Mutagenetix > Incidental Mutation

Incidental Mutation 'R9046:Kdm3a'

688046

Institutional Source

Beutler Lab

Gene Symbol

Kdm3a

Ensembl Gene

ENSMUSG00000053470

Gene Name

lysine (K)-specific demethylase 3A

Synonyms

1700105C21Rik, Jmjd1, Jmjd1a, Tsga, C230043E16Rik

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R9046 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

71565954-71609963 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 71572540 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 1007 (V1007A)

Ref Sequence

ENSEMBL: ENSMUSP00000065716 (fasta)

Gene Model

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

AlphaFold

Q6PCM1

Predicted Effect

probably damaging
Transcript: ENSMUST00000065509
AA Change: V1007A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: V1007A

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000167220
AA Change: V1007A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: V1007A

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 damaging
Transcript: ENSMUST00000207023
AA Change: V1007A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.8%

Validation Efficiency

99% (66/67)

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	T	C	11: 9,243,525 (GRCm39)	V1796A	probably benign	Het
Abca3	A	G	17: 24,617,477 (GRCm39)	D1058G	probably damaging	Het
Adgrg6	A	G	10: 14,323,858 (GRCm39)	V431A	probably benign	Het
Amdhd1	C	T	10: 93,363,087 (GRCm39)	D334N	probably damaging	Het
Ankrd50	A	T	3: 38,506,642 (GRCm39)	M252K	probably benign	Het
Anxa3	G	A	5: 96,976,626 (GRCm39)	R204Q	probably damaging	Het
Apmap	T	C	2: 150,426,093 (GRCm39)	T352A	probably benign	Het
Arhgef4	A	G	1: 34,850,846 (GRCm39)	E464G	possibly damaging	Het
Atp11b	T	A	3: 35,852,740 (GRCm39)		probably benign	Het
Brwd1	T	A	16: 95,829,402 (GRCm39)	S1100C	probably damaging	Het
Ccm2l	T	A	2: 152,916,720 (GRCm39)	I317N	probably damaging	Het
Ccr9	C	T	9: 123,608,831 (GRCm39)	T171I	probably benign	Het
Cdh23	A	T	10: 60,218,303 (GRCm39)		probably benign	Het
Dact1	A	G	12: 71,365,534 (GRCm39)	I735V	probably benign	Het
Dok6	C	A	18: 89,787,221 (GRCm39)	V14L	probably benign	Het
Dthd1	A	T	5: 62,984,603 (GRCm39)	Y436F	possibly damaging	Het
Fndc9	G	T	11: 46,128,889 (GRCm39)	W136L	probably damaging	Het
Gal3st1	G	A	11: 3,948,278 (GRCm39)	V162I	probably benign	Het
Gart	A	G	16: 91,418,561 (GRCm39)	S973P	probably damaging	Het
H2-T5	A	T	17: 36,476,035 (GRCm39)		probably null	Het
Hsp90ab1	G	A	17: 45,879,969 (GRCm39)	P516S	probably damaging	Het
Htr1a	G	C	13: 105,581,816 (GRCm39)	G352A	probably damaging	Het
Hycc2	T	C	1: 58,568,945 (GRCm39)	T545A	probably damaging	Het
Isg20	A	T	7: 78,569,823 (GRCm39)	R265*	probably null	Het
Kcmf1	C	T	6: 72,825,455 (GRCm39)	A213T	probably damaging	Het
Klhl25	A	G	7: 75,515,337 (GRCm39)	E81G	probably damaging	Het
Klhl6	C	A	16: 19,765,803 (GRCm39)	V600F	probably damaging	Het
Kmt2b	A	G	7: 30,285,479 (GRCm39)	V471A	probably benign	Het
Lap3	A	G	5: 45,652,562 (GRCm39)	T53A	probably damaging	Het
Lmntd1	A	T	6: 145,365,565 (GRCm39)	I188N	probably damaging	Het
Lrba	A	G	3: 86,302,543 (GRCm39)	I1868V	possibly damaging	Het
Mef2d	A	T	3: 88,074,825 (GRCm39)	Y337F	probably benign	Het
Mgat4e	T	C	1: 134,474,742 (GRCm39)	T7A	possibly damaging	Het
Myo3a	G	T	2: 22,448,367 (GRCm39)	L985F	probably damaging	Het
Myof	T	C	19: 37,923,112 (GRCm39)		probably benign	Het
Ncapg2	G	A	12: 116,376,145 (GRCm39)	G77S	probably benign	Het
Nostrin	G	T	2: 68,975,123 (GRCm39)	V13L	probably benign	Het
Nup155	TGGG	TGG	15: 8,157,919 (GRCm39)		probably null	Het
Or14j6	A	G	17: 38,215,145 (GRCm39)	K236R	probably damaging	Het
Or3a10	T	C	11: 73,935,284 (GRCm39)	D272G	probably damaging	Het
Or4a75	C	T	2: 89,448,496 (GRCm39)		probably benign	Het
Or5b101	T	C	19: 13,005,115 (GRCm39)	N193D	probably benign	Het
Parp4	A	C	14: 56,864,927 (GRCm39)	K1025T	probably damaging	Het
Parvb	T	C	15: 84,174,639 (GRCm39)	I144T	probably benign	Het
Peg10	GC	GCTCC	6: 4,756,452 (GRCm39)		probably benign	Het
Phf10	A	G	17: 15,175,160 (GRCm39)	V195A	probably damaging	Het
Prpf18	A	T	2: 4,640,464 (GRCm39)	M257K	possibly damaging	Het
Ptcd3	A	T	6: 71,870,364 (GRCm39)		probably null	Het
Ptprt	G	A	2: 161,372,361 (GRCm39)	T1437M	possibly damaging	Het
Ptx3	T	C	3: 66,132,153 (GRCm39)	F225L	probably damaging	Het
Rpl3l	A	G	17: 24,947,435 (GRCm39)	K50E	probably damaging	Het
Rubcn	T	C	16: 32,661,940 (GRCm39)	N427D	probably benign	Het
Serpinb8	G	A	1: 107,530,563 (GRCm39)	A114T	possibly damaging	Het
Sgsm1	A	G	5: 113,436,725 (GRCm39)	V35A	probably damaging	Het
Slc22a2	G	A	17: 12,834,234 (GRCm39)	A501T	probably null	Het
Slu7	G	A	11: 43,335,629 (GRCm39)	C455Y	probably damaging	Het
Src	C	A	2: 157,307,795 (GRCm39)	H235N	probably damaging	Het
Svopl	T	A	6: 37,998,531 (GRCm39)	M248L	probably benign	Het
Tbx6	G	A	7: 126,381,120 (GRCm39)		probably null	Het
Tprg1l	A	T	4: 154,242,913 (GRCm39)	I239N	probably damaging	Het
Trafd1	A	G	5: 121,513,189 (GRCm39)	F350L	probably benign	Het
Trpv3	A	G	11: 73,176,698 (GRCm39)	Y359C	probably damaging	Het
Vmn1r46	T	C	6: 89,953,585 (GRCm39)	S145P	probably damaging	Het
Vmn2r11	A	T	5: 109,202,850 (GRCm39)	F76I	probably benign	Het
Xpot	A	T	10: 121,432,149 (GRCm39)	C916*	probably null	Het
Zfp236	C	T	18: 82,637,042 (GRCm39)	E1415K	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
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
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
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'- TACAGATCCGGATTACTCAGAAC -3'
(R):5'- CATTTCACCAGCCGAGACTG -3'

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

Posted On

2021-11-19