Mutagenetix > Incidental Mutation

Incidental Mutation 'R7163:Kdm3a'

557729

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

045330-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.962) question?

Stock #

R7163 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

71565954-71609963 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 71609061 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 55 (D55E)

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: D55E

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

SMART Domains

Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: D55E

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: D55E

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

SMART Domains

Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: D55E

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: D55E

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000207023
AA Change: D55E

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930550C14Rik	A	G	9: 53,319,372 (GRCm39)	K4R	possibly damaging	Het
A830018L16Rik	G	A	1: 11,484,848 (GRCm39)	G19D	probably damaging	Het
Abca3	A	T	17: 24,583,916 (GRCm39)	M102L	probably benign	Het
Adam19	A	T	11: 46,022,544 (GRCm39)	Y499F	probably benign	Het
Adck2	T	C	6: 39,560,797 (GRCm39)	V444A	probably damaging	Het
Adck5	T	C	15: 76,478,016 (GRCm39)	V214A	probably damaging	Het
Agrn	G	A	4: 156,262,966 (GRCm39)	T437M	probably damaging	Het
Aox3	A	T	1: 58,158,671 (GRCm39)	I81F	probably damaging	Het
Bcl6	G	A	16: 23,784,976 (GRCm39)	R675*	probably null	Het
Blmh	A	G	11: 76,836,987 (GRCm39)	Y23C	unknown	Het
Cacnb1	A	G	11: 97,903,726 (GRCm39)	V109A	probably benign	Het
Ccdc27	C	T	4: 154,117,282 (GRCm39)	R555H	not run	Het
Cep170	A	C	1: 176,602,031 (GRCm39)	S358R	probably damaging	Het
Cfap46	A	T	7: 139,197,994 (GRCm39)		probably null	Het
Dclk1	G	T	3: 55,163,549 (GRCm39)	E214*	probably null	Het
Dhrs1	A	G	14: 55,976,838 (GRCm39)	L282P	probably benign	Het
Dlgap5	A	G	14: 47,637,095 (GRCm39)	L461P	probably damaging	Het
Elp2	G	T	18: 24,747,503 (GRCm39)	C185F	probably benign	Het
Fbxw7	T	C	3: 84,832,892 (GRCm39)		probably benign	Het
Fga	T	C	3: 82,933,571 (GRCm39)	V17A	probably benign	Het
Gdi1	G	A	X: 73,350,461 (GRCm39)	R55H	probably benign	Het
Gm43302	T	A	5: 105,441,493 (GRCm39)		probably null	Het
Gpatch8	TTCCTCCTCCTCCTCTTCCTCCTCCTC	TTCCTCCTCCTCCTCCTCTTCCTCCTCCTC	11: 102,371,014 (GRCm39)		probably benign	Het
Hcn1	A	T	13: 118,062,083 (GRCm39)	I450L	unknown	Het
Hydin	T	A	8: 111,329,968 (GRCm39)	C4901S	probably benign	Het
Ino80	A	T	2: 119,223,356 (GRCm39)	I1186N	probably damaging	Het
Ints7	T	A	1: 191,349,949 (GRCm39)	I781N	possibly damaging	Het
Irf2	T	A	8: 47,290,712 (GRCm39)	V178E	possibly damaging	Het
Iws1	T	A	18: 32,226,277 (GRCm39)	S722T	possibly damaging	Het
Jak1	G	A	4: 101,032,385 (GRCm39)	S407F	probably damaging	Het
Kdm5d	T	C	Y: 899,940 (GRCm39)	S169P	probably damaging	Het
Kif15	A	G	9: 122,846,722 (GRCm39)	N1348S	probably damaging	Het
Kpna7	G	A	5: 144,939,206 (GRCm39)	P187L	unknown	Het
Krt35	A	T	11: 99,986,984 (GRCm39)	F10Y	probably damaging	Het
Lemd1	G	T	1: 132,184,475 (GRCm39)	V131F	probably benign	Het
Mcf2l	G	A	8: 12,965,439 (GRCm39)	R4H	probably benign	Het
Megf6	C	T	4: 154,351,898 (GRCm39)	R1166C	probably damaging	Het
Mmp11	T	C	10: 75,762,410 (GRCm39)	I308V	possibly damaging	Het
Mrgpra4	A	G	7: 47,631,238 (GRCm39)	V121A	probably benign	Het
Myl2	T	A	5: 122,239,885 (GRCm39)	I26N	probably damaging	Het
Myo15a	A	G	11: 60,389,195 (GRCm39)	M862V		Het
Nckap5l	T	C	15: 99,331,354 (GRCm39)	H64R	probably damaging	Het
Nipsnap2	A	C	5: 129,821,774 (GRCm39)	E90A	probably benign	Het
Nup210	G	T	6: 91,050,313 (GRCm39)	N385K	probably damaging	Het
Or2h2	T	C	17: 37,396,937 (GRCm39)	N40S	probably damaging	Het
Or2t48	C	A	11: 58,419,994 (GRCm39)	E273*	probably null	Het
Or5m11b	T	A	2: 85,805,932 (GRCm39)	L115Q	probably damaging	Het
Or8c19-ps1	T	C	9: 38,220,345 (GRCm39)	F85L	probably damaging	Het
Or9e1	T	C	11: 58,732,012 (GRCm39)	V24A	probably benign	Het
Pcmt1	A	T	10: 7,513,922 (GRCm39)	M249K	probably benign	Het
Pde3a	T	C	6: 141,433,270 (GRCm39)	L767P	probably damaging	Het
Pde8a	T	C	7: 80,956,456 (GRCm39)	V285A	possibly damaging	Het
Pla2g4a	T	A	1: 149,716,416 (GRCm39)	K690*	probably null	Het
Plxna4	T	C	6: 32,473,691 (GRCm39)	H442R	probably benign	Het
Polr1b	A	G	2: 128,967,931 (GRCm39)	D1108G	probably benign	Het
Prkn	G	A	17: 12,280,434 (GRCm39)	C430Y	probably damaging	Het
Sec23ip	T	C	7: 128,364,257 (GRCm39)		probably null	Het
Slc24a3	A	G	2: 145,086,911 (GRCm39)	D57G	probably benign	Het
Sprtn	T	G	8: 125,625,044 (GRCm39)	F50V	probably damaging	Het
Srr	A	G	11: 74,803,828 (GRCm39)	F43S	probably damaging	Het
Szt2	A	G	4: 118,262,727 (GRCm39)	F17L	possibly damaging	Het
Taar1	G	T	10: 23,796,918 (GRCm39)	M205I	probably benign	Het
Tas2r143	A	G	6: 42,377,202 (GRCm39)	I11V	probably benign	Het
Tlx1	T	C	19: 45,139,655 (GRCm39)	S101P	probably damaging	Het
Tmeff2	T	C	1: 50,977,503 (GRCm39)		probably null	Het
Vhl	A	G	6: 113,606,451 (GRCm39)	D156G	possibly damaging	Het
Washc4	T	A	10: 83,426,897 (GRCm39)	D1068E	probably damaging	Het
Zfp513	A	G	5: 31,358,076 (GRCm39)	V101A	probably benign	Het
Zfp82	T	C	7: 29,761,669 (GRCm39)	R71G	probably benign	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
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'- TTTCAAAGACTTTCACGGTCTAGAG -3'
(R):5'- GTGGAAACCATGGTGCTCAC -3'

Sequencing Primer
(F):5'- AAGACTTTCACGGTCTAGAGTTCTG -3'
(R):5'- CTCACGCTCGGAGAAAGTTG -3'

Posted On

2019-06-26