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

C230043E16Rik, Jmjd1a, Tsga, 1700105C21Rik, Jmjd1

MMRRC Submission

038628-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.965) question?

Stock #

R0426 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

71588972-71632990 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 71600755 bp (GRCm38)

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

noncoding transcript
Transcript: ENSMUST00000206704

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206798

Predicted Effect

probably benign
Transcript: ENSMUST00000206916

Predicted Effect

probably damaging
Transcript: ENSMUST00000207023
AA Change: C687Y

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

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
A830010M20Rik	C	T	5: 107,510,373	T1603I	probably damaging	Het
Abca8b	G	T	11: 109,955,027		probably benign	Het
Acadl	A	T	1: 66,841,646	F320L	probably damaging	Het
Acsbg1	T	C	9: 54,622,746	D222G	probably benign	Het
Anapc15	A	G	7: 101,898,033	T39A	probably benign	Het
Ano3	A	T	2: 110,661,174	V919E	probably damaging	Het
Arhgef12	T	C	9: 42,970,990		probably null	Het
Atad5	T	A	11: 80,112,832	I1091N	probably benign	Het
Atf1	A	T	15: 100,232,827	H26L	possibly damaging	Het
Atp10a	T	C	7: 58,784,734	M252T	probably benign	Het
Cd55	C	T	1: 130,448,372	R347H	probably benign	Het
Cdc27	A	C	11: 104,513,027		probably null	Het
Cdh9	G	A	15: 16,823,454		probably null	Het
Cdk11b	T	C	4: 155,642,512		probably benign	Het
Cep70	A	G	9: 99,297,684	D567G	probably benign	Het
Cep78	A	T	19: 15,970,970	Y382*	probably null	Het
Col9a2	T	C	4: 121,044,660		probably benign	Het
Cyp2d12	G	A	15: 82,558,963	D409N	probably benign	Het
Ddx39	A	G	8: 83,721,769	T217A	probably benign	Het
Dennd1b	T	A	1: 139,170,196	D733E	probably benign	Het
Dicer1	A	G	12: 104,702,542	S1294P	probably damaging	Het
Dnah3	T	C	7: 119,943,572	E3539G	probably benign	Het
Dnmbp	A	G	19: 43,852,436		probably benign	Het
Dysf	T	C	6: 84,149,757	L1332P	probably damaging	Het
F5	A	G	1: 164,182,840	D380G	probably damaging	Het
Fam160a2	A	C	7: 105,389,473	C186W	probably damaging	Het
Fam171a1	T	C	2: 3,225,396	V522A	probably benign	Het
Galr2	C	A	11: 116,281,691	A69D	probably damaging	Het
Grk2	T	C	19: 4,290,600		probably null	Het
Gtf3c1	A	T	7: 125,663,016	Y1119*	probably null	Het
Hgd	A	T	16: 37,588,685		probably benign	Het
Ildr2	G	T	1: 166,308,899	V436L	probably benign	Het
Intu	G	A	3: 40,675,305	C355Y	probably damaging	Het
Irf2bpl	G	T	12: 86,883,096	P268T	probably benign	Het
Jarid2	T	C	13: 44,840,882		probably null	Het
Jup	A	T	11: 100,372,401	M716K	probably benign	Het
Kank1	G	A	19: 25,411,473	V809I	probably damaging	Het
Kdm1b	T	A	13: 47,064,244		probably benign	Het
Kdm5d	T	A	Y: 942,437		probably benign	Het
Kifap3	T	A	1: 163,865,552		probably benign	Het
Macf1	T	A	4: 123,483,660	K1400*	probably null	Het
Majin	A	G	19: 6,212,117		probably benign	Het
Mb21d1	G	A	9: 78,435,738		probably benign	Het
Mctp1	A	G	13: 77,020,821	I846V	probably benign	Het
Mrgpra2b	T	A	7: 47,464,127	I286F	possibly damaging	Het
Neil3	T	G	8: 53,609,396		probably benign	Het
Nox3	G	T	17: 3,695,563	N23K	probably damaging	Het
Nt5c3	T	C	6: 56,883,812	K219E	probably benign	Het
Olfr1458	G	A	19: 13,103,278	R3C	possibly damaging	Het
Olfr213	A	T	6: 116,540,485	N11Y	probably damaging	Het
Olfr389	T	A	11: 73,776,437	M297L	probably benign	Het
Olfr524	A	C	7: 140,202,116	F218C	possibly damaging	Het
Olfr548-ps1	T	A	7: 102,542,686	I250N	probably damaging	Het
Olfr954	T	C	9: 39,461,593	L54P	probably damaging	Het
Pacsin2	A	G	15: 83,379,795	V347A	possibly damaging	Het
Pcdhb7	A	T	18: 37,342,804	E331V	probably damaging	Het
Pcid2	A	C	8: 13,081,262		probably null	Het
Pcsk9	T	C	4: 106,450,077	D323G	possibly damaging	Het
Pdhb	T	C	14: 8,169,801	E203G	probably damaging	Het
Phlpp2	A	G	8: 109,928,463	Y630C	probably benign	Het
Pidd1	C	T	7: 141,439,133	A812T	probably damaging	Het
Plau	G	A	14: 20,842,314	R389H	probably benign	Het
Plekhg6	G	A	6: 125,364,629		probably null	Het
Ppox	T	C	1: 171,277,749	Y321C	probably damaging	Het
Pxdn	A	G	12: 29,987,066	N281S	possibly damaging	Het
Pycrl	A	T	15: 75,918,388	M138K	probably benign	Het
Radil	T	C	5: 142,497,873	Y526C	probably damaging	Het
Ranbp3	C	A	17: 56,707,169	D233E	probably benign	Het
Rhpn1	A	G	15: 75,711,872	Q402R	possibly damaging	Het
Sec23b	T	A	2: 144,568,612		probably benign	Het
Sel1l2	A	T	2: 140,240,912	L602*	probably null	Het
Sema5b	G	A	16: 35,646,355	G209D	probably damaging	Het
Svep1	T	C	4: 58,073,333	Y1992C	possibly damaging	Het
Syncrip	T	A	9: 88,456,259		probably benign	Het
Synj1	G	T	16: 90,967,354	A65E	probably damaging	Het
Taar2	G	A	10: 23,941,495	R311H	probably benign	Het
Tecrl	T	C	5: 83,354,763		probably benign	Het
Tenm4	G	T	7: 96,777,851	G698C	probably damaging	Het
Tmem209	G	A	6: 30,491,182	L259F	probably damaging	Het
Tmem247	G	A	17: 86,918,503	E124K	possibly damaging	Het
Tnks2	C	A	19: 36,852,821	A218E	probably damaging	Het
Tppp	T	A	13: 74,021,311	F57I	probably damaging	Het
Trim36	A	G	18: 46,172,525	W452R	probably damaging	Het
Vars2	A	T	17: 35,664,584	V262E	probably damaging	Het
Vmn2r92	C	T	17: 18,167,957	A408V	probably damaging	Het
Zfp516	G	T	18: 82,955,772	A32S	probably benign	Het
Zfy2	G	T	Y: 2,107,348	L429I	possibly 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
R0408:Kdm3a	UTSW	6	71611679	missense	probably benign	0.00
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
R8933:Kdm3a	UTSW	6	71600108	missense	probably benign	0.00
R9046:Kdm3a	UTSW	6	71595556	missense	probably damaging	1.00
R9211:Kdm3a	UTSW	6	71596690	missense	probably benign	0.07
RF053:Kdm3a	UTSW	6	71632049	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