Mutagenetix > Incidental Mutation

Incidental Mutation 'R4741:Jmjd1c'

358093

Institutional Source

Beutler Lab

Gene Symbol

Jmjd1c

Ensembl Gene

ENSMUSG00000037876

Gene Name

jumonji domain containing 1C

Synonyms

D630035I23Rik, TRIP8, 5430433L24Rik

MMRRC Submission

042026-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.662) question?

Stock #

R4741 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

66932189-67092105 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 67060718 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 737 (I737V)

Ref Sequence

ENSEMBL: ENSMUSP00000134246 (fasta)

Gene Model

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

AlphaFold

Q69ZK6

Predicted Effect

probably benign
Transcript: ENSMUST00000051446
AA Change: I1024V

PolyPhen 2 Score 0.289 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000056227
Gene: ENSMUSG00000037876
AA Change: I1024V

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

Predicted Effect

probably benign
Transcript: ENSMUST00000173689
AA Change: I843V

PolyPhen 2 Score 0.289 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000133700
Gene: ENSMUSG00000037876
AA Change: I843V

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000174317
AA Change: I737V

PolyPhen 2 Score 0.562 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000134246
Gene: ENSMUSG00000037876
AA Change: I737V

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

Predicted Effect

probably benign
Transcript: ENSMUST00000174408
AA Change: I1024V

PolyPhen 2 Score 0.427 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000134551
Gene: ENSMUSG00000037876
AA Change: I1024V

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

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.1%

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: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Angptl2	T	C	2: 33,136,200 (GRCm39)	Y462H	probably benign	Het
Arhgef12	A	G	9: 42,883,449 (GRCm39)	I1360T	possibly damaging	Het
Armc10	T	G	5: 21,856,834 (GRCm39)	L111R	probably damaging	Het
Atm	T	C	9: 53,364,907 (GRCm39)	K2628E	probably benign	Het
Best3	A	T	10: 116,859,901 (GRCm39)	N387I	probably benign	Het
Bltp1	A	G	3: 36,996,524 (GRCm39)	T1079A	probably damaging	Het
Brpf3	T	C	17: 29,036,758 (GRCm39)	F721S	possibly damaging	Het
Cacna1c	A	G	6: 118,590,271 (GRCm39)	S1411P	probably damaging	Het
Cldn8	G	A	16: 88,359,296 (GRCm39)	H210Y	probably benign	Het
Clip2	T	A	5: 134,545,123 (GRCm39)	T344S	probably benign	Het
Csmd1	A	C	8: 15,960,447 (GRCm39)	W3323G	probably damaging	Het
Doc2a	A	T	7: 126,450,617 (GRCm39)	T298S	possibly damaging	Het
Dpp9	T	C	17: 56,512,286 (GRCm39)	N234S	probably benign	Het
Dtx2	C	T	5: 136,055,371 (GRCm39)	R353C	probably benign	Het
Epm2aip1	A	G	9: 111,101,681 (GRCm39)	H218R	probably benign	Het
F2rl1	G	A	13: 95,650,651 (GRCm39)	T77M	probably damaging	Het
Fsd2	A	G	7: 81,201,643 (GRCm39)		probably null	Het
Grin2a	T	C	16: 9,481,376 (GRCm39)	Y475C	probably damaging	Het
H2-Ob	T	A	17: 34,461,545 (GRCm39)	S95T	possibly damaging	Het
Hddc3	A	G	7: 79,995,464 (GRCm39)	T160A	probably benign	Het
Hp	A	T	8: 110,302,104 (GRCm39)	C281*	probably null	Het
Ighg1	T	C	12: 113,290,178 (GRCm39)		probably benign	Het
Ints7	A	G	1: 191,351,747 (GRCm39)	I819V	probably benign	Het
Jam2	G	A	16: 84,609,840 (GRCm39)	V151M	probably damaging	Het
Krt74	C	T	15: 101,669,876 (GRCm39)		noncoding transcript	Het
Lnpep	T	C	17: 17,791,920 (GRCm39)	Y407C	probably damaging	Het
Lrp4	T	G	2: 91,341,912 (GRCm39)	C1842G	probably damaging	Het
Mug2	T	A	6: 122,056,572 (GRCm39)	N1172K	probably benign	Het
Npy6r	A	T	18: 44,408,791 (GRCm39)	T71S	probably damaging	Het
Nsd3	A	T	8: 26,163,382 (GRCm39)	I591F	probably damaging	Het
Oog2	A	C	4: 143,921,715 (GRCm39)	E208D	possibly damaging	Het
Otogl	A	G	10: 107,615,121 (GRCm39)	I1928T	probably benign	Het
Papss1	T	C	3: 131,324,860 (GRCm39)	L418P	probably damaging	Het
Pcdhb13	T	A	18: 37,576,571 (GRCm39)	D316E	probably benign	Het
Pcdhgb2	T	A	18: 37,824,737 (GRCm39)		probably null	Het
Ptcd3	T	A	6: 71,879,933 (GRCm39)	L108F	probably damaging	Het
Ralgps1	T	C	2: 33,226,599 (GRCm39)	S31G	probably benign	Het
Rnf225	A	T	7: 12,661,857 (GRCm39)	H12L	probably benign	Het
Ryr3	T	A	2: 112,633,613 (GRCm39)	M2047L	probably damaging	Het
Secisbp2l	C	T	2: 125,582,657 (GRCm39)	G933D	possibly damaging	Het
Serpinb3b	G	T	1: 107,082,200 (GRCm39)	Q355K	probably benign	Het
Slc8a2	T	A	7: 15,868,233 (GRCm39)	F155Y	probably damaging	Het
Taf1c	A	G	8: 120,330,134 (GRCm39)		probably benign	Het
Tln2	A	G	9: 67,293,837 (GRCm39)		probably null	Het
Tmpo	A	G	10: 90,998,506 (GRCm39)	V427A	probably benign	Het
Vmn1r17	A	T	6: 57,338,337 (GRCm39)	Y9*	probably null	Het
Vmn2r63	C	T	7: 42,577,544 (GRCm39)	M331I	probably benign	Het
Zdhhc1	CGGGGG	CGGGGGG	8: 106,210,376 (GRCm39)		probably null	Het
Zfand5	C	T	19: 21,253,845 (GRCm39)	T16I	probably damaging	Het
Zfp352	A	T	4: 90,113,177 (GRCm39)	K439M	possibly damaging	Het
Zfp786	G	A	6: 47,797,625 (GRCm39)	H438Y	probably damaging	Het
Zfp808	T	A	13: 62,319,763 (GRCm39)	C331S	probably damaging	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
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
R5514:Jmjd1c	UTSW	10	67,053,928 (GRCm39)	missense	probably damaging	1.00
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'- CGGTCTAATGCATCCACATCAG -3'
(R):5'- TCTTGGTGGCTCATTGACCAC -3'

Sequencing Primer
(F):5'- TCCACATCAGTAAAAGGTGACCTGG -3'
(R):5'- AGTTACTCTGGGGCAAACTC -3'

Posted On

2015-11-11