Mutagenetix > Incidental Mutation

Incidental Mutation 'R7090:Kdm3a'

550150

Institutional Source

Beutler Lab

Gene Symbol

Kdm3a

Ensembl Gene

ENSMUSG00000053470

Gene Name

lysine (K)-specific demethylase 3A

Synonyms

1700105C21Rik, Jmjd1, Jmjd1a, Tsga, C230043E16Rik

MMRRC Submission

045184-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R7090 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

71565954-71609963 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 71572529 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 1011 (T1011A)

Ref Sequence

ENSEMBL: ENSMUSP00000065716 (fasta)

Gene Model

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

AlphaFold

Q6PCM1

Predicted Effect

possibly damaging
Transcript: ENSMUST00000065509
AA Change: T1011A

PolyPhen 2 Score 0.691 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: T1011A

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000167220
AA Change: T1011A

PolyPhen 2 Score 0.691 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: T1011A

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000207023
AA Change: T1011A

PolyPhen 2 Score 0.691 (Sensitivity: 0.86; Specificity: 0.92)

Meta Mutation Damage Score

0.1293

Coding Region Coverage

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

Validation Efficiency

100% (66/66)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Calm3	A	T	7: 16,651,004 (GRCm39)	Y139*	probably null	Het
Ccdc27	T	C	4: 154,112,523 (GRCm39)	N584S	probably benign	Het
Cdh24	C	G	14: 54,876,964 (GRCm39)	G13A	probably damaging	Het
Chd8	T	C	14: 52,452,677 (GRCm39)	K1281E	probably damaging	Het
Clasp1	G	T	1: 118,409,816 (GRCm39)	G4C	probably benign	Het
Cul9	G	T	17: 46,811,765 (GRCm39)	P2488T	probably damaging	Het
Daam2	A	G	17: 49,789,973 (GRCm39)	V428A	probably damaging	Het
Dcaf8	A	G	1: 172,016,535 (GRCm39)	S441G	probably damaging	Het
Dchs2	A	G	3: 83,255,581 (GRCm39)	T2426A	probably benign	Het
Dnai3	C	A	3: 145,746,582 (GRCm39)	K881N	possibly damaging	Het
Dpys	A	G	15: 39,690,279 (GRCm39)	V358A	probably damaging	Het
Efhd1	A	G	1: 87,217,219 (GRCm39)	D112G	probably damaging	Het
Exoc1	T	C	5: 76,714,800 (GRCm39)	S120P	unknown	Het
Fyco1	A	G	9: 123,626,784 (GRCm39)	L1309S	probably damaging	Het
Gm14403	A	G	2: 177,201,114 (GRCm39)	N111S	possibly damaging	Het
Gm5901	A	G	7: 105,026,555 (GRCm39)	T108A	probably benign	Het
Idh2	TCCCAGG	T	7: 79,748,079 (GRCm39)		probably benign	Het
Itgb5	T	G	16: 33,705,464 (GRCm39)	D251E	probably damaging	Het
Kcnk15	T	C	2: 163,700,637 (GRCm39)	V292A	probably benign	Het
Kdm2a	A	T	19: 4,369,169 (GRCm39)	Y1149N	probably damaging	Het
Krt35	A	T	11: 99,986,498 (GRCm39)		probably null	Het
Lipn	T	A	19: 34,049,180 (GRCm39)	D115E	possibly damaging	Het
Lpin3	T	G	2: 160,738,672 (GRCm39)	L208R	probably damaging	Het
Ltf	C	A	9: 110,855,048 (GRCm39)	Q354K	probably benign	Het
Marf1	C	A	16: 13,929,566 (GRCm39)	C1680F	possibly damaging	Het
Mtss2	T	A	8: 111,456,656 (GRCm39)	V242E	probably damaging	Het
Myo7b	T	C	18: 32,131,765 (GRCm39)	Y477C	probably damaging	Het
Nbn	T	A	4: 15,981,350 (GRCm39)	S481T	probably benign	Het
Ncoa2	A	G	1: 13,257,062 (GRCm39)	Y146H	probably damaging	Het
Ntng1	A	T	3: 109,842,496 (GRCm39)	C92*	probably null	Het
Or10ad1b	C	T	15: 98,125,083 (GRCm39)	V150I	probably benign	Het
Or2n1b	G	A	17: 38,460,385 (GRCm39)	G302D	probably benign	Het
Or8k18	T	A	2: 86,085,420 (GRCm39)	N206Y	probably damaging	Het
Or8k31-ps1	T	C	2: 86,356,471 (GRCm39)	I17V	probably benign	Het
Os9	A	T	10: 126,935,547 (GRCm39)	S308T	probably benign	Het
Otx2	T	A	14: 48,896,192 (GRCm39)	T289S	probably benign	Het
Pakap	C	T	4: 57,648,042 (GRCm39)	A60V	probably benign	Het
Pigg	A	G	5: 108,484,378 (GRCm39)	T675A	possibly damaging	Het
Pink1	C	T	4: 138,042,912 (GRCm39)	E461K	probably damaging	Het
Pip5k1a	A	G	3: 94,967,809 (GRCm39)	S543P	possibly damaging	Het
Prkaa1	A	G	15: 5,206,611 (GRCm39)	T454A	probably benign	Het
Ptk2	G	A	15: 73,093,658 (GRCm39)	P854S	possibly damaging	Het
Rab31	C	T	17: 66,005,012 (GRCm39)	V83I	possibly damaging	Het
Rabggtb	G	T	3: 153,615,986 (GRCm39)	D117E	probably benign	Het
Rbl1	T	C	2: 156,994,820 (GRCm39)	H951R	probably benign	Het
Sapcd2	A	G	2: 25,266,091 (GRCm39)	S314G	probably benign	Het
Septin4	T	C	11: 87,475,264 (GRCm39)	L164P	probably damaging	Het
Shroom1	A	G	11: 53,356,760 (GRCm39)	E541G	probably damaging	Het
Slc26a7	C	A	4: 14,565,460 (GRCm39)	G208*	probably null	Het
Smco2	A	G	6: 146,772,711 (GRCm39)	I304M	probably damaging	Het
Spg7	T	C	8: 123,818,491 (GRCm39)		probably null	Het
Spocd1	T	C	4: 129,847,691 (GRCm39)	F552L		Het
St6galnac2	T	C	11: 116,568,461 (GRCm39)	D334G	probably damaging	Het
Sub1	A	G	15: 11,986,572 (GRCm39)	S92P	probably benign	Het
Syne2	T	C	12: 75,989,125 (GRCm39)	F1829L	probably benign	Het
Tdrd1	T	C	19: 56,839,833 (GRCm39)	V631A	probably benign	Het
Tdrd9	T	C	12: 111,958,904 (GRCm39)	S113P	probably benign	Het
Tgfbrap1	A	C	1: 43,110,725 (GRCm39)	V260G	probably damaging	Het
Tyw3	G	C	3: 154,299,426 (GRCm39)	S94R	probably benign	Het
Urb2	T	C	8: 124,757,338 (GRCm39)	V1015A	probably benign	Het
Usp5	A	G	6: 124,806,357 (GRCm39)	M1T	probably null	Het
Utrn	T	C	10: 12,560,260 (GRCm39)	D1343G	possibly damaging	Het
Vmn2r56	T	C	7: 12,449,254 (GRCm39)	Y328C	probably damaging	Het
Vmn2r99	A	T	17: 19,613,972 (GRCm39)	E564V	possibly damaging	Het
Zc3h8	T	C	2: 128,777,241 (GRCm39)	T133A	possibly damaging	Het

Other mutations in Kdm3a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02168:Kdm3a	APN	6	71,577,101 (GRCm39)	missense	probably damaging	1.00
IGL02219:Kdm3a	APN	6	71,577,718 (GRCm39)	missense	probably benign	0.01
IGL02423:Kdm3a	APN	6	71,590,987 (GRCm39)	splice site	probably benign
IGL02427:Kdm3a	APN	6	71,569,184 (GRCm39)	splice site	probably benign
IGL02519:Kdm3a	APN	6	71,588,570 (GRCm39)	missense	probably benign	0.04
IGL03143:Kdm3a	APN	6	71,573,845 (GRCm39)	missense	probably damaging	0.98
IGL03279:Kdm3a	APN	6	71,588,659 (GRCm39)	missense	probably benign
R0194:Kdm3a	UTSW	6	71,601,578 (GRCm39)	missense	probably null	0.44
R0408:Kdm3a	UTSW	6	71,588,663 (GRCm39)	missense	probably benign	0.00
R0426:Kdm3a	UTSW	6	71,577,739 (GRCm39)	missense	probably damaging	1.00
R0608:Kdm3a	UTSW	6	71,597,030 (GRCm39)	missense	probably benign	0.01
R1175:Kdm3a	UTSW	6	71,577,011 (GRCm39)	missense	possibly damaging	0.94
R1835:Kdm3a	UTSW	6	71,590,940 (GRCm39)	missense	probably benign	0.14
R3821:Kdm3a	UTSW	6	71,588,661 (GRCm39)	missense	probably benign	0.00
R5083:Kdm3a	UTSW	6	71,598,346 (GRCm39)	missense	probably damaging	1.00
R5536:Kdm3a	UTSW	6	71,588,920 (GRCm39)	missense	probably benign	0.31
R5903:Kdm3a	UTSW	6	71,609,234 (GRCm39)	start gained	probably benign
R5965:Kdm3a	UTSW	6	71,598,364 (GRCm39)	missense	probably benign	0.21
R6236:Kdm3a	UTSW	6	71,588,641 (GRCm39)	missense	probably benign	0.00
R6541:Kdm3a	UTSW	6	71,571,517 (GRCm39)	missense	possibly damaging	0.69
R6666:Kdm3a	UTSW	6	71,588,974 (GRCm39)	missense	probably benign	0.00
R7112:Kdm3a	UTSW	6	71,609,154 (GRCm39)	missense	probably benign
R7136:Kdm3a	UTSW	6	71,588,764 (GRCm39)	missense	probably benign	0.00
R7163:Kdm3a	UTSW	6	71,609,061 (GRCm39)	missense	probably damaging	1.00
R7608:Kdm3a	UTSW	6	71,577,731 (GRCm39)	missense	probably benign	0.01
R7614:Kdm3a	UTSW	6	71,568,937 (GRCm39)	missense	possibly damaging	0.82
R7683:Kdm3a	UTSW	6	71,576,438 (GRCm39)	missense	probably benign
R7687:Kdm3a	UTSW	6	71,576,476 (GRCm39)	missense	possibly damaging	0.64
R7868:Kdm3a	UTSW	6	71,572,473 (GRCm39)	missense	probably benign	0.31
R8447:Kdm3a	UTSW	6	71,588,881 (GRCm39)	missense	probably benign
R8476:Kdm3a	UTSW	6	71,588,693 (GRCm39)	missense	probably damaging	0.98
R8933:Kdm3a	UTSW	6	71,577,092 (GRCm39)	missense	probably benign	0.00
R9046:Kdm3a	UTSW	6	71,572,540 (GRCm39)	missense	probably damaging	1.00
R9211:Kdm3a	UTSW	6	71,573,674 (GRCm39)	missense	probably benign	0.07
R9569:Kdm3a	UTSW	6	71,584,434 (GRCm39)	missense	probably benign	0.02
R9727:Kdm3a	UTSW	6	71,569,094 (GRCm39)	nonsense	probably null
RF053:Kdm3a	UTSW	6	71,609,033 (GRCm39)	critical splice donor site	probably benign

Predicted Primers

PCR Primer
(F):5'- ACAGATCCGGATTACTCAGAAC -3'
(R):5'- TTTCACCAGCCGAGACTGAG -3'

Sequencing Primer
(F):5'- CAGATCCGGATTACTCAGAACTATTC -3'
(R):5'- TGAGGGCCAGCTGCTTGAAG -3'

Posted On

2019-05-15