Mutagenetix > Incidental Mutation

Incidental Mutation 'R0194:Kdm3a'

23295

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

038453-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.962) question?

Stock #

R0194 (G1)

Quality Score

210

Status

Validated

Chromosome

Chromosomal Location

71588972-71632990 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 71624594 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Arginine at position 151 (Q151R)

Ref Sequence

ENSEMBL: ENSMUSP00000145719 (fasta)

Gene Model

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

AlphaFold

Q6PCM1

Predicted Effect

probably null
Transcript: ENSMUST00000065509
AA Change: Q151R

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: Q151R

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

Predicted Effect

probably null
Transcript: ENSMUST00000167220
AA Change: Q151R

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: Q151R

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

Predicted Effect

probably null
Transcript: ENSMUST00000205289
AA Change: Q151R

PolyPhen 2 Score 0.441 (Sensitivity: 0.89; Specificity: 0.90)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206597

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206704

Predicted Effect

probably null
Transcript: ENSMUST00000207023
AA Change: Q151R

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)

Meta Mutation Damage Score

0.0823

Coding Region Coverage

1x: 98.6%
3x: 97.3%
10x: 91.4%
20x: 70.1%

Validation Efficiency

91% (439/482)

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: 102 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110043O21Rik	T	A	4: 35,197,207	D122V	probably damaging	Het
4930553M12Rik	T	A	4: 88,868,243	D46V	unknown	Het
Abcb9	A	G	5: 124,077,295	V461A	probably damaging	Het
Ackr4	T	A	9: 104,099,480	L89F	probably benign	Het
Acsf2	T	C	11: 94,561,370	T449A	probably benign	Het
Acsl4	C	G	X: 142,333,718	G489R	probably damaging	Het
Actl6a	T	A	3: 32,725,320	I399N	probably damaging	Het
Adamts19	G	A	18: 59,011,148	C934Y	probably null	Het
Adsl	A	G	15: 80,961,360	E40G	possibly damaging	Het
AI481877	T	A	4: 59,066,534		probably benign	Het
Alppl2	T	G	1: 87,088,743	D203A	probably damaging	Het
Asb10	C	A	5: 24,537,932	A268S	probably benign	Het
Atp9a	T	C	2: 168,643,885	S832G	probably benign	Het
Bckdha	A	T	7: 25,631,450	I297N	probably damaging	Het
Blm	G	A	7: 80,464,946		probably benign	Het
Cacna1h	A	G	17: 25,380,924		probably benign	Het
Camsap2	G	A	1: 136,292,948	Q298*	probably null	Het
Ccdc38	A	T	10: 93,565,912	K145*	probably null	Het
Cfap45	C	T	1: 172,541,327	T434M	probably benign	Het
Cfap54	A	T	10: 93,034,662		probably benign	Het
Clcn6	G	A	4: 148,012,756	P618L	probably damaging	Het
Copg1	T	C	6: 87,904,197		probably benign	Het
Dctd	T	A	8: 48,112,078	N79K	probably benign	Het
Dgkq	A	G	5: 108,654,644		probably benign	Het
Dntt	A	T	19: 41,038,970	T159S	possibly damaging	Het
Doc2g	G	A	19: 4,003,656	R29Q	probably benign	Het
Dsg3	A	G	18: 20,540,142	T957A	probably damaging	Het
Eif3c	T	A	7: 126,558,623		probably benign	Het
Ephb3	T	A	16: 21,218,109	D107E	probably benign	Het
Esrrb	A	T	12: 86,470,481	D108V	probably damaging	Het
Exo1	A	G	1: 175,892,030	K214E	probably damaging	Het
Fam186a	G	A	15: 99,941,763	T2200I	possibly damaging	Het
Fam227a	C	T	15: 79,640,669	W194*	probably null	Het
Foxn4	A	G	5: 114,259,748		probably null	Het
Gabbr2	T	C	4: 46,787,565	K366R	possibly damaging	Het
Garem2	T	A	5: 30,113,930	V130E	probably damaging	Het
Grin2b	A	G	6: 135,779,305	F474S	probably damaging	Het
H2-M10.6	G	T	17: 36,814,042	V284F	probably damaging	Het
Helz2	C	A	2: 181,232,759	G1981C	probably damaging	Het
Hivep1	G	T	13: 42,155,435	V384F	probably damaging	Het
Hmox1	A	G	8: 75,097,108	T135A	probably damaging	Het
Hpse	T	C	5: 100,719,512	D28G	probably benign	Het
Itm2b	G	T	14: 73,364,618	D213E	probably benign	Het
Jakmip1	T	A	5: 37,134,283	M692K	possibly damaging	Het
Limch1	C	A	5: 66,999,273	A517E	probably benign	Het
Lrit1	T	A	14: 37,061,720	L335Q	probably damaging	Het
Lrrc37a	A	G	11: 103,499,790	V1603A	possibly damaging	Het
Mbtps1	T	A	8: 119,535,369	N347I	probably damaging	Het
Mier1	A	T	4: 103,139,519		probably null	Het
Mt2	A	T	8: 94,172,848	M1L	probably damaging	Het
Mug1	A	T	6: 121,840,107	E45V	probably damaging	Het
Mybphl	A	G	3: 108,374,168	K67E	probably benign	Het
Myh4	A	G	11: 67,252,336	K1030R	probably damaging	Het
Myl3	T	A	9: 110,769,121	D176E	probably benign	Het
Ncapg2	A	G	12: 116,420,683		probably null	Het
Ndor1	T	C	2: 25,248,706		probably null	Het
Nedd4	T	G	9: 72,670,053	N53K	possibly damaging	Het
Nek11	C	A	9: 105,392,952	A24S	probably benign	Het
Nudt19	G	T	7: 35,551,514	P267T	probably benign	Het
Olfml2b	T	C	1: 170,681,115	M514T	possibly damaging	Het
Olfr304	A	T	7: 86,386,374	C95*	probably null	Het
Olfr424	A	T	1: 174,136,761	T6S	probably benign	Het
Olfr556	A	G	7: 102,670,199	D93G	probably benign	Het
Olfr699	C	A	7: 106,790,823	M59I	probably benign	Het
P3h1	T	A	4: 119,237,952	F302Y	probably damaging	Het
Pappa2	T	A	1: 158,765,101		probably benign	Het
Pex2	A	C	3: 5,561,364	H128Q	probably benign	Het
Phf11d	A	C	14: 59,352,731	L214R	probably damaging	Het
Plcg2	G	A	8: 117,573,397		probably benign	Het
Ppargc1b	A	C	18: 61,307,945	L634R	possibly damaging	Het
Prune1	A	T	3: 95,262,360	I177N	probably damaging	Het
Puf60	T	C	15: 76,070,485	D496G	probably damaging	Het
Rasl11b	A	G	5: 74,196,163		probably null	Het
Sdr42e1	A	T	8: 117,663,109	F264L	probably damaging	Het
Sec24b	A	T	3: 129,984,165		probably null	Het
Sgta	G	T	10: 81,051,059	P79T	probably benign	Het
Shisa9	C	T	16: 11,984,954	T125M	probably damaging	Het
Slc12a2	A	G	18: 57,930,211	D921G	probably damaging	Het
Slc13a5	C	T	11: 72,245,233	V494I	probably benign	Het
Slc13a5	T	A	11: 72,262,130	I42L	possibly damaging	Het
Spire2	G	A	8: 123,363,011		probably benign	Het
Sptbn4	G	A	7: 27,404,911	R962C	probably benign	Het
St8sia5	G	A	18: 77,254,724	V377I	probably benign	Het
Stag2	T	G	X: 42,206,137		probably benign	Het
Syne1	C	A	10: 5,424,311	M165I	probably benign	Het
Synm	C	A	7: 67,734,924	V997L	probably damaging	Het
Tacc1	A	G	8: 25,182,376	S279P	probably benign	Het
Tbc1d10a	T	C	11: 4,212,901		probably null	Het
Tbc1d19	A	G	5: 53,860,156	T302A	probably damaging	Het
Tecpr1	A	C	5: 144,218,517	N74K	probably damaging	Het
Tmem120a	T	C	5: 135,742,398	E28G	possibly damaging	Het
Tnfrsf1b	A	T	4: 145,224,812	I186N	probably benign	Het
Trim55	A	G	3: 19,661,861	D195G	probably benign	Het
Trpm3	G	T	19: 22,715,356		probably null	Het
Ttc39a	T	A	4: 109,444,179	S571T	probably benign	Het
Vwf	T	G	6: 125,643,297	I1646S	probably benign	Het
Wbp2nl	T	C	15: 82,314,282	F340S	possibly damaging	Het
Yeats2	T	C	16: 20,152,969	M1T	probably null	Het
Zfp236	T	A	18: 82,656,987	E460V	probably damaging	Het
Zfp277	G	A	12: 40,378,877		probably benign	Het
Zfp975	T	A	7: 42,662,492	K232N	probably benign	Het
Zxdc	T	C	6: 90,372,537		probably benign	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
R0408:Kdm3a	UTSW	6	71611679	missense	probably benign	0.00
R0426:Kdm3a	UTSW	6	71600755	missense	probably damaging	1.00
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
R9569:Kdm3a	UTSW	6	71607450	missense	probably benign	0.02
R9727:Kdm3a	UTSW	6	71592110	nonsense	probably null
RF053:Kdm3a	UTSW	6	71632049	critical splice donor site	probably benign

Predicted Primers

PCR Primer
(F):5'- CAAACTCACAGGCTATCTAACAGATGCT -3'
(R):5'- AGTGCTTGGAGACGCTGGGA -3'

Sequencing Primer
(F):5'- GGCTATCTAACAGATGCTATACAAC -3'
(R):5'- AGTTCCTGCTTCCAGAATGATG -3'

Posted On

2013-04-16