Mutagenetix > Incidental Mutation

Incidental Mutation 'R7868:Kdm3a'

607911

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

045920-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R7868 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

71565954-71609963 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 71572473 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 1029 (D1029E)

Ref Sequence

ENSEMBL: ENSMUSP00000065716 (fasta)

Gene Model

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

AlphaFold

Q6PCM1

Predicted Effect

probably benign
Transcript: ENSMUST00000065509
AA Change: D1029E

PolyPhen 2 Score 0.305 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: D1029E

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: D1029E

PolyPhen 2 Score 0.305 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: D1029E

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

probably benign
Transcript: ENSMUST00000207023
AA Change: D1029E

PolyPhen 2 Score 0.305 (Sensitivity: 0.90; Specificity: 0.89)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

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: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933415A04Rik	GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT	GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT	11: 43,478,257 (GRCm39)		probably null	Het
Acacb	A	G	5: 114,386,288 (GRCm39)	E2274G	probably benign	Het
Adam7	A	G	14: 68,770,090 (GRCm39)	I21T	possibly damaging	Het
Aldh3b3	C	T	19: 4,018,492 (GRCm39)	R57*	probably null	Het
Arhgap22	T	C	14: 33,086,473 (GRCm39)		probably benign	Het
B4galt5	G	T	2: 167,143,340 (GRCm39)	Y361*	probably null	Het
BC005537	C	T	13: 24,987,382 (GRCm39)	R7W	possibly damaging	Het
Bsn	G	T	9: 107,992,098 (GRCm39)	A1218D	possibly damaging	Het
Ccdc141	T	C	2: 76,938,756 (GRCm39)	D283G	probably damaging	Het
Ccdc33	T	A	9: 57,976,374 (GRCm39)	I547F	probably benign	Het
Chdh	A	G	14: 29,753,288 (GRCm39)	N66D	probably benign	Het
Ckap2l	T	A	2: 129,127,209 (GRCm39)	Q323L	probably damaging	Het
Cpvl	T	A	6: 53,951,745 (GRCm39)	I13F	possibly damaging	Het
Creb3l2	G	A	6: 37,312,804 (GRCm39)	P410L	probably damaging	Het
Dna2	T	C	10: 62,805,643 (GRCm39)	V960A	probably benign	Het
Dop1a	G	A	9: 86,384,037 (GRCm39)		probably null	Het
Dpysl5	A	T	5: 30,902,760 (GRCm39)	D64V	probably damaging	Het
Dysf	A	G	6: 84,091,081 (GRCm39)	Q1041R	probably benign	Het
Efcab7	T	C	4: 99,746,154 (GRCm39)	V242A	probably benign	Het
Ehbp1	G	A	11: 22,096,542 (GRCm39)	R341*	probably null	Het
Eif1ad8	G	T	12: 87,563,388 (GRCm39)		probably benign	Het
Fbxo32	A	T	15: 58,077,986 (GRCm39)	W8R	probably damaging	Het
Fpgs	T	C	2: 32,573,472 (GRCm39)	N455D	probably damaging	Het
Fsip1	G	A	2: 117,966,967 (GRCm39)	Q453*	probably null	Het
Gm8257	T	A	14: 44,894,754 (GRCm39)	E12V	probably damaging	Het
Lipo4	T	G	19: 33,488,968 (GRCm39)	Q205P	possibly damaging	Het
Lpar6	A	T	14: 73,476,435 (GRCm39)	N132I	probably damaging	Het
Lrp1b	C	T	2: 41,339,246 (GRCm39)	G866S		Het
Man2c1	T	C	9: 57,045,270 (GRCm39)	F460L	probably damaging	Het
Map3k7cl	T	C	16: 87,378,100 (GRCm39)	V72A	probably damaging	Het
Map4k1	A	T	7: 28,699,387 (GRCm39)		probably null	Het
Matn1	A	G	4: 130,682,311 (GRCm39)	E496G	probably damaging	Het
Mfsd2a	A	T	4: 122,850,648 (GRCm39)	V76E	possibly damaging	Het
Mmut	C	T	17: 41,257,934 (GRCm39)	R367C	probably damaging	Het
Mtpap	A	G	18: 4,380,673 (GRCm39)	E117G	probably damaging	Het
Muc17	T	A	5: 137,175,625 (GRCm39)	N15I		Het
Ndufa10	A	G	1: 92,388,169 (GRCm39)	Y275H	probably damaging	Het
Nlrc4	A	T	17: 74,755,047 (GRCm39)	H56Q	possibly damaging	Het
Nrde2	G	A	12: 100,097,446 (GRCm39)	R785C	possibly damaging	Het
Nsun4	C	A	4: 115,891,329 (GRCm39)	C350F	probably benign	Het
Or10x1	A	G	1: 174,196,551 (GRCm39)	T23A	probably benign	Het
Or51f23b	A	G	7: 102,402,812 (GRCm39)	L108P	possibly damaging	Het
Or8g2	T	A	9: 39,821,282 (GRCm39)	F61Y	probably benign	Het
Or9s14	G	A	1: 92,536,237 (GRCm39)	G226D	possibly damaging	Het
Pdcd7	T	A	9: 65,254,261 (GRCm39)	C280S	probably damaging	Het
Peak1	G	T	9: 56,167,754 (GRCm39)	T58K	probably damaging	Het
Phactr2	T	C	10: 13,108,353 (GRCm39)	E573G	probably damaging	Het
Pramel27	A	G	4: 143,578,154 (GRCm39)	H138R	possibly damaging	Het
Ptprz1	G	A	6: 23,000,963 (GRCm39)	A1018T	not run	Het
Ralgapa1	G	T	12: 55,659,423 (GRCm39)	D2032E	probably benign	Het
Rapgef4	T	A	2: 72,031,481 (GRCm39)	N488K	probably benign	Het
Slc1a2	A	G	2: 102,591,530 (GRCm39)	D420G	probably benign	Het
Smyd5	T	A	6: 85,421,297 (GRCm39)	L337Q	probably damaging	Het
Tenm4	G	A	7: 96,555,587 (GRCm39)	R2764H	possibly damaging	Het
Tex35	A	T	1: 156,926,908 (GRCm39)	Y195*	probably null	Het
Tln2	T	C	9: 67,255,508 (GRCm39)	K690E	probably damaging	Het
Trpc4	A	G	3: 54,209,707 (GRCm39)	T691A	probably benign	Het
Tsr1	T	A	11: 74,791,158 (GRCm39)	F246I	possibly damaging	Het
Ttn	ATATCTCTCCAGAGCCTCCCCTGGAGGAGTGGAGTATCTCTCCAGAGCCTCCCCTGGAGGAGTGGAGTATCTCTCCAGAGCCTCCCCTG	ATATCTCTCCAGAGCCTCCCCTGGAGGAGTGGAGTATCTCTCCAGAGCCTCCCCTG	2: 76,746,150 (GRCm39)		probably benign	Het
Ubr4	A	T	4: 139,187,344 (GRCm39)	Y669F	unknown	Het
Uox	A	C	3: 146,316,029 (GRCm39)	D12A	probably benign	Het
Wdr17	A	G	8: 55,149,302 (GRCm39)		probably null	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
R7090:Kdm3a	UTSW	6	71,572,529 (GRCm39)	missense	possibly damaging	0.69
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
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'- GAAGGACCATCTGTGTCCTCTTC -3'
(R):5'- CCTTTAGCCAGTGATGGTGTC -3'

Sequencing Primer
(F):5'- TGAACTCTACAGATCCGGATTACTC -3'
(R):5'- GTCGGGCGTGCATCATAAATTAAAC -3'

Posted On

2019-12-20