Incidental Mutation 'R4171:Kdm4c'
| ID |
368393 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4c
|
| Ensembl Gene |
ENSMUSG00000028397 |
| Gene Name |
lysine (K)-specific demethylase 4C |
| Synonyms |
Jmjd2c, 2410141F18Rik |
| MMRRC Submission |
041011-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4171 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
74160734-74324097 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 74199135 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Asparagine
at position 108
(Y108N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000077017
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030102]
[ENSMUST00000077851]
[ENSMUST00000149295]
|
| AlphaFold |
Q8VCD7 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000030102
AA Change: Y108N
PolyPhen 2
Score 0.729 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000030102
Gene: ENSMUSG00000028397
AA Change: Y108N
| Domain | Start | End | E-Value | Type |
|---|
|
JmjN
|
15 |
57 |
9.12e-14 |
SMART |
|
JmjC
|
144 |
310 |
1.31e-61 |
SMART |
|
low complexity region
|
361 |
374 |
N/A |
INTRINSIC |
|
low complexity region
|
386 |
400 |
N/A |
INTRINSIC |
|
PHD
|
687 |
745 |
3.3e-5 |
SMART |
|
PHD
|
807 |
863 |
8.71e-5 |
SMART |
|
TUDOR
|
875 |
932 |
2.96e-10 |
SMART |
|
TUDOR
|
933 |
989 |
2e-7 |
SMART |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000077851
AA Change: Y108N
PolyPhen 2
Score 0.729 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000077017
Gene: ENSMUSG00000028397
AA Change: Y108N
| Domain | Start | End | E-Value | Type |
|---|
|
JmjN
|
15 |
57 |
9.12e-14 |
SMART |
|
JmjC
|
144 |
310 |
1.31e-61 |
SMART |
|
low complexity region
|
361 |
374 |
N/A |
INTRINSIC |
|
low complexity region
|
386 |
400 |
N/A |
INTRINSIC |
|
PHD
|
687 |
745 |
3.3e-5 |
SMART |
|
PHD
|
807 |
863 |
8.71e-5 |
SMART |
|
TUDOR
|
875 |
932 |
2.96e-10 |
SMART |
|
TUDOR
|
933 |
989 |
2e-7 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000149295
|
| SMART Domains |
Protein: ENSMUSP00000118728
Gene: ENSMUSG00000028397
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:JmjN
|
17 |
49 |
9.4e-14 |
PFAM |
|
low complexity region
|
102 |
115 |
N/A |
INTRINSIC |
|
low complexity region
|
127 |
141 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156065
|
| Meta Mutation Damage Score |
0.5234 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.6%
|
| Validation Efficiency |
100% (42/42) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the Jumonji domain 2 (JMJD2) family. The encoded protein is a trimethylation-specific demethylase, and converts specific trimethylated histone residues to the dimethylated form. This enzymatic action regulates gene expression and chromosome segregation. Chromosomal aberrations and changes in expression of this gene may be found in tumor cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
PHENOTYPE: Mice homozygous for a null gene trap allele cannot be produced likely due to embryonic lethality. Mice heterozygous for a null gene trap allele exhibit reduced body weight and lower incidence and multiplicity of both benign and malignant tumors in mice treated with DMBA and TPA. [provided by MGI curators]
|
| Allele List at MGI |
All alleles(402) : Targeted, other(2) Gene trapped(400) |
| Other mutations in this stock |
Total: 37 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700012B07Rik |
G |
T |
11: 109,684,980 (GRCm39) |
C172* |
probably null |
Het |
| 2310022A10Rik |
A |
G |
7: 27,265,109 (GRCm39) |
N87S |
probably benign |
Het |
| Apmap |
A |
G |
2: 150,425,987 (GRCm39) |
V387A |
probably benign |
Het |
| B130024G19Rik |
C |
T |
7: 70,038,454 (GRCm39) |
|
noncoding transcript |
Het |
| Cd200r1 |
A |
G |
16: 44,613,127 (GRCm39) |
I244M |
probably damaging |
Het |
| Clic6 |
T |
C |
16: 92,293,949 (GRCm39) |
|
probably benign |
Het |
| Col11a1 |
A |
G |
3: 114,001,863 (GRCm39) |
D429G |
probably damaging |
Het |
| Dsg4 |
T |
A |
18: 20,591,636 (GRCm39) |
Y458* |
probably null |
Het |
| Elapor1 |
G |
T |
3: 108,368,259 (GRCm39) |
Q885K |
probably benign |
Het |
| Fbxl13 |
A |
G |
5: 21,748,786 (GRCm39) |
Y378H |
probably benign |
Het |
| Ifi203 |
A |
C |
1: 173,761,341 (GRCm39) |
|
probably benign |
Het |
| Ifna6 |
T |
C |
4: 88,746,038 (GRCm39) |
V129A |
probably benign |
Het |
| Igkv3-4 |
G |
A |
6: 70,649,324 (GRCm39) |
A108T |
probably damaging |
Het |
| Itga1 |
G |
A |
13: 115,167,422 (GRCm39) |
Q165* |
probably null |
Het |
| Lap3 |
T |
C |
5: 45,666,833 (GRCm39) |
S412P |
probably benign |
Het |
| Lrfn5 |
G |
A |
12: 61,890,168 (GRCm39) |
V486I |
probably damaging |
Het |
| Mep1b |
A |
T |
18: 21,228,163 (GRCm39) |
|
probably null |
Het |
| Mettl6 |
T |
C |
14: 31,215,624 (GRCm39) |
N52S |
probably damaging |
Het |
| Nup54 |
A |
G |
5: 92,565,343 (GRCm39) |
I458T |
possibly damaging |
Het |
| Or1e16 |
A |
C |
11: 73,286,365 (GRCm39) |
L161R |
probably damaging |
Het |
| Or6c204 |
G |
A |
10: 129,022,453 (GRCm39) |
A279V |
probably benign |
Het |
| Pecr |
A |
T |
1: 72,315,428 (GRCm39) |
N107K |
probably damaging |
Het |
| Pnpla6 |
A |
G |
8: 3,593,997 (GRCm39) |
Q1307R |
probably benign |
Het |
| Poll |
T |
C |
19: 45,544,492 (GRCm39) |
K310E |
probably damaging |
Het |
| Rab29 |
A |
G |
1: 131,795,475 (GRCm39) |
Q29R |
probably benign |
Het |
| Reg2 |
G |
A |
6: 78,383,574 (GRCm39) |
G99D |
probably damaging |
Het |
| Rftn2 |
G |
A |
1: 55,253,429 (GRCm39) |
S58L |
probably damaging |
Het |
| Rps6kb1 |
T |
C |
11: 86,435,405 (GRCm39) |
E43G |
possibly damaging |
Het |
| Sdk2 |
T |
C |
11: 113,757,815 (GRCm39) |
|
probably null |
Het |
| Slc38a6 |
T |
A |
12: 73,397,326 (GRCm39) |
Y323N |
probably benign |
Het |
| Sp100 |
T |
C |
1: 85,634,562 (GRCm39) |
S152P |
probably benign |
Het |
| Tmc5 |
A |
G |
7: 118,248,810 (GRCm39) |
Y605C |
probably damaging |
Het |
| Txndc17 |
T |
C |
11: 72,098,537 (GRCm39) |
Y30H |
probably damaging |
Het |
| Vmn1r44 |
T |
A |
6: 89,870,996 (GRCm39) |
F247L |
probably damaging |
Het |
| Zbtb39 |
C |
T |
10: 127,578,236 (GRCm39) |
T270I |
possibly damaging |
Het |
| Zfp512b |
G |
A |
2: 181,232,391 (GRCm39) |
|
probably null |
Het |
| Zwilch |
T |
A |
9: 64,065,997 (GRCm39) |
R255* |
probably null |
Het |
|
| Other mutations in Kdm4c |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00093:Kdm4c
|
APN |
4 |
74,263,738 (GRCm39) |
missense |
probably benign |
0.19 |
|
IGL00225:Kdm4c
|
APN |
4 |
74,263,804 (GRCm39) |
missense |
probably benign |
0.03 |
|
IGL00672:Kdm4c
|
APN |
4 |
74,261,751 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL00897:Kdm4c
|
APN |
4 |
74,291,921 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01479:Kdm4c
|
APN |
4 |
74,261,738 (GRCm39) |
missense |
probably benign |
0.18 |
|
IGL01707:Kdm4c
|
APN |
4 |
74,255,164 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02142:Kdm4c
|
APN |
4 |
74,225,253 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02268:Kdm4c
|
APN |
4 |
74,291,953 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
IGL02662:Kdm4c
|
APN |
4 |
74,323,058 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL03377:Kdm4c
|
APN |
4 |
74,189,492 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
3-1:Kdm4c
|
UTSW |
4 |
74,252,910 (GRCm39) |
missense |
probably benign |
0.00 |
|
BB002:Kdm4c
|
UTSW |
4 |
74,323,058 (GRCm39) |
missense |
probably damaging |
0.99 |
|
BB012:Kdm4c
|
UTSW |
4 |
74,323,058 (GRCm39) |
missense |
probably damaging |
0.99 |
|
PIT4434001:Kdm4c
|
UTSW |
4 |
74,189,569 (GRCm39) |
missense |
probably benign |
0.01 |
|
R0096:Kdm4c
|
UTSW |
4 |
74,275,580 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0096:Kdm4c
|
UTSW |
4 |
74,275,580 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0219:Kdm4c
|
UTSW |
4 |
74,291,857 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0309:Kdm4c
|
UTSW |
4 |
74,263,804 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0512:Kdm4c
|
UTSW |
4 |
74,252,031 (GRCm39) |
missense |
probably benign |
|
|
R1070:Kdm4c
|
UTSW |
4 |
74,291,865 (GRCm39) |
nonsense |
probably null |
|
|
R1518:Kdm4c
|
UTSW |
4 |
74,252,063 (GRCm39) |
missense |
probably benign |
|
|
R1713:Kdm4c
|
UTSW |
4 |
74,216,721 (GRCm39) |
missense |
probably benign |
0.10 |
|
R1769:Kdm4c
|
UTSW |
4 |
74,199,234 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
R1927:Kdm4c
|
UTSW |
4 |
74,263,720 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1962:Kdm4c
|
UTSW |
4 |
74,225,253 (GRCm39) |
intron |
probably benign |
|
|
R1992:Kdm4c
|
UTSW |
4 |
74,261,631 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R2389:Kdm4c
|
UTSW |
4 |
74,252,107 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2979:Kdm4c
|
UTSW |
4 |
74,291,965 (GRCm39) |
nonsense |
probably null |
|
|
R3966:Kdm4c
|
UTSW |
4 |
74,216,820 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4094:Kdm4c
|
UTSW |
4 |
74,229,915 (GRCm39) |
missense |
probably benign |
|
|
R4543:Kdm4c
|
UTSW |
4 |
74,248,997 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4581:Kdm4c
|
UTSW |
4 |
74,275,576 (GRCm39) |
splice site |
probably null |
|
|
R5019:Kdm4c
|
UTSW |
4 |
74,261,772 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5088:Kdm4c
|
UTSW |
4 |
74,252,936 (GRCm39) |
missense |
probably benign |
|
|
R5533:Kdm4c
|
UTSW |
4 |
74,233,886 (GRCm39) |
intron |
probably benign |
|
|
R5663:Kdm4c
|
UTSW |
4 |
74,317,585 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5691:Kdm4c
|
UTSW |
4 |
74,252,965 (GRCm39) |
missense |
probably benign |
|
|
R5775:Kdm4c
|
UTSW |
4 |
74,277,668 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5786:Kdm4c
|
UTSW |
4 |
74,277,722 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6002:Kdm4c
|
UTSW |
4 |
74,323,206 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R6375:Kdm4c
|
UTSW |
4 |
74,248,952 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6491:Kdm4c
|
UTSW |
4 |
74,291,873 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6790:Kdm4c
|
UTSW |
4 |
74,309,698 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6952:Kdm4c
|
UTSW |
4 |
74,275,587 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7157:Kdm4c
|
UTSW |
4 |
74,263,804 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7319:Kdm4c
|
UTSW |
4 |
74,255,200 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7925:Kdm4c
|
UTSW |
4 |
74,323,058 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7976:Kdm4c
|
UTSW |
4 |
74,295,906 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7990:Kdm4c
|
UTSW |
4 |
74,309,685 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8185:Kdm4c
|
UTSW |
4 |
74,291,821 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9079:Kdm4c
|
UTSW |
4 |
74,277,738 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9486:Kdm4c
|
UTSW |
4 |
74,252,966 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9546:Kdm4c
|
UTSW |
4 |
74,323,104 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R9547:Kdm4c
|
UTSW |
4 |
74,323,104 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
| Predicted Primers |
PCR Primer
(F):5'- AAGCCCTACTGATAAGGAACATAAGA -3'
(R):5'- TGTCACAGTTGTAGCATGTCA -3'
Sequencing Primer
(F):5'- CTCTGATACCACATGAGTGTA -3'
(R):5'- GCTCCATAAATAGGTGCCA -3'
|
| Posted On |
2016-02-04 |
Incidental Mutation