Incidental Mutation 'R3839:Ddx56'
| ID |
277059 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ddx56
|
| Ensembl Gene |
ENSMUSG00000004393 |
| Gene Name |
DEAD box helicase 56 |
| Synonyms |
D11Ertd619e, NOH61, DEAD (Asp-Glu-Ala-Asp) box polypeptide 56, 2600001H07Rik |
| MMRRC Submission |
040892-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.968)
|
| Stock # |
R3839 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
6208919-6217772 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 6217712 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 3
(D3G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000122368
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004507]
[ENSMUST00000004508]
[ENSMUST00000151446]
|
| AlphaFold |
Q9D0R4 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000004507
AA Change: D3G
PolyPhen 2
Score 0.078 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000004507
Gene: ENSMUSG00000004393
AA Change: D3G
| Domain | Start | End | E-Value | Type |
|---|
|
DEXDc
|
26 |
234 |
4.13e-46 |
SMART |
|
low complexity region
|
246 |
256 |
N/A |
INTRINSIC |
|
HELICc
|
272 |
380 |
2.42e-20 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000004508
|
| SMART Domains |
Protein: ENSMUSP00000004508
Gene: ENSMUSG00000004394
| Domain | Start | End | E-Value | Type |
|---|
|
EMP24_GP25L
|
29 |
222 |
3.21e-79 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130621
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139073
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000151446
AA Change: D3G
PolyPhen 2
Score 0.227 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000122368
Gene: ENSMUSG00000004393
AA Change: D3G
| Domain | Start | End | E-Value | Type |
|---|
|
DEXDc
|
26 |
216 |
3.65e-38 |
SMART |
|
low complexity region
|
228 |
236 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155874
|
| Meta Mutation Damage Score |
0.0926 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.8%
- 10x: 97.8%
- 20x: 96.4%
|
| Validation Efficiency |
98% (48/49) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The protein encoded by this gene shows ATPase activity in the presence of polynucleotides and associates with nucleoplasmic 65S preribosomal particles. This gene may be involved in ribosome synthesis, most likely during assembly of the large 60S ribosomal subunit. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700028I16Rik |
A |
G |
10: 82,648,219 (GRCm39) |
|
noncoding transcript |
Het |
| Abraxas2 |
T |
A |
7: 132,484,867 (GRCm39) |
S303R |
probably benign |
Het |
| Ackr3 |
G |
A |
1: 90,141,850 (GRCm39) |
S103N |
probably damaging |
Het |
| Arhgef25 |
T |
C |
10: 127,025,605 (GRCm39) |
T12A |
probably benign |
Het |
| Aspm |
C |
T |
1: 139,405,792 (GRCm39) |
H1560Y |
probably benign |
Het |
| Atg10 |
A |
T |
13: 91,085,499 (GRCm39) |
I150K |
probably damaging |
Het |
| AW551984 |
T |
C |
9: 39,509,204 (GRCm39) |
|
probably benign |
Het |
| Cald1 |
A |
T |
6: 34,722,700 (GRCm39) |
D122V |
probably damaging |
Het |
| Cc2d2a |
T |
C |
5: 43,876,056 (GRCm39) |
V1011A |
probably benign |
Het |
| Cdh9 |
G |
T |
15: 16,823,524 (GRCm39) |
E169* |
probably null |
Het |
| Cmbl |
T |
C |
15: 31,582,144 (GRCm39) |
V47A |
probably damaging |
Het |
| Col9a2 |
C |
G |
4: 120,911,455 (GRCm39) |
R599G |
probably damaging |
Het |
| Ctnnd2 |
T |
A |
15: 31,009,174 (GRCm39) |
|
probably null |
Het |
| Cyp4a10 |
A |
C |
4: 115,382,544 (GRCm39) |
E278A |
possibly damaging |
Het |
| Dnajb2 |
G |
A |
1: 75,218,124 (GRCm39) |
|
probably null |
Het |
| Eif3d |
T |
A |
15: 77,848,300 (GRCm39) |
T211S |
probably benign |
Het |
| Fam13c |
C |
T |
10: 70,378,478 (GRCm39) |
S336L |
probably damaging |
Het |
| Garnl3 |
C |
T |
2: 32,879,558 (GRCm39) |
G923S |
probably benign |
Het |
| Gcnt4 |
A |
T |
13: 97,083,522 (GRCm39) |
R273* |
probably null |
Het |
| Gldc |
T |
A |
19: 30,096,075 (GRCm39) |
|
probably benign |
Het |
| Glra2 |
C |
T |
X: 164,072,612 (GRCm39) |
V85I |
probably benign |
Het |
| Gm10608 |
CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA |
CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA |
9: 118,989,784 (GRCm39) |
|
probably null |
Het |
| Gpam |
T |
C |
19: 55,068,890 (GRCm39) |
N450S |
probably benign |
Het |
| Gpr156 |
T |
A |
16: 37,808,962 (GRCm39) |
V228D |
probably damaging |
Het |
| Hivep2 |
C |
A |
10: 14,004,713 (GRCm39) |
T437K |
probably benign |
Het |
| Hmgcr |
A |
G |
13: 96,795,597 (GRCm39) |
I324T |
probably benign |
Het |
| Itga3 |
A |
G |
11: 94,948,095 (GRCm39) |
|
probably null |
Het |
| Itih1 |
T |
A |
14: 30,657,785 (GRCm39) |
N429Y |
probably damaging |
Het |
| Klhl40 |
A |
G |
9: 121,609,482 (GRCm39) |
Y453C |
possibly damaging |
Het |
| Mid1ip1 |
T |
C |
X: 10,584,620 (GRCm39) |
V51A |
possibly damaging |
Het |
| Msn |
C |
A |
X: 95,203,805 (GRCm39) |
Q303K |
probably damaging |
Het |
| Nap1l1 |
T |
A |
10: 111,331,183 (GRCm39) |
|
probably null |
Het |
| Rala |
A |
T |
13: 18,067,759 (GRCm39) |
C91S |
probably damaging |
Het |
| Rps9 |
A |
G |
7: 3,709,823 (GRCm39) |
|
probably benign |
Het |
| Sdr16c5 |
C |
A |
4: 4,006,601 (GRCm39) |
M230I |
probably damaging |
Het |
| Sec14l3 |
A |
G |
11: 4,021,544 (GRCm39) |
|
probably null |
Het |
| Senp2 |
T |
C |
16: 21,828,485 (GRCm39) |
S32P |
probably damaging |
Het |
| Skor1 |
A |
C |
9: 63,051,730 (GRCm39) |
S746R |
probably damaging |
Het |
| Slc17a4 |
C |
T |
13: 24,085,752 (GRCm39) |
R387H |
probably benign |
Het |
| Slc47a1 |
G |
T |
11: 61,243,884 (GRCm39) |
|
probably benign |
Het |
| Slit3 |
A |
T |
11: 35,399,064 (GRCm39) |
N143I |
probably benign |
Het |
| Tpbg |
T |
C |
9: 85,725,167 (GRCm39) |
|
probably benign |
Het |
| Tubb2a |
G |
T |
13: 34,259,294 (GRCm39) |
N165K |
probably benign |
Het |
| Usp14 |
A |
G |
18: 10,024,532 (GRCm39) |
|
probably null |
Het |
| Vmn2r109 |
A |
G |
17: 20,774,704 (GRCm39) |
V217A |
probably damaging |
Het |
| Zfp108 |
A |
G |
7: 23,959,981 (GRCm39) |
I191V |
probably benign |
Het |
|
| Other mutations in Ddx56 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01061:Ddx56
|
APN |
11 |
6,214,671 (GRCm39) |
splice site |
probably null |
|
|
IGL01764:Ddx56
|
APN |
11 |
6,215,692 (GRCm39) |
missense |
probably null |
0.05 |
|
IGL02858:Ddx56
|
APN |
11 |
6,217,667 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL03075:Ddx56
|
APN |
11 |
6,211,632 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0972:Ddx56
|
UTSW |
11 |
6,217,718 (GRCm39) |
start codon destroyed |
probably null |
0.99 |
|
R1652:Ddx56
|
UTSW |
11 |
6,217,679 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1744:Ddx56
|
UTSW |
11 |
6,216,396 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1793:Ddx56
|
UTSW |
11 |
6,216,934 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1869:Ddx56
|
UTSW |
11 |
6,213,993 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R1917:Ddx56
|
UTSW |
11 |
6,213,937 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2415:Ddx56
|
UTSW |
11 |
6,211,727 (GRCm39) |
unclassified |
probably benign |
|
|
R4445:Ddx56
|
UTSW |
11 |
6,215,770 (GRCm39) |
splice site |
probably null |
|
|
R5041:Ddx56
|
UTSW |
11 |
6,214,178 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6925:Ddx56
|
UTSW |
11 |
6,213,980 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7412:Ddx56
|
UTSW |
11 |
6,211,720 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8401:Ddx56
|
UTSW |
11 |
6,214,199 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9088:Ddx56
|
UTSW |
11 |
6,209,612 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9382:Ddx56
|
UTSW |
11 |
6,215,516 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1177:Ddx56
|
UTSW |
11 |
6,217,445 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTCCTGGATCAACGTAGGTCG -3'
(R):5'- TAGCCAAAACGCGGTCGATC -3'
Sequencing Primer
(F):5'- GCGACCAGCCCAAATCGG -3'
(R):5'- ACAATTCGGAGGGCGTTC -3'
|
| Posted On |
2015-04-06 |
Incidental Mutation