Mutagenetix > Incidental Mutation

Incidental Mutation 'R1835:Kdm3a'

205158

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

039862-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.960) question?

Stock #

R1835 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

71588972-71632990 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 71613956 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 295 (T295S)

Ref Sequence

ENSEMBL: ENSMUSP00000145719 (fasta)

Gene Model

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

AlphaFold

Q6PCM1

Predicted Effect

probably benign
Transcript: ENSMUST00000065509
AA Change: T295S

PolyPhen 2 Score 0.087 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000065716
Gene: ENSMUSG00000053470
AA Change: T295S

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: ENSMUST00000167220
AA Change: T295S

PolyPhen 2 Score 0.087 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000128789
Gene: ENSMUSG00000053470
AA Change: T295S

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
AA Change: T295S

PolyPhen 2 Score 0.141 (Sensitivity: 0.92; Specificity: 0.86)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205470

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206597

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206704

Predicted Effect

probably benign
Transcript: ENSMUST00000206916

Predicted Effect

probably benign
Transcript: ENSMUST00000207023
AA Change: T295S

PolyPhen 2 Score 0.087 (Sensitivity: 0.93; Specificity: 0.85)

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 94.9%
20x: 91.0%

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610507B11Rik	G	T	11: 78,287,750	V1993F	probably damaging	Het
4933425L06Rik	C	A	13: 105,082,194	A12E	unknown	Het
Acss2	T	A	2: 155,558,630	Y530N	probably damaging	Het
Adam4	T	C	12: 81,419,559	I763V	probably benign	Het
Aipl1	T	G	11: 72,030,499	K190T	possibly damaging	Het
Alms1	T	A	6: 85,678,503	S3344T	possibly damaging	Het
Alpi	A	G	1: 87,099,414	V381A	possibly damaging	Het
Ankfn1	A	T	11: 89,447,618	S365R	probably benign	Het
Aox2	G	A	1: 58,308,991	A623T	probably benign	Het
Apc	T	A	18: 34,317,077	L2308Q	probably damaging	Het
Atp9b	C	T	18: 80,778,883	V501I	probably benign	Het
Baz2b	T	C	2: 59,901,819	E1994G	probably benign	Het
Cacna1a	T	C	8: 84,581,357		probably null	Het
Cacna1h	C	A	17: 25,392,076	V583L	probably benign	Het
Cd55	T	C	1: 130,447,609		probably benign	Het
Cep192	T	A	18: 67,804,424	S75T	possibly damaging	Het
Cfap54	T	A	10: 92,962,375	D1674V	probably benign	Het
Churc1	T	C	12: 76,773,297	F27L	possibly damaging	Het
Coro1c	A	G	5: 113,848,543	I280T	probably benign	Het
Creb1	C	T	1: 64,550,950	Q32*	probably null	Het
Cyp2b9	A	G	7: 26,200,783	T339A	probably benign	Het
Dctn3	T	C	4: 41,720,813	R51G	probably damaging	Het
Ddb1	T	C	19: 10,626,593	V888A	probably damaging	Het
Disp1	A	G	1: 183,089,000	Y619H	probably damaging	Het
Dnajc9	T	C	14: 20,388,334	D96G	possibly damaging	Het
Eepd1	A	G	9: 25,482,868	T143A	possibly damaging	Het
Eps8	T	A	6: 137,522,279	K204*	probably null	Het
Ercc5	T	A	1: 44,180,875	S1102R	probably benign	Het
Ergic2	T	A	6: 148,189,581	Y211F	possibly damaging	Het
Fam135b	G	T	15: 71,490,711	L274M	probably damaging	Het
Fat3	G	A	9: 15,998,088	T2206I	probably damaging	Het
Fat4	A	G	3: 38,983,571	I3791V	probably benign	Het
Gemin4	A	G	11: 76,213,296	M213T	possibly damaging	Het
Gnai3	T	C	3: 108,118,407	M119V	probably benign	Het
Heatr5b	A	T	17: 78,773,563	L1420Q	probably damaging	Het
Herc2	G	T	7: 56,206,765	G3918*	probably null	Het
Ints9	A	G	14: 65,032,256	Y465C	probably damaging	Het
Ist1	A	G	8: 109,678,883	V175A	probably damaging	Het
Kcnj12	T	C	11: 61,069,557	L227P	possibly damaging	Het
Kcnq5	T	C	1: 21,466,387	S416G	probably benign	Het
Kif1c	T	A	11: 70,708,971	M479K	probably damaging	Het
Kif20b	T	C	19: 34,956,038	L83P	probably damaging	Het
Kndc1	A	G	7: 139,927,711	E1194G	probably damaging	Het
Llgl1	A	G	11: 60,704,730	M81V	probably benign	Het
Map4k5	C	A	12: 69,824,662	M495I	probably damaging	Het
Mest	C	T	6: 30,742,791	R146C	probably benign	Het
Mettl24	T	A	10: 40,737,816		probably null	Het
Mical1	T	C	10: 41,483,535	S586P	probably benign	Het
Mrgpra3	G	T	7: 47,589,946	Y77*	probably null	Het
Mss51	A	T	14: 20,483,178	C408*	probably null	Het
Myh6	T	C	14: 54,957,401	T666A	probably benign	Het
Myo10	T	C	15: 25,805,587	C1685R	possibly damaging	Het
Naip5	A	T	13: 100,223,218	Y503*	probably null	Het
Neil1	A	C	9: 57,146,604	F144C	probably damaging	Het
Nipbl	T	A	15: 8,343,517	I1082F	possibly damaging	Het
Nkiras1	T	C	14: 18,276,732	V7A	probably damaging	Het
Ntng2	G	A	2: 29,197,057	Q384*	probably null	Het
Ocrl	T	A	X: 47,962,116	I74N	probably damaging	Het
Olfr137	A	T	17: 38,305,312	S50T	probably benign	Het
Olfr1385	A	T	11: 49,494,670	I46F	probably damaging	Het
Olfr1408	A	G	1: 173,130,815	V134A	probably benign	Het
Olfr381	A	C	11: 73,486,374	V150G	probably benign	Het
Olfr535	A	G	7: 140,492,709	S24G	probably benign	Het
Olfr761	C	T	17: 37,952,385	G213E	possibly damaging	Het
Patj	A	G	4: 98,491,590	D151G	probably benign	Het
Plpbp	T	C	8: 27,049,231	V126A	probably damaging	Het
Pold2	A	G	11: 5,873,454	L325P	possibly damaging	Het
Ppp1r12c	A	C	7: 4,483,651	S480A	probably damaging	Het
Pum1	T	C	4: 130,701,048	S124P	possibly damaging	Het
Pwp2	C	G	10: 78,179,091	G353A	probably damaging	Het
Reln	C	A	5: 21,979,002	Q1666H	probably damaging	Het
Rnf19a	T	C	15: 36,265,925	I9V	probably benign	Het
Ryr2	T	C	13: 11,769,878	H1063R	probably benign	Het
Samd14	C	G	11: 95,023,600	D361E	probably damaging	Het
Samd15	A	T	12: 87,201,843	N365I	probably damaging	Het
Sec16b	A	G	1: 157,531,312	H105R	probably benign	Het
Sez6	T	C	11: 77,953,503	S51P	probably benign	Het
Sh3bp1	T	A	15: 78,905,150	L236Q	probably damaging	Het
Sspo	C	T	6: 48,457,340	T991I	probably damaging	Het
Suco	A	T	1: 161,859,500	L97*	probably null	Het
Tab1	C	A	15: 80,148,296	R35S	probably benign	Het
Tet3	C	A	6: 83,404,163	S341I	possibly damaging	Het
Tlr1	A	T	5: 64,925,700	D511E	probably benign	Het
Tmem132b	A	C	5: 125,785,899	D656A	probably damaging	Het
Tmtc4	T	A	14: 122,941,988		probably null	Het
Trmo	T	C	4: 46,380,158	T404A	probably damaging	Het
Trpm1	A	G	7: 64,230,268	K790E	probably damaging	Het
Ulk4	C	A	9: 121,168,184	R774M	probably null	Het
Ush2a	C	T	1: 188,451,818	L1440F	probably benign	Het
Usp16	A	G	16: 87,480,907	K682E	probably damaging	Het
Virma	T	C	4: 11,540,511	S1471P	probably benign	Het
Vmn1r177	A	T	7: 23,865,686	I255N	probably damaging	Het
Vmn2r61	A	T	7: 42,266,652	R230*	probably null	Het
Vps13c	T	A	9: 67,993,013	F3671L	probably benign	Het
Washc5	T	C	15: 59,359,340	N358S	possibly damaging	Het
Wdr72	A	G	9: 74,151,617	K331E	probably damaging	Het
Zfp986	A	T	4: 145,899,235	K155I	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
R0194:Kdm3a	UTSW	6	71624594	missense	probably null	0.44
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
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'- TTGAAGGCCCCTGGTCAATC -3'
(R):5'- AGATCAGCTTGTAACCTTACAGG -3'

Sequencing Primer
(F):5'- TGGTCAATCCGTCCCAAGGAG -3'
(R):5'- TTTTTGAAAACCAGGGTGCTC -3'

Posted On

2014-06-23