
IGL03276:Kdm4d	APN	9	14464542	missense	probably benign	0.04
IGL03379:Kdm4d	APN	9	14463843	missense	probably damaging	1.00
R0220:Kdm4d	UTSW	9	14463122	missense	probably benign
R0755:Kdm4d	UTSW	9	14464295	missense	probably damaging	0.99
R1195:Kdm4d	UTSW	9	14463099	missense	probably benign
R1195:Kdm4d	UTSW	9	14463099	missense	probably benign
R1195:Kdm4d	UTSW	9	14463099	missense	probably benign
R1455:Kdm4d	UTSW	9	14464395	missense	probably damaging	0.98
R1552:Kdm4d	UTSW	9	14464029	missense	probably damaging	1.00
R1692:Kdm4d	UTSW	9	14464511	missense	probably benign	0.43
R1871:Kdm4d	UTSW	9	14464383	missense	probably damaging	1.00
R1892:Kdm4d	UTSW	9	14464317	missense	probably benign	0.14
R4792:Kdm4d	UTSW	9	14463390	missense	probably benign
R5211:Kdm4d	UTSW	9	14463104	missense	probably benign	0.04
R5352:Kdm4d	UTSW	9	14464358	missense	probably damaging	1.00
R6692:Kdm4d	UTSW	9	14463065	missense	probably benign
R7014:Kdm4d	UTSW	9	14464179	missense	probably damaging	0.99
R7198:Kdm4d	UTSW	9	14464020	missense	probably damaging	1.00
R7260:Kdm4d	UTSW	9	14463158	missense	probably benign	0.05
R8116:Kdm4d	UTSW	9	14463941	missense	probably damaging	1.00
R8134:Kdm4d	UTSW	9	14463236	missense	probably damaging	1.00
R8354:Kdm4d	UTSW	9	14463939	missense	possibly damaging	0.80
R9006:Kdm4d	UTSW	9	14463537	missense	probably benign	0.01
R9197:Kdm4d	UTSW	9	14464241	missense	probably damaging	1.00
R9298:Kdm4d	UTSW	9	14464040	missense	probably damaging	1.00
R9300:Kdm4d	UTSW	9	14464040	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCACAGCATACCAGGTCTTG -3'
(R):5'- TCTTAATAGCAACTCCCCTGCAG -3'

Sequencing Primer
(F):5'- GGGCTGCCCAAAGTGTAG -3'
(R):5'- GCAGGCGTGTTCACCCAATAC -3'

Posted On

2016-06-15