Mutagenetix > Incidental Mutations

Incidental Mutation 'R1455:Kdm4d'

161733

Institutional Source

Beutler Lab

Gene Symbol

Kdm4d

Ensembl Gene

ENSMUSG00000053914

Gene Name

lysine (K)-specific demethylase 4D

Synonyms

Jmjd2d

MMRRC Submission

039510-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1455 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

14462548-14500482 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 14464395 bp

Zygosity

Heterozygous

Amino Acid Change

Alanine to Serine at position 56 (A56S)

Ref Sequence

ENSEMBL: ENSMUSP00000061632 (fasta)

Gene Model

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000058796
AA Change: A56S

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000061632
Gene: ENSMUSG00000053914
AA Change: A56S

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

possibly damaging
Transcript: ENSMUST00000115647
AA Change: A56S

PolyPhen 2 Score 0.721 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000111311
Gene: ENSMUSG00000053914
AA Change: A56S

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: 98.9%
3x: 97.9%
10x: 94.8%
20x: 87.9%

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: 41 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921509C19Rik	T	C	2: 151,472,904	N285D	possibly damaging	Het
9230110C19Rik	T	G	9: 8,022,456	N255T	probably benign	Het
Adam9	T	G	8: 24,993,109	M227L	probably benign	Het
Ankrd35	A	G	3: 96,678,155	D21G	probably damaging	Het
Arhgap32	C	T	9: 32,260,085	A1387V	probably benign	Het
Atg4d	T	A	9: 21,270,801	V306E	probably damaging	Het
Brsk1	G	A	7: 4,704,251	V268M	probably damaging	Het
Clec4a4	A	G	6: 123,012,799	E133G	possibly damaging	Het
Col24a1	T	A	3: 145,460,838	L1076H	probably damaging	Het
Ddah1	G	T	3: 145,889,109	R208L	probably benign	Het
Dysf	A	G	6: 84,113,386	N960S	probably benign	Het
Egln2	A	G	7: 27,160,371	Y306H	probably damaging	Het
Fgfr1	T	C	8: 25,562,276	V293A	possibly damaging	Het
Gja3	A	G	14: 57,036,385	Y177H	probably damaging	Het
Glul	T	A	1: 153,907,099		probably null	Het
Gprc5a	G	A	6: 135,079,247	V231I	probably benign	Het
Lingo4	G	A	3: 94,399,392		probably benign	Het
Map6	A	G	7: 99,268,214	T65A	probably damaging	Het
Mmrn2	T	C	14: 34,399,132	I653T	probably benign	Het
Ndufa12	A	G	10: 94,203,314	T70A	probably benign	Het
Nfe2l3	C	A	6: 51,457,764	P435T	possibly damaging	Het
Npc1l1	A	T	11: 6,228,174	V412E	possibly damaging	Het
Olfr303	A	T	7: 86,394,595	F301Y	probably damaging	Het
Olfr33	A	T	7: 102,713,998	Y138*	probably null	Het
Pcnx	T	C	12: 81,973,234	F1344L	probably damaging	Het
Pi4ka	A	G	16: 17,363,954	V297A	probably benign	Het
Pole2	G	A	12: 69,207,929	L381F	probably benign	Het
Pramel7	T	C	2: 87,489,723	T409A	probably benign	Het
Proc	C	G	18: 32,123,398	M405I	probably damaging	Het
Serinc2	C	A	4: 130,264,340	A105S	probably damaging	Het
Slc4a10	G	T	2: 62,286,930	K744N	probably damaging	Het
Spdye4c	A	T	2: 128,596,558	I279F	probably damaging	Het
Srcap	G	T	7: 127,530,650	R568L	probably damaging	Het
Stag3	T	A	5: 138,311,735	M1215K	probably benign	Het
Tenm3	C	T	8: 48,279,048	A1274T	possibly damaging	Het
Tet2	A	G	3: 133,473,645	V1253A	possibly damaging	Het
Tns2	C	T	15: 102,108,934	R281C	probably damaging	Het
Trip12	T	C	1: 84,759,100	I800V	probably benign	Het
Zfc3h1	T	C	10: 115,412,108	I1072T	probably benign	Het
Zfp148	T	A	16: 33,495,465		probably null	Het
Zfp941	A	G	7: 140,812,774	V224A	probably benign	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
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
R5113:Kdm4d	UTSW	9	14464113	missense	probably damaging	1.00
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

Predicted Primers

PCR Primer
(F):5'- GGTGACTCATACAGGCGATTCTTCC -3'
(R):5'- ATCACATGCACAGAGGCTGTCAGG -3'

Sequencing Primer
(F):5'- CTTCAAAATCCAGGTGTGGC -3'
(R):5'- AGGAGATTCGGCTCCATCAC -3'

Posted On

2014-03-14