Mutagenetix > Incidental Mutations

Incidental Mutation 'R6895:Jmjd1c'

538293

Institutional Source

Beutler Lab

Gene Symbol

Jmjd1c

Ensembl Gene

ENSMUSG00000037876

Gene Name

jumonji domain containing 1C

Synonyms

TRIP8, D630035I23Rik, 5430433L24Rik

MMRRC Submission

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.608) question?

Stock #

R6895 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

67096125-67256326 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 67217090 bp

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 220 (I220V)

Ref Sequence

ENSEMBL: ENSMUSP00000134551 (fasta)

Gene Model

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

Predicted Effect

probably benign
Transcript: ENSMUST00000051446
AA Change: I220V

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000056227
Gene: ENSMUSG00000037876
AA Change: I220V

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: I39V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000133700
Gene: ENSMUSG00000037876
AA Change: I39V

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 benign
Transcript: ENSMUST00000174408
AA Change: I220V

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000134551
Gene: ENSMUSG00000037876
AA Change: I220V

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.3%
20x: 97.7%

Validation Efficiency

100% (45/45)

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: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ankrd29	A	G	18: 12,260,989	V256A	probably benign	Het
Arid4a	A	G	12: 71,063,302	D139G	probably benign	Het
AU040320	T	C	4: 126,791,930	W100R	probably damaging	Het
C4bp	T	C	1: 130,636,206	*470W	probably null	Het
Capn8	C	A	1: 182,628,669	D661E	possibly damaging	Het
Car14	T	C	3: 95,898,160	T334A	probably benign	Het
Chd6	T	A	2: 160,988,340	T1012S	probably damaging	Het
Csmd3	T	C	15: 47,666,514		probably null	Het
Dnaaf2	A	G	12: 69,197,663	V208A	probably benign	Het
Dnah11	A	G	12: 117,995,191	W2986R	probably damaging	Het
Epb42	G	A	2: 121,036,623		probably benign	Het
Fam120a	A	G	13: 48,892,021	F780L	probably benign	Het
Gm4788	G	A	1: 139,740,472	P308S	possibly damaging	Het
Gpt2	G	A	8: 85,518,052	E325K	probably benign	Het
Grid2	T	C	6: 64,395,299	F655S	probably damaging	Het
Homer3	T	C	8: 70,285,305	S2P	probably damaging	Het
Hydin	T	C	8: 110,312,251	V207A	probably benign	Het
Inpp5j	T	C	11: 3,495,557		probably null	Het
Jak1	C	T	4: 101,154,537		probably null	Het
Kat6a	T	G	8: 22,935,783	S1115A	possibly damaging	Het
Larp4	T	G	15: 100,007,730		probably null	Het
Lrrc72	T	G	12: 36,209,718	D43A	probably damaging	Het
Mptx2	A	C	1: 173,277,685	V13G	probably benign	Het
Nmbr	A	T	10: 14,769,960	*258Y	probably null	Het
Nup210l	C	T	3: 90,159,924	A757V	probably damaging	Het
Nup62	A	G	7: 44,829,733	K391E	possibly damaging	Het
Nup93	T	A	8: 94,243,686	I71K	probably damaging	Het
Olfr294	A	T	7: 86,616,115	C177S	probably damaging	Het
Olfr916	A	C	9: 38,658,089	L101R	probably damaging	Het
Pik3cg	A	G	12: 32,204,347	M547T	possibly damaging	Het
Ropn1	A	T	16: 34,677,298	I187F	possibly damaging	Het
Rtp3	T	C	9: 110,987,196	R96G	possibly damaging	Het
Sfrp5	A	T	19: 42,199,788	S197R	probably damaging	Het
Slc12a6	A	G	2: 112,355,095	H903R	probably damaging	Het
Slc26a3	G	T	12: 31,463,524	A482S	probably damaging	Het
Slc2a12	G	T	10: 22,692,185	A504S	probably damaging	Het
Slitrk5	C	A	14: 111,681,653	P903Q	probably damaging	Het
Tas2r123	A	T	6: 132,847,170	H10L	probably benign	Het
Tex46	T	C	4: 136,612,901	V99A	probably benign	Het
Top2b	T	C	14: 16,413,604	V1024A	probably benign	Het
Ugt2b36	G	A	5: 87,092,298	T76I	probably benign	Het
Usp31	G	T	7: 121,653,176	T747K	probably benign	Het
Vmn2r111	T	C	17: 22,559,051	N549S	possibly damaging	Het

Other mutations in Jmjd1c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01062:Jmjd1c	APN	10	67226715	missense	probably damaging	1.00
IGL01604:Jmjd1c	APN	10	67249762	missense	probably damaging	1.00
IGL01753:Jmjd1c	APN	10	67232015	missense	probably damaging	1.00
IGL02081:Jmjd1c	APN	10	67219526	missense	probably benign	0.02
IGL02128:Jmjd1c	APN	10	67243869	missense	probably damaging	1.00
IGL02134:Jmjd1c	APN	10	67220392	missense	possibly damaging	0.87
IGL02215:Jmjd1c	APN	10	67220322	missense	probably damaging	1.00
IGL02408:Jmjd1c	APN	10	67226382	missense	probably benign	0.00
IGL02502:Jmjd1c	APN	10	67225861	missense	probably benign	0.13
IGL02546:Jmjd1c	APN	10	67225336	missense	possibly damaging	0.94
IGL02943:Jmjd1c	APN	10	67219654	missense	probably damaging	0.99
IGL03171:Jmjd1c	APN	10	67225498	missense	possibly damaging	0.89
IGL03261:Jmjd1c	APN	10	67232070	missense	probably damaging	0.99
accordion	UTSW	10	67233414	missense	probably damaging	0.99
PIT4378001:Jmjd1c	UTSW	10	67229913	missense	probably damaging	1.00
R0126:Jmjd1c	UTSW	10	67219326	missense	probably damaging	0.98
R0133:Jmjd1c	UTSW	10	67240808	missense	probably benign	0.22
R0201:Jmjd1c	UTSW	10	67219109	missense	unknown
R0396:Jmjd1c	UTSW	10	67219523	missense	possibly damaging	0.82
R0401:Jmjd1c	UTSW	10	67220382	missense	probably damaging	1.00
R0452:Jmjd1c	UTSW	10	67255482	missense	probably benign	0.28
R0488:Jmjd1c	UTSW	10	67240727	missense	probably damaging	0.99
R0504:Jmjd1c	UTSW	10	67225755	missense	probably damaging	1.00
R0555:Jmjd1c	UTSW	10	67225789	missense	probably benign	0.01
R0673:Jmjd1c	UTSW	10	67226809	missense	probably damaging	1.00
R0718:Jmjd1c	UTSW	10	67218946	splice site	probably null
R0755:Jmjd1c	UTSW	10	67096599	intron	probably benign
R1142:Jmjd1c	UTSW	10	67225345	missense	probably damaging	1.00
R1196:Jmjd1c	UTSW	10	67239236	splice site	probably benign
R1413:Jmjd1c	UTSW	10	67249750	missense	probably damaging	1.00
R1619:Jmjd1c	UTSW	10	67219875	missense	probably benign	0.25
R1676:Jmjd1c	UTSW	10	67224809	missense	probably benign	0.02
R1751:Jmjd1c	UTSW	10	67225690	missense	probably benign
R1950:Jmjd1c	UTSW	10	67239922	missense	possibly damaging	0.71
R1968:Jmjd1c	UTSW	10	67225440	missense	probably damaging	1.00
R2049:Jmjd1c	UTSW	10	67157998	nonsense	probably null
R2061:Jmjd1c	UTSW	10	67218426	missense	probably damaging	1.00
R2202:Jmjd1c	UTSW	10	67239463	splice site	probably null
R2203:Jmjd1c	UTSW	10	67239463	splice site	probably null
R2256:Jmjd1c	UTSW	10	67225294	missense	probably damaging	1.00
R2312:Jmjd1c	UTSW	10	67238850	missense	probably damaging	0.98
R2349:Jmjd1c	UTSW	10	67255500	missense	probably benign
R2392:Jmjd1c	UTSW	10	67229904	missense	probably damaging	1.00
R3015:Jmjd1c	UTSW	10	67157932	missense	probably damaging	1.00
R3110:Jmjd1c	UTSW	10	67240084	splice site	probably benign
R4043:Jmjd1c	UTSW	10	67219466	missense	possibly damaging	0.55
R4097:Jmjd1c	UTSW	10	67219008	missense	probably benign	0.09
R4118:Jmjd1c	UTSW	10	67219753	missense	probably damaging	0.96
R4193:Jmjd1c	UTSW	10	67096681	intron	probably benign
R4352:Jmjd1c	UTSW	10	67244809	missense	probably damaging	1.00
R4577:Jmjd1c	UTSW	10	67249750	missense	probably damaging	1.00
R4630:Jmjd1c	UTSW	10	67157974	nonsense	probably null
R4717:Jmjd1c	UTSW	10	67158051	nonsense	probably null
R4741:Jmjd1c	UTSW	10	67224939	missense	possibly damaging	0.56
R4774:Jmjd1c	UTSW	10	67224792	missense	possibly damaging	0.45
R4836:Jmjd1c	UTSW	10	67233446	missense	probably benign	0.21
R4914:Jmjd1c	UTSW	10	67218971	missense	probably damaging	1.00
R4939:Jmjd1c	UTSW	10	67246137	missense	possibly damaging	0.93
R5211:Jmjd1c	UTSW	10	67232016	missense	probably damaging	1.00
R5215:Jmjd1c	UTSW	10	67240701	missense	possibly damaging	0.93
R5514:Jmjd1c	UTSW	10	67218149	missense	probably damaging	1.00
R5530:Jmjd1c	UTSW	10	67249762	missense	probably damaging	1.00
R5624:Jmjd1c	UTSW	10	67233414	missense	probably damaging	0.99
R5640:Jmjd1c	UTSW	10	67226078	missense	probably benign	0.10
R5654:Jmjd1c	UTSW	10	67230006	missense	probably benign	0.10
R5742:Jmjd1c	UTSW	10	67220333	missense	probably benign	0.02
R5764:Jmjd1c	UTSW	10	67226512	missense	probably damaging	1.00
R6118:Jmjd1c	UTSW	10	67240012	missense	probably damaging	1.00
R6163:Jmjd1c	UTSW	10	67248048	missense	possibly damaging	0.46
R6256:Jmjd1c	UTSW	10	67220408	missense	probably damaging	1.00
R6266:Jmjd1c	UTSW	10	67249660	missense	probably damaging	0.96
R6358:Jmjd1c	UTSW	10	67225939	missense	probably benign
R6430:Jmjd1c	UTSW	10	67224160	missense	possibly damaging	0.87
R6455:Jmjd1c	UTSW	10	67226016	missense	probably benign	0.10
R6887:Jmjd1c	UTSW	10	67189820	missense	possibly damaging	0.74
R7041:Jmjd1c	UTSW	10	67220609	missense	possibly damaging	0.90
R7095:Jmjd1c	UTSW	10	67219632	missense	probably benign	0.39
R7113:Jmjd1c	UTSW	10	67158001	missense	probably damaging	0.98
R7225:Jmjd1c	UTSW	10	67226065	missense	probably benign	0.00
R7249:Jmjd1c	UTSW	10	67189817	missense	probably benign	0.01
R7361:Jmjd1c	UTSW	10	67218364	missense	probably benign	0.10
R7383:Jmjd1c	UTSW	10	67189758	missense	probably benign	0.14
R7460:Jmjd1c	UTSW	10	67217036	missense	probably benign	0.24
R7475:Jmjd1c	UTSW	10	67225313	missense	probably benign	0.22
R7502:Jmjd1c	UTSW	10	67232015	missense	probably damaging	0.99
R7745:Jmjd1c	UTSW	10	67217045	missense	probably damaging	0.96
RF011:Jmjd1c	UTSW	10	67220199	missense	possibly damaging	0.47
Z1088:Jmjd1c	UTSW	10	67238174	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- GGTAATTCCTAAGTATTCCTAAGTGGG -3'
(R):5'- CTCCATAGGTGTGCTGTGAC -3'

Sequencing Primer
(F):5'- GGGAATGTCTTCATTTAAGAAATCCC -3'
(R):5'- CTTTAATCCCAGTGCTCAGGAGG -3'

Posted On

2018-11-06