Mutagenetix > Incidental Mutations

Incidental Mutation 'R0408:Kdm3a'

40085

Institutional Source

Beutler Lab

Gene Symbol

Kdm3a

Ensembl Gene

ENSMUSG00000053470

Gene Name

lysine (K)-specific demethylase 3A

Synonyms

C230043E16Rik, Jmjd1a, Tsga, 1700105C21Rik, Jmjd1

MMRRC Submission

038610-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.962) question?

Stock #

R0408 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

71588972-71632990 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 71611679 bp

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Asparagine at position 449 (D449N)

Ref Sequence

ENSEMBL: ENSMUSP00000145959 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000065509] [ENSMUST00000167220] [ENSMUST00000205289] [ENSMUST00000207023]

Predicted Effect

probably benign
Transcript: ENSMUST00000065509
AA Change: D449N

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: D449N

Domain	Start	End	E-Value	Type
low complexity region	853	859	N/A	INTRINSIC
JmjC	1060	1283	1.6e-56	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000167220
AA Change: D449N

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: D449N

Domain	Start	End	E-Value	Type
low complexity region	853	859	N/A	INTRINSIC
JmjC	1060	1283	1.6e-56	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000205289
AA Change: D449N

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205470

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206597

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206704

Predicted Effect

probably benign
Transcript: ENSMUST00000206916

Predicted Effect

probably benign
Transcript: ENSMUST00000207023
AA Change: D449N

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.6%
20x: 93.7%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a zinc finger protein that contains a jumonji domain and may play a role in hormone-dependent transcriptional activation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
PHENOTYPE: Male mice homozygous for a hypomorphic allele display infertility, oligoasthenoteratozoospermia, small testis, and impaired spermiogenesis. Mice homozygous for a null allele exhibit abnormal spermatogenesis and obesity associated with hyperlipidemia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb1b	T	A	5: 8,853,446	N1032K	probably damaging	Het
Abcc8	A	G	7: 46,107,033	I1416T	probably damaging	Het
Aco2	T	C	15: 81,913,118		probably null	Het
Akap13	C	T	7: 75,746,796	L2514F	probably damaging	Het
Aldh1a3	A	G	7: 66,406,050	V331A	probably damaging	Het
Arid3a	T	A	10: 79,950,833	D473E	probably benign	Het
Atg9a	A	G	1: 75,185,295	S536P	probably damaging	Het
Atxn7	A	T	14: 14,100,317	S668C	probably damaging	Het
Bcar3	A	T	3: 122,508,384	I243F	probably damaging	Het
Bend6	G	A	1: 33,862,753	P183S	probably damaging	Het
Bfsp2	A	T	9: 103,480,100	S43T	probably benign	Het
Camk4	G	A	18: 33,129,792	D136N	probably damaging	Het
Ceacam3	G	T	7: 17,151,883		probably benign	Het
Chrm3	T	C	13: 9,877,933	I356V	probably benign	Het
Clec9a	T	A	6: 129,419,569	I133N	possibly damaging	Het
Ctnnd2	T	C	15: 30,634,677	L157P	probably damaging	Het
Ddhd2	T	C	8: 25,739,587		probably null	Het
Def8	T	C	8: 123,459,917	V436A	probably damaging	Het
Dock10	T	C	1: 80,540,476	K1293R	probably benign	Het
Dync1h1	T	G	12: 110,631,692	D1772E	probably benign	Het
Ephx4	G	T	5: 107,413,521	G72C	probably damaging	Het
Fam136a	T	G	6: 86,366,725	V68G	possibly damaging	Het
Fam69c	T	A	18: 84,720,363		probably null	Het
Fcgrt	T	C	7: 45,101,939	E195G	probably damaging	Het
Fut9	T	A	4: 25,620,319	Q165L	possibly damaging	Het
Glb1l	T	C	1: 75,208,835	Y77C	probably damaging	Het
Gm16286	T	C	18: 80,211,814	S108P	probably damaging	Het
Gpr26	T	C	7: 131,967,520	V198A	possibly damaging	Het
Gpr26	C	A	7: 131,974,272		probably null	Het
Gsdma3	A	C	11: 98,635,338	E296A	probably benign	Het
Hyou1	G	T	9: 44,384,692	G385W	probably damaging	Het
Il17rb	T	C	14: 29,996,680	S482G	probably benign	Het
Itgb4	A	T	11: 116,007,602	R1715W	probably damaging	Het
Jak2	A	G	19: 29,286,317	S411G	probably benign	Het
Kif1bp	T	C	10: 62,566,053	I23M	probably benign	Het
Klhl26	T	C	8: 70,452,480	D226G	probably damaging	Het
Klra1	T	A	6: 130,377,774	I94F	probably benign	Het
Lama3	A	G	18: 12,456,837	D808G	probably benign	Het
Lrp1b	C	T	2: 40,677,591	M272I	probably damaging	Het
Masp2	A	G	4: 148,606,039	D251G	probably benign	Het
Mob3b	T	C	4: 35,083,991	D66G	probably damaging	Het
Myo7a	T	C	7: 98,056,781	Q1863R	probably damaging	Het
Olfr119	G	A	17: 37,701,299	V210I	probably benign	Het
Olfr1195	A	T	2: 88,683,655	F26I	probably benign	Het
Pdgfd	T	A	9: 6,293,928	Y167*	probably null	Het
Pfas	A	G	11: 69,001,105		probably null	Het
Plin1	T	A	7: 79,722,646	T393S	probably damaging	Het
Prdm15	A	T	16: 97,835,786	N110K	possibly damaging	Het
Prune2	T	A	19: 17,122,310	V1726D	probably benign	Het
Sestd1	T	A	2: 77,191,793	D518V	probably damaging	Het
Setd2	C	T	9: 110,594,242	P344S	probably damaging	Het
Slc22a1	A	T	17: 12,656,941	I462N	probably damaging	Het
Slc6a1	G	A	6: 114,302,800	V142I	probably benign	Het
Tbc1d14	G	T	5: 36,571,299	T241K	possibly damaging	Het
Uaca	T	C	9: 60,871,859	L1176P	possibly damaging	Het
Ube2g1	G	C	11: 72,672,965	G52A	probably damaging	Het
Utrn	A	G	10: 12,384,190	*957R	probably null	Het
Vmn2r125	A	T	4: 156,350,858	E177V	probably damaging	Het
Vmn2r86	A	G	10: 130,446,854	F631S	probably damaging	Het
Zc3h13	T	A	14: 75,292,186	C42*	probably null	Het
Zc3h14	T	G	12: 98,763,823	V13G	probably damaging	Het
Zfat	A	T	15: 68,180,292	V551D	probably benign	Het
Zfp618	C	T	4: 63,086,572	R70W	probably damaging	Het

Other mutations in Kdm3a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02168:Kdm3a	APN	6	71600117	missense	probably damaging	1.00
IGL02219:Kdm3a	APN	6	71600734	missense	probably benign	0.01
IGL02423:Kdm3a	APN	6	71614003	splice site	probably benign
IGL02427:Kdm3a	APN	6	71592200	splice site	probably benign
IGL02519:Kdm3a	APN	6	71611586	missense	probably benign	0.04
IGL03143:Kdm3a	APN	6	71596861	missense	probably damaging	0.98
IGL03279:Kdm3a	APN	6	71611675	missense	probably benign
R0194:Kdm3a	UTSW	6	71624594	missense	probably null	0.44
R0426:Kdm3a	UTSW	6	71600755	missense	probably damaging	1.00
R0608:Kdm3a	UTSW	6	71620046	missense	probably benign	0.01
R1175:Kdm3a	UTSW	6	71600027	missense	possibly damaging	0.94
R1835:Kdm3a	UTSW	6	71613956	missense	probably benign	0.14
R3821:Kdm3a	UTSW	6	71611677	missense	probably benign	0.00
R5083:Kdm3a	UTSW	6	71621362	missense	probably damaging	1.00
R5536:Kdm3a	UTSW	6	71611936	missense	probably benign	0.31
R5903:Kdm3a	UTSW	6	71632250	start gained	probably benign
R5965:Kdm3a	UTSW	6	71621380	missense	probably benign	0.21
R6236:Kdm3a	UTSW	6	71611657	missense	probably benign	0.00
R6541:Kdm3a	UTSW	6	71594533	missense	possibly damaging	0.69
R6666:Kdm3a	UTSW	6	71611990	missense	probably benign	0.00
R7090:Kdm3a	UTSW	6	71595545	missense	possibly damaging	0.69
R7112:Kdm3a	UTSW	6	71632170	missense	probably benign
R7136:Kdm3a	UTSW	6	71611780	missense	probably benign	0.00
R7163:Kdm3a	UTSW	6	71632077	missense	probably damaging	1.00
R7608:Kdm3a	UTSW	6	71600747	missense	probably benign	0.01
R7614:Kdm3a	UTSW	6	71591953	missense	possibly damaging	0.82
R7683:Kdm3a	UTSW	6	71599454	missense	probably benign
R7687:Kdm3a	UTSW	6	71599492	missense	possibly damaging	0.64
R7868:Kdm3a	UTSW	6	71595489	missense	probably benign	0.31
R8447:Kdm3a	UTSW	6	71611897	missense	probably benign
R8476:Kdm3a	UTSW	6	71611709	missense	probably damaging	0.98
RF053:Kdm3a	UTSW	6	71632049	critical splice donor site	probably benign

Predicted Primers

PCR Primer
(F):5'- GTGTACCATCTTCTCTGCACTAAGAGC -3'
(R):5'- AATTCTGAGTGAGCCCAAAGGTAGC -3'

Sequencing Primer
(F):5'- ACTTGAACTACCTGTGTGAGAGC -3'
(R):5'- GAGCCCAAAGGTAGCTGTATCC -3'

Posted On

2013-05-23