Mutagenetix > Incidental Mutations

Incidental Mutation 'R6772:Kdm4a'

532196

Institutional Source

Beutler Lab

Gene Symbol

Kdm4a

Ensembl Gene

ENSMUSG00000033326

Gene Name

lysine (K)-specific demethylase 4A

Synonyms

Jmjd2, D4Ertd222e, JHDM3A, Jmjd2a

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.788) question?

Stock #

R6772 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

118136957-118180043 bp(-) (GRCm38)

Type of Mutation

critical splice acceptor site

DNA Base Change (assembly)

T to C at 118142555 bp

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000102014 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000050288] [ENSMUST00000050288] [ENSMUST00000050288] [ENSMUST00000097911] [ENSMUST00000097911] [ENSMUST00000097911] [ENSMUST00000106403] [ENSMUST00000106403] [ENSMUST00000106403] [ENSMUST00000106406] [ENSMUST00000106406] [ENSMUST00000106406]

Predicted Effect

probably null
Transcript: ENSMUST00000050288

SMART Domains

Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.87e-8	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000050288

SMART Domains

Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.87e-8	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000050288

SMART Domains

Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.87e-8	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000097911

SMART Domains

Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.41e-10	SMART
TUDOR	955	1011	4.77e-14	SMART
low complexity region	1032	1044	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000097911

SMART Domains

Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.41e-10	SMART
TUDOR	955	1011	4.77e-14	SMART
low complexity region	1032	1044	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000097911

SMART Domains

Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.41e-10	SMART
TUDOR	955	1011	4.77e-14	SMART
low complexity region	1032	1044	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000106403

SMART Domains

Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.41e-10	SMART
TUDOR	955	1011	4.77e-14	SMART
low complexity region	1032	1044	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000106403

SMART Domains

Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.41e-10	SMART
TUDOR	955	1011	4.77e-14	SMART
low complexity region	1032	1044	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000106403

SMART Domains

Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.41e-10	SMART
TUDOR	955	1011	4.77e-14	SMART
low complexity region	1032	1044	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000106406

SMART Domains

Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.41e-10	SMART
TUDOR	955	1011	4.77e-14	SMART
low complexity region	1032	1044	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000106406

SMART Domains

Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.41e-10	SMART
TUDOR	955	1011	4.77e-14	SMART
low complexity region	1032	1044	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000106406

SMART Domains

Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.41e-10	SMART
TUDOR	955	1011	4.77e-14	SMART
low complexity region	1032	1044	N/A	INTRINSIC

Meta Mutation Damage Score

0.9505

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.8%
20x: 96.7%

Validation Efficiency

97% (36/37)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the Jumonji domain 2 (JMJD2) family and encodes a protein containing a JmjN domain, a JmjC domain, a JD2H domain, two TUDOR domains, and two PHD-type zinc fingers. This nuclear protein functions as a trimethylation-specific demethylase, converting specific trimethylated histone residues to the dimethylated form, and as a transcriptional repressor. [provided by RefSeq, Apr 2009]

Allele List at MGI

Other mutations in this stock

Total: 36 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca16	A	T	7: 120,527,053	D1144V	probably damaging	Het
Ankrd13a	A	G	5: 114,801,743	H477R	probably benign	Het
Anxa3	A	T	5: 96,811,113	I27F	probably damaging	Het
Aplf	T	C	6: 87,663,799	E76G	possibly damaging	Het
Bbs1	A	G	19: 4,906,590		probably benign	Het
Camk2a	T	C	18: 60,969,020	S332P	probably benign	Het
Casz1	T	A	4: 148,943,206	F1013L	probably damaging	Het
Cd109	A	T	9: 78,680,810	I707F	possibly damaging	Het
Cd4	G	A	6: 124,872,458	T202I	probably benign	Het
Celsr1	A	G	15: 86,030,782	S997P	probably benign	Het
Cfap77	T	C	2: 29,054,939	T24A	probably damaging	Het
Dscaml1	G	A	9: 45,710,311	R1019H	probably damaging	Het
Epb41l4b	C	A	4: 57,063,140	V517F	probably benign	Het
Exosc10	G	A	4: 148,581,134	D818N	probably damaging	Het
Furin	C	T	7: 80,393,492	G324S	probably damaging	Het
Idh2	TCCCAGG	T	7: 80,098,331		probably benign	Het
Ifi206	T	C	1: 173,481,207	M408V	unknown	Het
Neo1	T	A	9: 58,902,976	Q1064L	probably damaging	Het
Nphp4	G	A	4: 152,544,406	V750I	probably benign	Het
Pcdhac1	T	C	18: 37,090,236	V34A	probably benign	Het
Pdk4	T	C	6: 5,487,141	I302V	probably benign	Het
Prl6a1	A	G	13: 27,319,048	D209G	probably damaging	Het
Pspn	T	C	17: 56,999,515	Q138R	probably benign	Het
Ptgs2	A	G	1: 150,102,078	Y134C	probably damaging	Het
Rlbp1	G	A	7: 79,384,050		probably benign	Het
Rpia	T	C	6: 70,785,548	I108V	probably benign	Het
Tcaf1	A	T	6: 42,675,276	H757Q	probably damaging	Het
Ttc8	A	C	12: 98,943,589	S143R	probably damaging	Het
Uba6	A	G	5: 86,147,073		probably null	Het
Ubr4	A	T	4: 139,467,230	K4280*	probably null	Het
Vmn2r15	C	A	5: 109,286,372	S822I	probably damaging	Het
Vps53	A	T	11: 76,179,498	M1K	probably null	Het
Zfp362	A	G	4: 128,790,260	M18T	possibly damaging	Het
Zfp429	A	G	13: 67,390,198	C376R	probably damaging	Het
Zfyve9	T	C	4: 108,639,269	N1395S	probably damaging	Het
Zmynd8	T	A	2: 165,807,601	Q857H	probably benign	Het

Other mutations in Kdm4a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01670:Kdm4a	APN	4	118160501	missense	probably damaging	1.00
IGL01845:Kdm4a	APN	4	118160459	missense	possibly damaging	0.85
IGL02009:Kdm4a	APN	4	118160169	missense	probably benign	0.01
IGL02296:Kdm4a	APN	4	118177465	missense	probably damaging	1.00
IGL02366:Kdm4a	APN	4	118160506	critical splice acceptor site	probably null
IGL02606:Kdm4a	APN	4	118160289	missense	probably benign	0.00
IGL02673:Kdm4a	APN	4	118168572	missense	probably benign	0.00
R0245:Kdm4a	UTSW	4	118175689	missense	probably benign	0.05
R0326:Kdm4a	UTSW	4	118161706	missense	probably benign	0.00
R0551:Kdm4a	UTSW	4	118138231	makesense	probably null
R0603:Kdm4a	UTSW	4	118142511	missense	probably damaging	1.00
R0652:Kdm4a	UTSW	4	118175689	missense	probably benign	0.05
R0799:Kdm4a	UTSW	4	118146992	splice site	probably null
R0847:Kdm4a	UTSW	4	118164498	missense	probably damaging	0.96
R1307:Kdm4a	UTSW	4	118175642	missense	probably benign	0.02
R1572:Kdm4a	UTSW	4	118138949	missense	possibly damaging	0.89
R1869:Kdm4a	UTSW	4	118138871	missense	probably null	1.00
R1902:Kdm4a	UTSW	4	118160399	missense	probably benign	0.38
R1903:Kdm4a	UTSW	4	118160399	missense	probably benign	0.38
R2135:Kdm4a	UTSW	4	118142459	missense	probably damaging	1.00
R3856:Kdm4a	UTSW	4	118153231	missense	probably damaging	1.00
R4687:Kdm4a	UTSW	4	118144083	missense	probably damaging	1.00
R4940:Kdm4a	UTSW	4	118161754	missense	probably benign	0.00
R5115:Kdm4a	UTSW	4	118162581	missense	possibly damaging	0.75
R5229:Kdm4a	UTSW	4	118146605	missense	probably damaging	0.99
R5305:Kdm4a	UTSW	4	118160501	missense	probably damaging	1.00
R5423:Kdm4a	UTSW	4	118138908	missense	probably damaging	1.00
R5750:Kdm4a	UTSW	4	118142199	intron	probably benign
R5849:Kdm4a	UTSW	4	118161840	missense	probably benign	0.17
R5876:Kdm4a	UTSW	4	118138876	missense	probably damaging	0.98
R6564:Kdm4a	UTSW	4	118177439	missense	probably benign	0.18
R6982:Kdm4a	UTSW	4	118153439	splice site	probably null
R7410:Kdm4a	UTSW	4	118143918	missense	possibly damaging	0.64
R7418:Kdm4a	UTSW	4	118160243	missense	probably damaging	0.99
Z1176:Kdm4a	UTSW	4	118153190	missense	probably benign	0.00
Z1176:Kdm4a	UTSW	4	118177502	missense	probably benign	0.41
Z1177:Kdm4a	UTSW	4	118147169	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CGGCAATAACAAGAAGATGTCC -3'
(R):5'- CTAGTTGGCTTGGAGCTCAG -3'

Sequencing Primer
(F):5'- GAAGCCGCTTTCAGACATTAC -3'
(R):5'- CTCAGAGCTCATGTGAGTGGC -3'

Posted On

2018-08-29