Incidental Mutation 'R6566:Khdc4'
| ID |
522659 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Khdc4
|
| Ensembl Gene |
ENSMUSG00000028060 |
| Gene Name |
KH domain containing 4, pre-mRNA splicing factor |
| Synonyms |
2810403A07Rik |
| MMRRC Submission |
044690-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.247)
|
| Stock # |
R6566 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
88593110-88620231 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 88618961 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Methionine
at position 555
(T555M)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000029696
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029696]
[ENSMUST00000198042]
[ENSMUST00000198078]
[ENSMUST00000199684]
|
| AlphaFold |
Q3TCX3 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000029696
AA Change: T555M
PolyPhen 2
Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000029696
Gene: ENSMUSG00000028060
AA Change: T555M
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
21 |
66 |
N/A |
INTRINSIC |
|
Blast:KH
|
103 |
185 |
2e-28 |
BLAST |
|
PDB:2YQR|A
|
229 |
340 |
6e-76 |
PDB |
|
Blast:KH
|
233 |
319 |
1e-36 |
BLAST |
|
SCOP:d1k1ga_
|
233 |
327 |
4e-16 |
SMART |
|
low complexity region
|
344 |
384 |
N/A |
INTRINSIC |
|
low complexity region
|
425 |
436 |
N/A |
INTRINSIC |
|
low complexity region
|
442 |
458 |
N/A |
INTRINSIC |
|
low complexity region
|
499 |
510 |
N/A |
INTRINSIC |
|
low complexity region
|
566 |
579 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000122484
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000197300
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000198042
|
| SMART Domains |
Protein: ENSMUSP00000142773
Gene: ENSMUSG00000028060
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
21 |
66 |
N/A |
INTRINSIC |
|
Blast:KH
|
103 |
185 |
7e-29 |
BLAST |
|
PDB:2YQR|A
|
229 |
340 |
2e-77 |
PDB |
|
Blast:KH
|
233 |
319 |
2e-37 |
BLAST |
|
SCOP:d1k1ga_
|
233 |
327 |
3e-16 |
SMART |
|
low complexity region
|
344 |
384 |
N/A |
INTRINSIC |
|
low complexity region
|
425 |
436 |
N/A |
INTRINSIC |
|
low complexity region
|
442 |
458 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000198078
|
| SMART Domains |
Protein: ENSMUSP00000142760
Gene: ENSMUSG00000028060
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
21 |
66 |
N/A |
INTRINSIC |
|
Blast:KH
|
103 |
185 |
5e-29 |
BLAST |
|
PDB:2YQR|A
|
229 |
340 |
1e-77 |
PDB |
|
Blast:KH
|
233 |
319 |
3e-37 |
BLAST |
|
SCOP:d1k1ga_
|
233 |
327 |
4e-17 |
SMART |
|
low complexity region
|
410 |
421 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000198721
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000199684
|
| SMART Domains |
Protein: ENSMUSP00000142353
Gene: ENSMUSG00000028060
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
21 |
66 |
N/A |
INTRINSIC |
|
Blast:KH
|
103 |
185 |
7e-29 |
BLAST |
|
PDB:2YQR|A
|
229 |
340 |
2e-77 |
PDB |
|
Blast:KH
|
233 |
319 |
2e-37 |
BLAST |
|
SCOP:d1k1ga_
|
233 |
327 |
3e-16 |
SMART |
|
low complexity region
|
344 |
384 |
N/A |
INTRINSIC |
|
low complexity region
|
425 |
436 |
N/A |
INTRINSIC |
|
low complexity region
|
442 |
458 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000200622
|
| Meta Mutation Damage Score |
0.6329 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.3%
- 20x: 97.6%
|
| Validation Efficiency |
100% (36/36) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 34 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcd2 |
A |
G |
15: 91,075,321 (GRCm39) |
I164T |
probably damaging |
Het |
| Adad2 |
C |
T |
8: 120,340,971 (GRCm39) |
P164S |
probably benign |
Het |
| Adcy3 |
T |
A |
12: 4,244,324 (GRCm39) |
L278H |
probably damaging |
Het |
| Aldh16a1 |
A |
C |
7: 44,792,651 (GRCm39) |
D670E |
probably benign |
Het |
| Bcat1 |
A |
G |
6: 144,961,210 (GRCm39) |
M131T |
probably damaging |
Het |
| Dcstamp |
T |
C |
15: 39,617,732 (GRCm39) |
F47S |
possibly damaging |
Het |
| Dsg1b |
T |
C |
18: 20,530,499 (GRCm39) |
F385L |
probably damaging |
Het |
| Exoc8 |
A |
C |
8: 125,622,783 (GRCm39) |
L528R |
probably damaging |
Het |
| Fat4 |
T |
C |
3: 39,011,275 (GRCm39) |
V2125A |
possibly damaging |
Het |
| Gm57859 |
C |
T |
11: 113,578,824 (GRCm39) |
P73L |
probably damaging |
Het |
| Hecw1 |
T |
C |
13: 14,471,868 (GRCm39) |
D600G |
probably damaging |
Het |
| Ice2 |
G |
A |
9: 69,323,511 (GRCm39) |
V669I |
probably benign |
Het |
| Lsr |
T |
A |
7: 30,671,508 (GRCm39) |
Y75F |
possibly damaging |
Het |
| Mrps30 |
C |
A |
13: 118,523,662 (GRCm39) |
V37L |
probably benign |
Het |
| Myl10 |
G |
C |
5: 136,726,825 (GRCm39) |
V70L |
probably benign |
Het |
| Or6c217 |
T |
A |
10: 129,737,947 (GRCm39) |
I211L |
probably benign |
Het |
| Pign |
A |
G |
1: 105,565,906 (GRCm39) |
|
probably null |
Het |
| Plcd3 |
A |
G |
11: 102,964,626 (GRCm39) |
Y582H |
probably damaging |
Het |
| Rad9b |
A |
G |
5: 122,490,630 (GRCm39) |
W29R |
probably damaging |
Het |
| Rb1cc1 |
T |
A |
1: 6,319,316 (GRCm39) |
F912I |
probably benign |
Het |
| Rgs16 |
C |
T |
1: 153,619,546 (GRCm39) |
S184L |
unknown |
Het |
| Runx2 |
A |
G |
17: 45,125,375 (GRCm39) |
|
probably null |
Het |
| Serpina1f |
T |
A |
12: 103,659,794 (GRCm39) |
I163F |
probably damaging |
Het |
| Serpina9 |
T |
C |
12: 103,963,296 (GRCm39) |
E404G |
possibly damaging |
Het |
| Slc4a4 |
T |
C |
5: 89,297,192 (GRCm39) |
S511P |
possibly damaging |
Het |
| Speg |
A |
T |
1: 75,365,107 (GRCm39) |
E390V |
probably damaging |
Het |
| Syne3 |
A |
G |
12: 104,912,966 (GRCm39) |
V614A |
probably benign |
Het |
| Tmc5 |
T |
C |
7: 118,247,067 (GRCm39) |
S524P |
probably damaging |
Het |
| Tuba4a |
G |
A |
1: 75,193,930 (GRCm39) |
T51I |
probably damaging |
Het |
| Tymp |
T |
A |
15: 89,257,803 (GRCm39) |
T421S |
probably benign |
Het |
| Uvssa |
A |
G |
5: 33,549,520 (GRCm39) |
R394G |
possibly damaging |
Het |
| Wdr7 |
T |
G |
18: 63,888,126 (GRCm39) |
I533S |
possibly damaging |
Het |
| Zbtb5 |
G |
A |
4: 44,994,508 (GRCm39) |
T292M |
probably damaging |
Het |
| Zfp944 |
T |
G |
17: 22,558,726 (GRCm39) |
K174Q |
possibly damaging |
Het |
|
| Other mutations in Khdc4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
R0085:Khdc4
|
UTSW |
3 |
88,619,046 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0271:Khdc4
|
UTSW |
3 |
88,593,636 (GRCm39) |
splice site |
probably benign |
|
|
R1160:Khdc4
|
UTSW |
3 |
88,616,169 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2348:Khdc4
|
UTSW |
3 |
88,616,183 (GRCm39) |
missense |
probably benign |
0.01 |
|
R3121:Khdc4
|
UTSW |
3 |
88,596,599 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3546:Khdc4
|
UTSW |
3 |
88,600,443 (GRCm39) |
splice site |
probably benign |
|
|
R3548:Khdc4
|
UTSW |
3 |
88,600,443 (GRCm39) |
splice site |
probably benign |
|
|
R4688:Khdc4
|
UTSW |
3 |
88,593,824 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5249:Khdc4
|
UTSW |
3 |
88,604,032 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5393:Khdc4
|
UTSW |
3 |
88,603,913 (GRCm39) |
missense |
probably benign |
0.08 |
|
R5558:Khdc4
|
UTSW |
3 |
88,600,403 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5579:Khdc4
|
UTSW |
3 |
88,607,582 (GRCm39) |
missense |
probably benign |
|
|
R5782:Khdc4
|
UTSW |
3 |
88,618,985 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R5809:Khdc4
|
UTSW |
3 |
88,616,192 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6415:Khdc4
|
UTSW |
3 |
88,607,279 (GRCm39) |
missense |
probably benign |
0.25 |
|
R6765:Khdc4
|
UTSW |
3 |
88,593,736 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6939:Khdc4
|
UTSW |
3 |
88,593,824 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7248:Khdc4
|
UTSW |
3 |
88,600,886 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7311:Khdc4
|
UTSW |
3 |
88,619,002 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R7852:Khdc4
|
UTSW |
3 |
88,604,043 (GRCm39) |
missense |
probably benign |
0.06 |
|
R8294:Khdc4
|
UTSW |
3 |
88,603,915 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8948:Khdc4
|
UTSW |
3 |
88,617,219 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8988:Khdc4
|
UTSW |
3 |
88,607,286 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9053:Khdc4
|
UTSW |
3 |
88,596,582 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9221:Khdc4
|
UTSW |
3 |
88,593,853 (GRCm39) |
missense |
probably benign |
0.01 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCATCAACGTTATGGGGTGAC -3'
(R):5'- CAGAACAGGTCCCAGAGTCTTG -3'
Sequencing Primer
(F):5'- CCATTGACCCTGTGGCTACAAAATG -3'
(R):5'- TCACTGAGGGTCAAAGCTCTGTC -3'
|
| Posted On |
2018-06-06 |
Incidental Mutation