Mutagenetix > Incidental Mutation

Incidental Mutation 'R0426:Kdm3a'

38640

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

038628-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.962) question?

Stock #

R0426 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

71565954-71609963 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 71577739 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Tyrosine at position 687 (C687Y)

Ref Sequence

ENSEMBL: ENSMUSP00000145959 (fasta)

Gene Model

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

AlphaFold

Q6PCM1

Predicted Effect

probably damaging
Transcript: ENSMUST00000065509
AA Change: C687Y

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: C687Y

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: C687Y

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: C687Y

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: ENSMUST00000205289
AA Change: C687Y

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205470

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205505

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206050

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206339

Predicted Effect

probably damaging
Transcript: ENSMUST00000207023
AA Change: C687Y

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Predicted Effect

probably benign
Transcript: ENSMUST00000206916

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206798

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206704

Meta Mutation Damage Score

0.9604

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.9%

Validation Efficiency

96% (86/90)

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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8b	G	T	11: 109,845,853 (GRCm39)		probably benign	Het
Acadl	A	T	1: 66,880,805 (GRCm39)	F320L	probably damaging	Het
Acsbg1	T	C	9: 54,530,030 (GRCm39)	D222G	probably benign	Het
Anapc15	A	G	7: 101,547,240 (GRCm39)	T39A	probably benign	Het
Ano3	A	T	2: 110,491,519 (GRCm39)	V919E	probably damaging	Het
Arhgef12	T	C	9: 42,882,286 (GRCm39)		probably null	Het
Atad5	T	A	11: 80,003,658 (GRCm39)	I1091N	probably benign	Het
Atf1	A	T	15: 100,130,708 (GRCm39)	H26L	possibly damaging	Het
Atp10a	T	C	7: 58,434,482 (GRCm39)	M252T	probably benign	Het
Btbd8	C	T	5: 107,658,239 (GRCm39)	T1603I	probably damaging	Het
Cd55	C	T	1: 130,376,109 (GRCm39)	R347H	probably benign	Het
Cdc27	A	C	11: 104,403,853 (GRCm39)		probably null	Het
Cdh9	G	A	15: 16,823,540 (GRCm39)		probably null	Het
Cdk11b	T	C	4: 155,726,969 (GRCm39)		probably benign	Het
Cep70	A	G	9: 99,179,737 (GRCm39)	D567G	probably benign	Het
Cep78	A	T	19: 15,948,334 (GRCm39)	Y382*	probably null	Het
Cgas	G	A	9: 78,343,020 (GRCm39)		probably benign	Het
Col9a2	T	C	4: 120,901,857 (GRCm39)		probably benign	Het
Cyp2d12	G	A	15: 82,443,164 (GRCm39)	D409N	probably benign	Het
Ddx39a	A	G	8: 84,448,398 (GRCm39)	T217A	probably benign	Het
Dennd1b	T	A	1: 139,097,934 (GRCm39)	D733E	probably benign	Het
Dicer1	A	G	12: 104,668,801 (GRCm39)	S1294P	probably damaging	Het
Dnah3	T	C	7: 119,542,795 (GRCm39)	E3539G	probably benign	Het
Dnmbp	A	G	19: 43,840,875 (GRCm39)		probably benign	Het
Dysf	T	C	6: 84,126,739 (GRCm39)	L1332P	probably damaging	Het
F5	A	G	1: 164,010,409 (GRCm39)	D380G	probably damaging	Het
Fam171a1	T	C	2: 3,226,433 (GRCm39)	V522A	probably benign	Het
Fhip1b	A	C	7: 105,038,680 (GRCm39)	C186W	probably damaging	Het
Galr2	C	A	11: 116,172,517 (GRCm39)	A69D	probably damaging	Het
Grk2	T	C	19: 4,340,628 (GRCm39)		probably null	Het
Gtf3c1	A	T	7: 125,262,188 (GRCm39)	Y1119*	probably null	Het
Hgd	A	T	16: 37,409,047 (GRCm39)		probably benign	Het
Ildr2	G	T	1: 166,136,468 (GRCm39)	V436L	probably benign	Het
Intu	G	A	3: 40,629,735 (GRCm39)	C355Y	probably damaging	Het
Irf2bpl	G	T	12: 86,929,870 (GRCm39)	P268T	probably benign	Het
Jarid2	T	C	13: 44,994,358 (GRCm39)		probably null	Het
Jup	A	T	11: 100,263,227 (GRCm39)	M716K	probably benign	Het
Kank1	G	A	19: 25,388,837 (GRCm39)	V809I	probably damaging	Het
Kdm1b	T	A	13: 47,217,720 (GRCm39)		probably benign	Het
Kdm5d	T	A	Y: 942,437 (GRCm39)		probably benign	Het
Kifap3	T	A	1: 163,693,121 (GRCm39)		probably benign	Het
Macf1	T	A	4: 123,377,453 (GRCm39)	K1400*	probably null	Het
Majin	A	G	19: 6,262,147 (GRCm39)		probably benign	Het
Mctp1	A	G	13: 77,168,940 (GRCm39)	I846V	probably benign	Het
Mrgpra2b	T	A	7: 47,113,875 (GRCm39)	I286F	possibly damaging	Het
Neil3	T	G	8: 54,062,431 (GRCm39)		probably benign	Het
Nox3	G	T	17: 3,745,838 (GRCm39)	N23K	probably damaging	Het
Nt5c3	T	C	6: 56,860,797 (GRCm39)	K219E	probably benign	Het
Or1e29	T	A	11: 73,667,263 (GRCm39)	M297L	probably benign	Het
Or52b4i	T	A	7: 102,191,893 (GRCm39)	I250N	probably damaging	Het
Or5b105	G	A	19: 13,080,642 (GRCm39)	R3C	possibly damaging	Het
Or6b13	A	C	7: 139,782,029 (GRCm39)	F218C	possibly damaging	Het
Or6d13	A	T	6: 116,517,446 (GRCm39)	N11Y	probably damaging	Het
Or8g34	T	C	9: 39,372,889 (GRCm39)	L54P	probably damaging	Het
Pacsin2	A	G	15: 83,263,996 (GRCm39)	V347A	possibly damaging	Het
Pcdhb7	A	T	18: 37,475,857 (GRCm39)	E331V	probably damaging	Het
Pcid2	A	C	8: 13,131,262 (GRCm39)		probably null	Het
Pcsk9	T	C	4: 106,307,274 (GRCm39)	D323G	possibly damaging	Het
Pdhb	T	C	14: 8,169,801 (GRCm38)	E203G	probably damaging	Het
Phlpp2	A	G	8: 110,655,095 (GRCm39)	Y630C	probably benign	Het
Pidd1	C	T	7: 141,019,046 (GRCm39)	A812T	probably damaging	Het
Plau	G	A	14: 20,892,382 (GRCm39)	R389H	probably benign	Het
Plekhg6	G	A	6: 125,341,592 (GRCm39)		probably null	Het
Ppox	T	C	1: 171,105,322 (GRCm39)	Y321C	probably damaging	Het
Pxdn	A	G	12: 30,037,065 (GRCm39)	N281S	possibly damaging	Het
Pycr3	A	T	15: 75,790,237 (GRCm39)	M138K	probably benign	Het
Radil	T	C	5: 142,483,628 (GRCm39)	Y526C	probably damaging	Het
Ranbp3	C	A	17: 57,014,169 (GRCm39)	D233E	probably benign	Het
Rhpn1	A	G	15: 75,583,721 (GRCm39)	Q402R	possibly damaging	Het
Sec23b	T	A	2: 144,410,532 (GRCm39)		probably benign	Het
Sel1l2	A	T	2: 140,082,832 (GRCm39)	L602*	probably null	Het
Sema5b	G	A	16: 35,466,725 (GRCm39)	G209D	probably damaging	Het
Svep1	T	C	4: 58,073,333 (GRCm39)	Y1992C	possibly damaging	Het
Syncrip	T	A	9: 88,338,312 (GRCm39)		probably benign	Het
Synj1	G	T	16: 90,764,242 (GRCm39)	A65E	probably damaging	Het
Taar2	G	A	10: 23,817,393 (GRCm39)	R311H	probably benign	Het
Tecrl	T	C	5: 83,502,610 (GRCm39)		probably benign	Het
Tenm4	G	T	7: 96,427,058 (GRCm39)	G698C	probably damaging	Het
Tmem209	G	A	6: 30,491,181 (GRCm39)	L259F	probably damaging	Het
Tmem247	G	A	17: 87,225,931 (GRCm39)	E124K	possibly damaging	Het
Tnks2	C	A	19: 36,830,221 (GRCm39)	A218E	probably damaging	Het
Tppp	T	A	13: 74,169,430 (GRCm39)	F57I	probably damaging	Het
Trim36	A	G	18: 46,305,592 (GRCm39)	W452R	probably damaging	Het
Vars2	A	T	17: 35,975,476 (GRCm39)	V262E	probably damaging	Het
Vmn2r92	C	T	17: 18,388,219 (GRCm39)	A408V	probably damaging	Het
Zfp516	G	T	18: 82,973,897 (GRCm39)	A32S	probably benign	Het
Zfy2	G	T	Y: 2,107,348 (GRCm39)	L429I	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
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
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'- ATCCCTCCTTCCTGAAATGGGCAC -3'
(R):5'- TCAGAAACCCTCTGTACCTCAGGC -3'

Sequencing Primer
(F):5'- TACTATGCAGTCCCTGAGAGC -3'
(R):5'- GCCTAAATGGCTTATTGATTTTTGC -3'

Posted On

2013-05-23