Mutagenetix > Incidental Mutation

Incidental Mutation 'R9647:Kdm4a'

726782

Institutional Source

Beutler Lab

Gene Symbol

Kdm4a

Ensembl Gene

ENSMUSG00000033326

Gene Name

lysine (K)-specific demethylase 4A

Synonyms

D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2

MMRRC Submission

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.631) question?

Stock #

R9647 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

117994154-118037240 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 118003790 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 762 (M762K)

Ref Sequence

ENSEMBL: ENSMUSP00000095524 (fasta)

Gene Model

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

AlphaFold

Q8BW72

Predicted Effect

probably benign
Transcript: ENSMUST00000050288
AA Change: M762K

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: M762K

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 benign
Transcript: ENSMUST00000097911
AA Change: M762K

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: M762K

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: ENSMUST00000106403
AA Change: M762K

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: M762K

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: ENSMUST00000106406
AA Change: M762K

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: M762K

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc5	C	A	16: 20,195,310 (GRCm39)	R729L	probably benign	Het
Actr3b	T	C	5: 26,037,408 (GRCm39)	S295P	probably benign	Het
Alb	G	A	5: 90,620,544 (GRCm39)		probably null	Het
Ank2	T	A	3: 126,792,623 (GRCm39)	N756I	possibly damaging	Het
Ankar	A	G	1: 72,689,307 (GRCm39)	Y1275H	probably damaging	Het
Ankrd11	C	T	8: 123,617,682 (GRCm39)	A2057T	probably benign	Het
Birc6	G	A	17: 74,999,305 (GRCm39)	V4678M	probably damaging	Het
Bmpr1a	A	G	14: 34,136,694 (GRCm39)	V499A	probably benign	Het
Ccdc142	A	G	6: 83,079,259 (GRCm39)	N199D	probably benign	Het
Ccdc179	G	T	7: 51,663,311 (GRCm39)	Y38*	probably null	Het
Cdhr2	A	T	13: 54,867,394 (GRCm39)	M438L	probably benign	Het
Cfap74	A	T	4: 155,549,373 (GRCm39)	Q78L	unknown	Het
Crocc	A	T	4: 140,774,335 (GRCm39)	S155T	probably benign	Het
Depdc5	T	A	5: 33,081,567 (GRCm39)	H576Q	possibly damaging	Het
Dhx30	A	T	9: 109,922,214 (GRCm39)	L156Q	probably damaging	Het
Dido1	T	A	2: 180,315,068 (GRCm39)	T795S	probably benign	Het
Dlx1	T	C	2: 71,360,476 (GRCm39)	S47P	probably benign	Het
Dspp	G	A	5: 104,323,636 (GRCm39)	A260T	possibly damaging	Het
Ephx2	T	C	14: 66,326,957 (GRCm39)	T413A	probably benign	Het
Erp44	A	C	4: 48,205,166 (GRCm39)	L276V	probably benign	Het
Fastkd5	T	A	2: 130,457,729 (GRCm39)	Q287L	probably damaging	Het
Foxh1	T	A	15: 76,553,460 (GRCm39)	H114L	possibly damaging	Het
Fry	A	T	5: 150,292,984 (GRCm39)	L410F	probably damaging	Het
Gamt	T	A	10: 80,095,672 (GRCm39)	H86L	probably damaging	Het
Gdpd5	G	T	7: 99,104,241 (GRCm39)	R483L	probably benign	Het
Gm17067	A	C	7: 42,357,569 (GRCm39)	V311G	probably benign	Het
Gpatch2	C	T	1: 187,054,542 (GRCm39)	T422I	probably damaging	Het
Gpi1	A	G	7: 33,901,879 (GRCm39)	I546T	probably damaging	Het
Gyg1	A	C	3: 20,177,007 (GRCm39)	S328A	probably benign	Het
Heatr1	T	A	13: 12,441,679 (GRCm39)	V1491E	probably benign	Het
Hrob	A	T	11: 102,146,586 (GRCm39)	Q287H	possibly damaging	Het
Ildr2	T	C	1: 166,137,038 (GRCm39)	S626P	probably benign	Het
Insr	T	G	8: 3,205,874 (GRCm39)	E1305A	probably benign	Het
Iqca1	T	A	1: 89,998,258 (GRCm39)	T572S	probably benign	Het
Lama1	A	G	17: 68,024,170 (GRCm39)	I89M		Het
Larp7	T	C	3: 127,334,211 (GRCm39)	K539E	probably damaging	Het
Mmadhc	C	A	2: 50,186,482 (GRCm39)		probably benign	Het
Mmp2	A	G	8: 93,567,114 (GRCm39)	D478G	probably damaging	Het
Nat10	T	C	2: 103,578,538 (GRCm39)	Q222R	probably benign	Het
Nlgn1	A	T	3: 25,488,182 (GRCm39)	Y718N	probably damaging	Het
Nlrp5	A	T	7: 23,107,576 (GRCm39)	E83V	probably benign	Het
Odc1	T	C	12: 17,598,614 (GRCm39)	V218A	possibly damaging	Het
Or10al4	A	T	17: 38,037,796 (GRCm39)	I294F	probably damaging	Het
Or11g26	G	C	14: 50,753,552 (GRCm39)	R297T	probably damaging	Het
Or9r3	A	G	10: 129,948,029 (GRCm39)	I210T	probably damaging	Het
Oxsr1	G	A	9: 119,083,932 (GRCm39)	S324F	probably damaging	Het
Pclo	C	T	5: 14,731,788 (GRCm39)	T304M		Het
Pgghg	A	G	7: 140,526,743 (GRCm39)	R687G	possibly damaging	Het
Plxna4	A	G	6: 32,228,044 (GRCm39)	S521P	probably damaging	Het
Rasgrp4	A	G	7: 28,839,917 (GRCm39)	S172G	probably damaging	Het
Rora	A	G	9: 69,255,450 (GRCm39)	D78G	probably damaging	Het
Sec1	G	T	7: 45,328,556 (GRCm39)	R164S	probably benign	Het
Sesn3	A	G	9: 14,225,999 (GRCm39)	N245D	probably benign	Het
Slc44a5	T	A	3: 153,953,370 (GRCm39)	W251R	possibly damaging	Het
Ssr2	T	C	3: 88,487,206 (GRCm39)	V7A	possibly damaging	Het
Syne2	A	G	12: 76,151,875 (GRCm39)	D1912G	possibly damaging	Het
Tcea2	C	A	2: 181,322,984 (GRCm39)	T1N	probably benign	Het
Tmem131l	T	C	3: 83,836,018 (GRCm39)	Y697C	probably damaging	Het
Tmx4	T	C	2: 134,481,588 (GRCm39)	M112V	probably benign	Het
Tom1	G	T	8: 75,785,495 (GRCm39)	A330S	probably benign	Het
Trip4	A	T	9: 65,765,616 (GRCm39)	L361*	probably null	Het
Trmt9b	T	C	8: 36,979,210 (GRCm39)	I271T	probably benign	Het
Trp73	T	G	4: 154,165,788 (GRCm39)	T142P	probably damaging	Het
Trpm5	T	A	7: 142,634,498 (GRCm39)	D683V	possibly damaging	Het
Trpm7	T	C	2: 126,667,562 (GRCm39)	I810V	probably damaging	Het
Trps1	A	T	15: 50,524,944 (GRCm39)	S995R	probably benign	Het
Ttn	C	A	2: 76,608,269 (GRCm39)	E17885*	probably null	Het
Uggt2	A	T	14: 119,256,312 (GRCm39)	Y1120N	probably damaging	Het
Unc13a	A	T	8: 72,104,882 (GRCm39)	N793K	probably damaging	Het
Vcf1	T	C	11: 113,568,146 (GRCm39)	D103G	probably damaging	Het
Vmn2r94	T	C	17: 18,463,884 (GRCm39)	H802R	probably benign	Het
Vmn2r-ps158	T	C	7: 42,697,171 (GRCm39)	C743R	probably damaging	Het
Zdhhc5	A	T	2: 84,524,750 (GRCm39)	M190K	probably benign	Het
Zfp719	A	T	7: 43,233,602 (GRCm39)	N7I	possibly damaging	Het
Zfp735	A	G	11: 73,580,600 (GRCm39)	Y33C	probably damaging	Het
Zgrf1	C	T	3: 127,355,251 (GRCm39)	T159I	probably benign	Het
Zzef1	A	T	11: 72,760,651 (GRCm39)	T1325S	probably benign	Het

Other mutations in Kdm4a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01670:Kdm4a	APN	4	118,017,698 (GRCm39)	missense	probably damaging	1.00
IGL01845:Kdm4a	APN	4	118,017,656 (GRCm39)	missense	possibly damaging	0.85
IGL02009:Kdm4a	APN	4	118,017,366 (GRCm39)	missense	probably benign	0.01
IGL02296:Kdm4a	APN	4	118,034,662 (GRCm39)	missense	probably damaging	1.00
IGL02366:Kdm4a	APN	4	118,017,703 (GRCm39)	critical splice acceptor site	probably null
IGL02606:Kdm4a	APN	4	118,017,486 (GRCm39)	missense	probably benign	0.00
IGL02673:Kdm4a	APN	4	118,025,769 (GRCm39)	missense	probably benign	0.00
R0245:Kdm4a	UTSW	4	118,032,886 (GRCm39)	missense	probably benign	0.05
R0326:Kdm4a	UTSW	4	118,018,903 (GRCm39)	missense	probably benign	0.00
R0551:Kdm4a	UTSW	4	117,995,428 (GRCm39)	makesense	probably null
R0603:Kdm4a	UTSW	4	117,999,708 (GRCm39)	missense	probably damaging	1.00
R0652:Kdm4a	UTSW	4	118,032,886 (GRCm39)	missense	probably benign	0.05
R0799:Kdm4a	UTSW	4	118,004,189 (GRCm39)	splice site	probably null
R0847:Kdm4a	UTSW	4	118,021,695 (GRCm39)	missense	probably damaging	0.96
R1307:Kdm4a	UTSW	4	118,032,839 (GRCm39)	missense	probably benign	0.02
R1572:Kdm4a	UTSW	4	117,996,146 (GRCm39)	missense	possibly damaging	0.89
R1869:Kdm4a	UTSW	4	117,996,068 (GRCm39)	missense	probably null	1.00
R1902:Kdm4a	UTSW	4	118,017,596 (GRCm39)	missense	probably benign	0.38
R1903:Kdm4a	UTSW	4	118,017,596 (GRCm39)	missense	probably benign	0.38
R2135:Kdm4a	UTSW	4	117,999,656 (GRCm39)	missense	probably damaging	1.00
R3856:Kdm4a	UTSW	4	118,010,428 (GRCm39)	missense	probably damaging	1.00
R4687:Kdm4a	UTSW	4	118,001,280 (GRCm39)	missense	probably damaging	1.00
R4940:Kdm4a	UTSW	4	118,018,951 (GRCm39)	missense	probably benign	0.00
R5115:Kdm4a	UTSW	4	118,019,778 (GRCm39)	missense	possibly damaging	0.75
R5229:Kdm4a	UTSW	4	118,003,802 (GRCm39)	missense	probably damaging	0.99
R5305:Kdm4a	UTSW	4	118,017,698 (GRCm39)	missense	probably damaging	1.00
R5423:Kdm4a	UTSW	4	117,996,105 (GRCm39)	missense	probably damaging	1.00
R5750:Kdm4a	UTSW	4	117,999,396 (GRCm39)	intron	probably benign
R5849:Kdm4a	UTSW	4	118,019,037 (GRCm39)	missense	probably benign	0.17
R5876:Kdm4a	UTSW	4	117,996,073 (GRCm39)	missense	probably damaging	0.98
R6564:Kdm4a	UTSW	4	118,034,636 (GRCm39)	missense	probably benign	0.18
R6772:Kdm4a	UTSW	4	117,999,752 (GRCm39)	critical splice acceptor site	probably null
R6982:Kdm4a	UTSW	4	118,010,636 (GRCm39)	splice site	probably null
R7410:Kdm4a	UTSW	4	118,001,115 (GRCm39)	missense	possibly damaging	0.64
R7418:Kdm4a	UTSW	4	118,017,440 (GRCm39)	missense	probably damaging	0.99
R8808:Kdm4a	UTSW	4	117,999,480 (GRCm39)	missense	unknown
R8956:Kdm4a	UTSW	4	118,019,013 (GRCm39)	missense	possibly damaging	0.69
R8958:Kdm4a	UTSW	4	117,999,573 (GRCm39)	missense	probably benign	0.08
R9233:Kdm4a	UTSW	4	118,004,193 (GRCm39)	critical splice donor site	probably null
R9281:Kdm4a	UTSW	4	117,995,728 (GRCm39)	missense	probably damaging	1.00
R9647:Kdm4a	UTSW	4	118,017,399 (GRCm39)	missense	probably benign
Z1176:Kdm4a	UTSW	4	118,034,699 (GRCm39)	missense	probably benign	0.41
Z1176:Kdm4a	UTSW	4	118,010,387 (GRCm39)	missense	probably benign	0.00
Z1177:Kdm4a	UTSW	4	118,004,366 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- AGATCCACTGGCTCTGACATC -3'
(R):5'- GGGAGCTGTACCAGTGAATC -3'

Sequencing Primer
(F):5'- GGCTCTGACATCTCCGAGTAC -3'
(R):5'- GTACCAGTGAATCCACAGTTTCTGAC -3'

Posted On

2022-10-06