Mutagenetix > Incidental Mutations

Incidental Mutation 'R1572:Kdm4a'

170827

Institutional Source

Beutler Lab

Gene Symbol

Kdm4a

Ensembl Gene

ENSMUSG00000033326

Gene Name

lysine (K)-specific demethylase 4A

Synonyms

Jmjd2, D4Ertd222e, JHDM3A, Jmjd2a

MMRRC Submission

039611-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.787) question?

Stock #

R1572 (G1)

Quality Score

154

Status

Validated

Chromosome

Chromosomal Location

118136957-118180043 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 118138949 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 961 (E961G)

Ref Sequence

ENSEMBL: ENSMUSP00000102014 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030263] [ENSMUST00000050288] [ENSMUST00000097911] [ENSMUST00000097912] [ENSMUST00000106403] [ENSMUST00000106406] [ENSMUST00000106410]

AlphaFold

Q8BW72

Predicted Effect

probably benign
Transcript: ENSMUST00000030263

SMART Domains

Protein: ENSMUSP00000030263
Gene: ENSMUSG00000028538

Domain	Start	End	E-Value	Type
transmembrane domain	5	27	N/A	INTRINSIC
low complexity region	37	47	N/A	INTRINSIC
Pfam:Glyco_transf_29	102	373	5.7e-75	PFAM

Predicted Effect

probably benign
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

possibly damaging
Transcript: ENSMUST00000097911
AA Change: E961G

PolyPhen 2 Score 0.888 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: E961G

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 benign
Transcript: ENSMUST00000097912

SMART Domains

Protein: ENSMUSP00000095525
Gene: ENSMUSG00000028538

Domain	Start	End	E-Value	Type
transmembrane domain	5	27	N/A	INTRINSIC
Pfam:Glyco_transf_29	86	357	5.4e-75	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000106403
AA Change: E961G

PolyPhen 2 Score 0.888 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: E961G

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

possibly damaging
Transcript: ENSMUST00000106406
AA Change: E961G

PolyPhen 2 Score 0.888 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: E961G

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 benign
Transcript: ENSMUST00000106410

SMART Domains

Protein: ENSMUSP00000102018
Gene: ENSMUSG00000028538

Domain	Start	End	E-Value	Type
transmembrane domain	5	27	N/A	INTRINSIC
low complexity region	37	47	N/A	INTRINSIC
Pfam:Glyco_transf_29	106	372	4.7e-63	PFAM

Meta Mutation Damage Score

0.2302

Coding Region Coverage

1x: 98.7%
3x: 97.5%
10x: 92.9%
20x: 80.7%

Validation Efficiency

97% (130/134)

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: 112 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310030G06Rik	G	A	9: 50,740,673	T85M	probably damaging	Het
5430419D17Rik	T	A	7: 131,244,831	Y777*	probably null	Het
Actn1	A	G	12: 80,172,957		probably benign	Het
Afap1l1	A	T	18: 61,737,499	S603T	probably damaging	Het
Ahcy	T	C	2: 155,068,931	Y39C	probably benign	Het
Ankmy2	T	C	12: 36,186,942		probably null	Het
Anxa13	A	T	15: 58,348,807		noncoding transcript	Het
Aoc1	T	C	6: 48,905,786	S221P	possibly damaging	Het
Arhgef10	C	A	8: 14,991,211	A770D	possibly damaging	Het
Arhgef19	A	G	4: 141,254,754	D707G	probably benign	Het
Arhgef3	G	A	14: 27,401,735	R444H	probably damaging	Het
Asphd1	T	C	7: 126,949,099	I11V	probably benign	Het
Atp2b1	A	G	10: 98,994,675	M333V	probably benign	Het
BC051665	T	C	13: 60,785,027	Y40C	probably damaging	Het
Ccdc87	T	A	19: 4,840,313	S278T	probably benign	Het
Chaf1b	G	A	16: 93,901,230	G463D	possibly damaging	Het
Chrna4	T	C	2: 181,029,307	T219A	possibly damaging	Het
Clcnkb	T	G	4: 141,407,095	T584P	possibly damaging	Het
Clptm1l	T	C	13: 73,607,747	S161P	probably benign	Het
Cmya5	T	C	13: 93,094,269	E1437G	possibly damaging	Het
Col13a1	A	T	10: 61,866,426		probably null	Het
Col3a1	T	C	1: 45,345,968	S82P	possibly damaging	Het
Cpeb3	A	T	19: 37,139,082	M383K	probably benign	Het
Cr2	T	A	1: 195,163,314	H111L	probably damaging	Het
Cttnbp2	T	C	6: 18,375,975	S1522G	possibly damaging	Het
Cul3	T	C	1: 80,282,789	D281G	possibly damaging	Het
Cyp2c70	T	G	19: 40,183,982	K72T	probably benign	Het
Cyp39a1	A	T	17: 43,680,129	I110F	probably damaging	Het
Cyp46a1	T	A	12: 108,351,939	M203K	probably null	Het
Cyp8b1	A	T	9: 121,914,958	V436D	possibly damaging	Het
Ddx17	T	C	15: 79,538,565	D324G	probably damaging	Het
Dopey2	A	G	16: 93,770,153	N1274S	probably damaging	Het
Dscaml1	G	A	9: 45,721,333	V1166I	probably benign	Het
Dsp	T	C	13: 38,195,738	V1554A	probably damaging	Het
Dusp27	C	T	1: 166,099,455	V863M	possibly damaging	Het
Efr3a	T	A	15: 65,854,792		probably null	Het
Egfem1	A	T	3: 29,648,271	N223I	probably benign	Het
Egr2	T	C	10: 67,539,975	S147P	probably damaging	Het
Elmo3	A	G	8: 105,308,301	T408A	probably benign	Het
Flnb	A	G	14: 7,883,908	D378G	probably damaging	Het
Foxj2	T	A	6: 122,833,261	M193K	probably benign	Het
Gm6327	A	G	16: 12,760,156		noncoding transcript	Het
Gm7694	T	C	1: 170,302,766	H21R	probably benign	Het
Gpr107	A	G	2: 31,167,025	D43G	probably damaging	Het
Grid2	T	A	6: 64,429,694	Y679*	probably null	Het
Grin2c	G	A	11: 115,256,074	P432S	possibly damaging	Het
H2-M10.1	A	G	17: 36,325,733	F60L	possibly damaging	Het
Hectd4	A	G	5: 121,301,878	D1147G	possibly damaging	Het
Idua	G	T	5: 108,680,589	A223S	probably benign	Het
Ifi206	T	C	1: 173,486,853	Q7R	probably benign	Het
Itgad	T	A	7: 128,203,234	V986E	probably damaging	Het
Itsn2	G	A	12: 4,650,044	R670H	probably benign	Het
Klra5	T	A	6: 129,906,622	I91L	probably damaging	Het
Kntc1	A	G	5: 123,772,113	T525A	probably damaging	Het
Lct	A	G	1: 128,294,195	F1536L	probably benign	Het
Lmod1	T	A	1: 135,363,933	D175E	probably benign	Het
Lonrf1	A	C	8: 36,233,972	D361E	probably benign	Het
Lrrc19	T	C	4: 94,638,429	Y297C	probably damaging	Het
Mast4	T	C	13: 102,736,923	E1787G	possibly damaging	Het
Mpp2	G	A	11: 102,060,548	A452V	probably benign	Het
Msh2	T	C	17: 87,718,652	V686A	possibly damaging	Het
Mthfd1	C	T	12: 76,270,419	Q15*	probably null	Het
Mtnr1b	A	T	9: 15,863,142	I207N	probably damaging	Het
Nid2	A	G	14: 19,805,412	T1207A	probably benign	Het
Nin	A	T	12: 70,038,750	V1569D	probably damaging	Het
Nov	T	A	15: 54,749,252	M219K	possibly damaging	Het
Nrcam	T	A	12: 44,537,364		probably benign	Het
Nsd1	T	A	13: 55,246,969	H897Q	probably damaging	Het
Olfr102	A	T	17: 37,313,480	N301K	probably benign	Het
Olfr1364	T	A	13: 21,574,310	I49F	possibly damaging	Het
Olfr77	G	T	9: 19,920,912	K234N	probably benign	Het
Olfr979	A	G	9: 40,001,194	F11S	probably benign	Het
Paip1	T	C	13: 119,451,784		probably benign	Het
Pcnx3	G	A	19: 5,685,347	R484*	probably null	Het
Pdxk	A	G	10: 78,447,980	Y127H	probably damaging	Het
Phf20	T	A	2: 156,287,834	V442E	probably benign	Het
Phlpp1	G	A	1: 106,392,789	D1505N	probably damaging	Het
Pkhd1	T	C	1: 20,347,440	T2496A	probably benign	Het
Pkhd1l1	A	G	15: 44,543,473	T2369A	probably benign	Het
Plod2	T	A	9: 92,603,067		probably benign	Het
Pnpla7	T	A	2: 25,015,251	M617K	possibly damaging	Het
Ppp1r16a	C	T	15: 76,693,669	Q328*	probably null	Het
Prkch	T	A	12: 73,649,357		probably null	Het
Prr12	G	A	7: 45,028,800	H1974Y	unknown	Het
Prr16	A	G	18: 51,302,970	I174V	probably benign	Het
Prss45	A	T	9: 110,838,429	T39S	probably benign	Het
Pum1	T	A	4: 130,718,204	D161E	probably damaging	Het
Rad51ap2	A	G	12: 11,457,112	D345G	probably damaging	Het
Ralgapb	A	G	2: 158,446,199		probably benign	Het
Rasgrp3	A	G	17: 75,500,734	H262R	possibly damaging	Het
Rnf213	T	A	11: 119,436,611	I1809N	probably damaging	Het
Ryr1	A	G	7: 29,062,191	L3177P	probably damaging	Het
Scyl2	C	A	10: 89,650,956	R230L	probably damaging	Het
Sfxn2	T	C	19: 46,582,476		probably benign	Het
Slc18b1	T	C	10: 23,798,741		probably benign	Het
Spata31d1d	T	C	13: 59,728,191	H510R	probably benign	Het
Stab1	A	T	14: 31,150,823	N1109K	probably damaging	Het
Sult3a2	A	G	10: 33,781,977	S47P	probably damaging	Het
Tenm3	T	C	8: 48,228,993	N2518S	possibly damaging	Het
Tex21	G	T	12: 76,206,891	P416Q	probably benign	Het
Tex38	T	C	4: 115,780,306	N100S	probably benign	Het
Thsd4	A	C	9: 60,394,553		probably benign	Het
Ticrr	T	C	7: 79,681,824	V723A	probably damaging	Het
Tmprss15	A	G	16: 79,090,829	V30A	probably benign	Het
Uba3	A	G	6: 97,185,337		probably benign	Het
Ubr1	T	C	2: 120,935,319		probably benign	Het
Uchl4	A	T	9: 64,235,731	I165L	probably benign	Het
Vmn2r112	A	T	17: 22,603,144	T268S	possibly damaging	Het
Wfdc3	T	C	2: 164,744,194		probably benign	Het
Zfp282	T	A	6: 47,892,867	L282Q	probably damaging	Het
Zfp422	A	T	6: 116,626,784	C85S	probably damaging	Het
Zfp790	A	T	7: 29,828,139	Q83L	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
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
R6772:Kdm4a	UTSW	4	118142555	critical splice acceptor site	probably null
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
R8808:Kdm4a	UTSW	4	118142283	missense	unknown
R8956:Kdm4a	UTSW	4	118161816	missense	possibly damaging	0.69
R8958:Kdm4a	UTSW	4	118142376	missense	probably benign	0.08
R9233:Kdm4a	UTSW	4	118146996	critical splice donor site	probably null
R9281:Kdm4a	UTSW	4	118138531	missense	probably damaging	1.00
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'- AGAGCAAAGACAAGCTTCTTGCCC -3'
(R):5'- TTCCTCCATAGCAGAGCAGCTCAG -3'

Sequencing Primer
(F):5'- AGCTTCTTGCCCGAGGAAAC -3'
(R):5'- AGACCTTGTTTGACGGACC -3'

Posted On

2014-04-13