Mutagenetix > Incidental Mutation

Incidental Mutation 'R5514:Jmjd1c'

440245

Institutional Source

Beutler Lab

Gene Symbol

Jmjd1c

Ensembl Gene

ENSMUSG00000037876

Gene Name

jumonji domain containing 1C

Synonyms

D630035I23Rik, TRIP8, 5430433L24Rik

MMRRC Submission

043074-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.655) question?

Stock #

R5514 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

66932189-67092105 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 67053928 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 263 (S263T)

Ref Sequence

ENSEMBL: ENSMUSP00000134551 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000051446] [ENSMUST00000173689] [ENSMUST00000174317] [ENSMUST00000174408]

AlphaFold

Q69ZK6

Predicted Effect

probably damaging
Transcript: ENSMUST00000051446
AA Change: S263T

PolyPhen 2 Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000056227
Gene: ENSMUSG00000037876
AA Change: S263T

Domain	Start	End	E-Value	Type
Blast:JmjC	143	2236	N/A	BLAST
JmjC	2264	2488	3.29e-53	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173187

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173661

Predicted Effect

probably damaging
Transcript: ENSMUST00000173689
AA Change: S82T

PolyPhen 2 Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000133700
Gene: ENSMUSG00000037876
AA Change: S82T

Domain	Start	End	E-Value	Type
Blast:JmjC	1	2056	N/A	BLAST
JmjC	2084	2308	3.29e-53	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000174317

SMART Domains

Protein: ENSMUSP00000134246
Gene: ENSMUSG00000037876

Domain	Start	End	E-Value	Type
Blast:JmjC	1	744	N/A	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000174408
AA Change: S263T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000134551
Gene: ENSMUSG00000037876
AA Change: S263T

Domain	Start	End	E-Value	Type
Blast:JmjC	143	2237	N/A	BLAST
JmjC	2265	2489	3.29e-53	SMART

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.5%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene interacts with thyroid hormone receptors and contains a jumonji domain. It is a candidate histone demethylase and is thought to be a coactivator for key transcription factors. It plays a role in the DNA-damage response pathway by demethylating the mediator of DNA damage checkpoint 1 (MDC1) protein, and is required for the survival of acute myeloid leukemia. Mutations in this gene are associated with Rett syndrome and intellectual disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
PHENOTYPE: Mice homozygous for a null allele exhibit an age-dependent male infertility phenotype, characterized by early loss of undifferentiated spermatogonia, and a progressive reduction in testis size/weight and male germ cells, partly due to increased male germ cell apoptosis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam17	T	C	12: 21,390,520 (GRCm39)	S382G	probably damaging	Het
Agr2	G	A	12: 36,046,090 (GRCm39)	V74I	probably benign	Het
Aldh3a1	T	C	11: 61,108,867 (GRCm39)	S423P	probably damaging	Het
Ampd1	C	T	3: 102,986,488 (GRCm39)	H56Y	possibly damaging	Het
Arhgef2	C	A	3: 88,550,304 (GRCm39)	P670T	probably benign	Het
Blk	T	G	14: 63,615,930 (GRCm39)	D333A	probably damaging	Het
Bmi1	T	C	2: 18,686,714 (GRCm39)	I31T	probably damaging	Het
Cacna1d	G	A	14: 30,072,790 (GRCm39)	Q62*	probably null	Het
Ccdc88c	A	G	12: 100,879,698 (GRCm39)	S1801P	probably damaging	Het
Cdkal1	C	T	13: 29,961,270 (GRCm39)	A100T	probably damaging	Het
Cfap251	G	T	5: 123,425,829 (GRCm39)		probably null	Het
Chst4	G	T	8: 110,756,606 (GRCm39)	S419Y	probably damaging	Het
Cntn4	T	C	6: 106,649,844 (GRCm39)	I680T	probably damaging	Het
Ddx55	T	C	5: 124,694,875 (GRCm39)	V101A	probably damaging	Het
Ddx60	A	T	8: 62,411,091 (GRCm39)	E451V	probably damaging	Het
Dffa	T	A	4: 149,190,772 (GRCm39)		probably null	Het
Dgkd	A	G	1: 87,861,832 (GRCm39)	R796G	probably damaging	Het
Dzank1	T	A	2: 144,323,605 (GRCm39)	M614L	probably benign	Het
Elf2	G	T	3: 51,215,555 (GRCm39)	Q52K	probably damaging	Het
Fcamr	T	A	1: 130,741,793 (GRCm39)	L522Q	probably damaging	Het
Fscn2	T	C	11: 120,258,858 (GRCm39)	Y468H	probably damaging	Het
Gm12689	T	C	4: 99,184,402 (GRCm39)	I85T	unknown	Het
Gm4787	A	G	12: 81,425,102 (GRCm39)	V352A	possibly damaging	Het
Gtsf1	T	C	15: 103,336,802 (GRCm39)	Q13R	probably benign	Het
Itpkb	G	A	1: 180,241,474 (GRCm39)	V715M	probably damaging	Het
Krba1	T	G	6: 48,390,429 (GRCm39)	L736R	probably damaging	Het
Lrrc8d	C	G	5: 105,960,650 (GRCm39)	F353L	probably damaging	Het
Lrrc8d	G	A	5: 105,960,651 (GRCm39)	E354K	probably benign	Het
Mtor	T	A	4: 148,630,901 (GRCm39)	V2286E	probably damaging	Het
Mybbp1a	T	A	11: 72,341,462 (GRCm39)	V1100E	possibly damaging	Het
Myo5a	G	A	9: 75,061,048 (GRCm39)	G518D	probably damaging	Het
Nalcn	A	T	14: 123,521,123 (GRCm39)	I1594N	probably benign	Het
Nav1	C	G	1: 135,398,299 (GRCm39)	G761A	probably benign	Het
Ncoa2	A	T	1: 13,251,445 (GRCm39)	L276H	probably damaging	Het
Ndufaf7	T	C	17: 79,245,051 (GRCm39)	Y57H	probably damaging	Het
Nfkb2	A	G	19: 46,299,847 (GRCm39)	Y807C	probably damaging	Het
Nid2	A	T	14: 19,852,535 (GRCm39)	Q1081L	probably damaging	Het
Nkain2	T	A	10: 31,827,189 (GRCm39)	I134F	probably damaging	Het
Nmu	A	C	5: 76,497,979 (GRCm39)	S69A	probably damaging	Het
Or4c15b	A	T	2: 89,112,817 (GRCm39)	I220N	probably damaging	Het
Or5t7	T	C	2: 86,507,225 (GRCm39)	I151V	probably benign	Het
Pard3	A	G	8: 128,153,086 (GRCm39)	R886G	probably damaging	Het
Pde6b	G	T	5: 108,571,317 (GRCm39)	Q423H	probably benign	Het
Pip5k1b	A	T	19: 24,327,505 (GRCm39)	D450E	probably damaging	Het
Plcg1	T	C	2: 160,595,275 (GRCm39)		probably null	Het
Pnpt1	T	C	11: 29,103,246 (GRCm39)	S504P	possibly damaging	Het
Pomt2	A	T	12: 87,175,797 (GRCm39)	D312E	probably damaging	Het
Ppp1r1b	T	C	11: 98,246,228 (GRCm39)	L70P	probably damaging	Het
Prr5	C	A	15: 84,587,096 (GRCm39)	P282Q	probably benign	Het
Reln	A	T	5: 22,176,883 (GRCm39)	W1928R	possibly damaging	Het
Sacm1l	A	T	9: 123,415,419 (GRCm39)	R465*	probably null	Het
Sema7a	A	G	9: 57,863,046 (GRCm39)	Y239C	probably damaging	Het
Slc35e2	C	T	4: 155,694,483 (GRCm39)	P10L	probably benign	Het
Svep1	T	C	4: 58,044,054 (GRCm39)	T3531A	possibly damaging	Het
Tjp1	A	T	7: 65,004,609 (GRCm39)	W19R	probably damaging	Het
Tmc2	T	A	2: 130,083,564 (GRCm39)	M507K	possibly damaging	Het
Unc13a	A	G	8: 72,095,795 (GRCm39)	Y1241H	probably damaging	Het
Upp1	C	T	11: 9,081,771 (GRCm39)	P103S	probably damaging	Het
Vldlr	A	G	19: 27,221,624 (GRCm39)	E663G	probably damaging	Het
Vmn2r68	G	A	7: 84,886,767 (GRCm39)	T49I	possibly damaging	Het
Xirp2	A	T	2: 67,335,465 (GRCm39)	M95L	probably benign	Het

Other mutations in Jmjd1c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01062:Jmjd1c	APN	10	67,062,494 (GRCm39)	missense	probably damaging	1.00
IGL01604:Jmjd1c	APN	10	67,085,541 (GRCm39)	missense	probably damaging	1.00
IGL01753:Jmjd1c	APN	10	67,067,794 (GRCm39)	missense	probably damaging	1.00
IGL02081:Jmjd1c	APN	10	67,055,305 (GRCm39)	missense	probably benign	0.02
IGL02128:Jmjd1c	APN	10	67,079,648 (GRCm39)	missense	probably damaging	1.00
IGL02134:Jmjd1c	APN	10	67,056,171 (GRCm39)	missense	possibly damaging	0.87
IGL02215:Jmjd1c	APN	10	67,056,101 (GRCm39)	missense	probably damaging	1.00
IGL02408:Jmjd1c	APN	10	67,062,161 (GRCm39)	missense	probably benign	0.00
IGL02502:Jmjd1c	APN	10	67,061,640 (GRCm39)	missense	probably benign	0.13
IGL02546:Jmjd1c	APN	10	67,061,115 (GRCm39)	missense	possibly damaging	0.94
IGL02943:Jmjd1c	APN	10	67,055,433 (GRCm39)	missense	probably damaging	0.99
IGL03171:Jmjd1c	APN	10	67,061,277 (GRCm39)	missense	possibly damaging	0.89
IGL03261:Jmjd1c	APN	10	67,067,849 (GRCm39)	missense	probably damaging	0.99
Accordion	UTSW	10	67,069,193 (GRCm39)	missense	probably damaging	0.99
PIT4378001:Jmjd1c	UTSW	10	67,065,692 (GRCm39)	missense	probably damaging	1.00
R0126:Jmjd1c	UTSW	10	67,055,105 (GRCm39)	missense	probably damaging	0.98
R0133:Jmjd1c	UTSW	10	67,076,587 (GRCm39)	missense	probably benign	0.22
R0201:Jmjd1c	UTSW	10	67,054,888 (GRCm39)	missense	unknown
R0396:Jmjd1c	UTSW	10	67,055,302 (GRCm39)	missense	possibly damaging	0.82
R0401:Jmjd1c	UTSW	10	67,056,161 (GRCm39)	missense	probably damaging	1.00
R0452:Jmjd1c	UTSW	10	67,091,261 (GRCm39)	missense	probably benign	0.28
R0488:Jmjd1c	UTSW	10	67,076,506 (GRCm39)	missense	probably damaging	0.99
R0504:Jmjd1c	UTSW	10	67,061,534 (GRCm39)	missense	probably damaging	1.00
R0555:Jmjd1c	UTSW	10	67,061,568 (GRCm39)	missense	probably benign	0.01
R0673:Jmjd1c	UTSW	10	67,062,588 (GRCm39)	missense	probably damaging	1.00
R0718:Jmjd1c	UTSW	10	67,054,725 (GRCm39)	splice site	probably null
R0755:Jmjd1c	UTSW	10	66,932,378 (GRCm39)	intron	probably benign
R1142:Jmjd1c	UTSW	10	67,061,124 (GRCm39)	missense	probably damaging	1.00
R1196:Jmjd1c	UTSW	10	67,075,015 (GRCm39)	splice site	probably benign
R1413:Jmjd1c	UTSW	10	67,085,529 (GRCm39)	missense	probably damaging	1.00
R1619:Jmjd1c	UTSW	10	67,055,654 (GRCm39)	missense	probably benign	0.25
R1676:Jmjd1c	UTSW	10	67,060,588 (GRCm39)	missense	probably benign	0.02
R1751:Jmjd1c	UTSW	10	67,061,469 (GRCm39)	missense	probably benign
R1950:Jmjd1c	UTSW	10	67,075,701 (GRCm39)	missense	possibly damaging	0.71
R1968:Jmjd1c	UTSW	10	67,061,219 (GRCm39)	missense	probably damaging	1.00
R2049:Jmjd1c	UTSW	10	66,993,777 (GRCm39)	nonsense	probably null
R2061:Jmjd1c	UTSW	10	67,054,205 (GRCm39)	missense	probably damaging	1.00
R2202:Jmjd1c	UTSW	10	67,075,242 (GRCm39)	splice site	probably null
R2203:Jmjd1c	UTSW	10	67,075,242 (GRCm39)	splice site	probably null
R2256:Jmjd1c	UTSW	10	67,061,073 (GRCm39)	missense	probably damaging	1.00
R2312:Jmjd1c	UTSW	10	67,074,629 (GRCm39)	missense	probably damaging	0.98
R2349:Jmjd1c	UTSW	10	67,091,279 (GRCm39)	missense	probably benign
R2392:Jmjd1c	UTSW	10	67,065,683 (GRCm39)	missense	probably damaging	1.00
R3015:Jmjd1c	UTSW	10	66,993,711 (GRCm39)	missense	probably damaging	1.00
R3110:Jmjd1c	UTSW	10	67,075,863 (GRCm39)	splice site	probably benign
R4043:Jmjd1c	UTSW	10	67,055,245 (GRCm39)	missense	possibly damaging	0.55
R4097:Jmjd1c	UTSW	10	67,054,787 (GRCm39)	missense	probably benign	0.09
R4118:Jmjd1c	UTSW	10	67,055,532 (GRCm39)	missense	probably damaging	0.96
R4193:Jmjd1c	UTSW	10	66,932,460 (GRCm39)	intron	probably benign
R4352:Jmjd1c	UTSW	10	67,080,588 (GRCm39)	missense	probably damaging	1.00
R4577:Jmjd1c	UTSW	10	67,085,529 (GRCm39)	missense	probably damaging	1.00
R4630:Jmjd1c	UTSW	10	66,993,753 (GRCm39)	nonsense	probably null
R4717:Jmjd1c	UTSW	10	66,993,830 (GRCm39)	nonsense	probably null
R4741:Jmjd1c	UTSW	10	67,060,718 (GRCm39)	missense	possibly damaging	0.56
R4774:Jmjd1c	UTSW	10	67,060,571 (GRCm39)	missense	possibly damaging	0.45
R4836:Jmjd1c	UTSW	10	67,069,225 (GRCm39)	missense	probably benign	0.21
R4914:Jmjd1c	UTSW	10	67,054,750 (GRCm39)	missense	probably damaging	1.00
R4939:Jmjd1c	UTSW	10	67,081,916 (GRCm39)	missense	possibly damaging	0.93
R5211:Jmjd1c	UTSW	10	67,067,795 (GRCm39)	missense	probably damaging	1.00
R5215:Jmjd1c	UTSW	10	67,076,480 (GRCm39)	missense	possibly damaging	0.93
R5530:Jmjd1c	UTSW	10	67,085,541 (GRCm39)	missense	probably damaging	1.00
R5624:Jmjd1c	UTSW	10	67,069,193 (GRCm39)	missense	probably damaging	0.99
R5640:Jmjd1c	UTSW	10	67,061,857 (GRCm39)	missense	probably benign	0.10
R5654:Jmjd1c	UTSW	10	67,065,785 (GRCm39)	missense	probably benign	0.10
R5742:Jmjd1c	UTSW	10	67,056,112 (GRCm39)	missense	probably benign	0.02
R5764:Jmjd1c	UTSW	10	67,062,291 (GRCm39)	missense	probably damaging	1.00
R6118:Jmjd1c	UTSW	10	67,075,791 (GRCm39)	missense	probably damaging	1.00
R6163:Jmjd1c	UTSW	10	67,083,827 (GRCm39)	missense	possibly damaging	0.46
R6256:Jmjd1c	UTSW	10	67,056,187 (GRCm39)	missense	probably damaging	1.00
R6266:Jmjd1c	UTSW	10	67,085,439 (GRCm39)	missense	probably damaging	0.96
R6358:Jmjd1c	UTSW	10	67,061,718 (GRCm39)	missense	probably benign
R6430:Jmjd1c	UTSW	10	67,059,939 (GRCm39)	missense	possibly damaging	0.87
R6455:Jmjd1c	UTSW	10	67,061,795 (GRCm39)	missense	probably benign	0.10
R6887:Jmjd1c	UTSW	10	67,025,599 (GRCm39)	missense	possibly damaging	0.74
R6895:Jmjd1c	UTSW	10	67,052,869 (GRCm39)	missense	probably benign	0.00
R7041:Jmjd1c	UTSW	10	67,056,388 (GRCm39)	missense	possibly damaging	0.90
R7095:Jmjd1c	UTSW	10	67,055,411 (GRCm39)	missense	probably benign	0.39
R7113:Jmjd1c	UTSW	10	66,993,780 (GRCm39)	missense	probably damaging	0.98
R7225:Jmjd1c	UTSW	10	67,061,844 (GRCm39)	missense	probably benign	0.00
R7249:Jmjd1c	UTSW	10	67,025,596 (GRCm39)	missense	probably benign	0.01
R7361:Jmjd1c	UTSW	10	67,054,143 (GRCm39)	missense	probably benign	0.10
R7383:Jmjd1c	UTSW	10	67,025,537 (GRCm39)	missense	probably benign	0.14
R7460:Jmjd1c	UTSW	10	67,052,815 (GRCm39)	missense	probably benign	0.24
R7475:Jmjd1c	UTSW	10	67,061,092 (GRCm39)	missense	probably benign	0.22
R7502:Jmjd1c	UTSW	10	67,067,794 (GRCm39)	missense	probably damaging	0.99
R7699:Jmjd1c	UTSW	10	67,054,195 (GRCm39)	missense	probably benign	0.10
R7745:Jmjd1c	UTSW	10	67,052,824 (GRCm39)	missense	probably damaging	0.96
R7897:Jmjd1c	UTSW	10	67,075,644 (GRCm39)	missense	probably damaging	0.96
R7908:Jmjd1c	UTSW	10	67,061,621 (GRCm39)	missense	probably benign
R7911:Jmjd1c	UTSW	10	67,067,774 (GRCm39)	missense	probably damaging	1.00
R7967:Jmjd1c	UTSW	10	67,085,461 (GRCm39)	missense	probably damaging	1.00
R8058:Jmjd1c	UTSW	10	67,090,274 (GRCm39)	missense	not run
R8224:Jmjd1c	UTSW	10	67,080,628 (GRCm39)	missense	noncoding transcript
R8251:Jmjd1c	UTSW	10	67,075,068 (GRCm39)	missense	noncoding transcript
R8797:Jmjd1c	UTSW	10	67,060,616 (GRCm39)	missense	probably benign
R8833:Jmjd1c	UTSW	10	67,054,162 (GRCm39)	missense	probably benign	0.03
R9262:Jmjd1c	UTSW	10	67,083,793 (GRCm39)	missense	probably benign	0.39
R9354:Jmjd1c	UTSW	10	67,059,875 (GRCm39)	missense	probably damaging	0.99
R9373:Jmjd1c	UTSW	10	66,932,495 (GRCm39)	intron	probably benign
R9477:Jmjd1c	UTSW	10	66,993,734 (GRCm39)	nonsense	probably null
R9519:Jmjd1c	UTSW	10	66,993,798 (GRCm39)	missense	possibly damaging	0.80
R9701:Jmjd1c	UTSW	10	67,060,745 (GRCm39)	missense	possibly damaging	0.94
R9802:Jmjd1c	UTSW	10	67,060,745 (GRCm39)	missense	possibly damaging	0.94
RF011:Jmjd1c	UTSW	10	67,055,978 (GRCm39)	missense	possibly damaging	0.47
Z1088:Jmjd1c	UTSW	10	67,073,953 (GRCm39)	missense	probably benign
Z1176:Jmjd1c	UTSW	10	67,073,953 (GRCm39)	missense	probably benign
Z1177:Jmjd1c	UTSW	10	67,081,904 (GRCm39)	missense	probably damaging	0.98
Z1177:Jmjd1c	UTSW	10	67,073,953 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CCCTAATTGATTAGCGCCCC -3'
(R):5'- CAGCTTGAGAGTTCATTGCTGG -3'

Sequencing Primer
(F):5'- AGCAGGTGGTATTGTACAAATTTG -3'
(R):5'- AGAGTTCATTGCTGGTCTGGGAC -3'

Posted On

2016-11-08