Incidental Mutation 'D3080:Smyd3'
| ID |
112 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smyd3
|
| Ensembl Gene |
ENSMUSG00000055067 |
| Gene Name |
SET and MYND domain containing 3 |
| Synonyms |
2410008A19Rik, Zmynd1 |
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
D3080
of strain
grasshopper
|
| Quality Score |
|
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
178779525-179345606 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 178913987 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 239
(Y239H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000117410
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000128302]
|
| AlphaFold |
Q9CWR2 |
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000068437
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000128302
AA Change: Y239H
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000117410
Gene: ENSMUSG00000055067
AA Change: Y239H
| Domain | Start | End | E-Value | Type |
|---|
|
SET
|
4 |
246 |
1.04e-11 |
SMART |
|
low complexity region
|
410 |
420 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000131684
|
| Meta Mutation Damage Score |
0.8145 |
| Coding Region Coverage |
|
| Validation Efficiency |
82% (141/173) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a histone methyltransferase which functions in RNA polymerase II complexes by an interaction with a specific RNA helicase. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
PHENOTYPE: No abnormal phenotype was observed in a high-throughput screen, nor in a pathology assessment. [provided by MGI curators]
|
| Allele List at MGI |
All alleles(34) : Targeted, other(5) Gene trapped(29)
|
| Other mutations in this stock |
Total: 20 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2310003L06Rik |
C |
A |
5: 88,119,846 (GRCm39) |
P201Q |
possibly damaging |
Het |
| Bdp1 |
A |
T |
13: 100,160,129 (GRCm39) |
S2417R |
probably benign |
Het |
| Ccdc168 |
C |
A |
1: 44,106,495 (GRCm39) |
|
|
Het |
| Dscaml1 |
A |
T |
9: 45,595,623 (GRCm39) |
H783L |
probably benign |
Het |
| Fbxl5 |
A |
T |
5: 43,915,708 (GRCm39) |
M568K |
probably benign |
Het |
| Gab1 |
T |
A |
8: 81,493,007 (GRCm39) |
D710V |
probably damaging |
Homo |
| Gabrr2 |
T |
C |
4: 33,084,466 (GRCm39) |
F128S |
probably damaging |
Het |
| Hyou1 |
T |
A |
9: 44,295,774 (GRCm39) |
V343E |
probably damaging |
Het |
| Nlrp4a |
A |
G |
7: 26,143,766 (GRCm39) |
T44A |
probably benign |
Het |
| Nsd3 |
C |
A |
8: 26,203,572 (GRCm39) |
T1362N |
possibly damaging |
Homo |
| Or6f2 |
G |
A |
7: 139,756,275 (GRCm39) |
V81M |
possibly damaging |
Het |
| Pcm1 |
T |
A |
8: 41,728,976 (GRCm39) |
N649K |
probably damaging |
Homo |
| Pde4dip |
T |
C |
3: 97,674,146 (GRCm39) |
K257E |
probably damaging |
Het |
| Pfpl |
G |
A |
19: 12,406,196 (GRCm39) |
R149Q |
probably damaging |
Homo |
| Pou2f2 |
G |
T |
7: 24,796,558 (GRCm39) |
|
probably benign |
Het |
| Rptn |
A |
G |
3: 93,303,135 (GRCm39) |
D156G |
possibly damaging |
Het |
| Sec31a |
T |
C |
5: 100,511,691 (GRCm39) |
D1107G |
probably damaging |
Het |
| Stoml3 |
T |
C |
3: 53,405,415 (GRCm39) |
F32S |
probably benign |
Het |
| Tnnc1 |
C |
A |
14: 30,932,147 (GRCm39) |
D62E |
probably damaging |
Homo |
| Vsig10 |
C |
T |
5: 117,481,884 (GRCm39) |
A358V |
probably damaging |
Het |
|
| Other mutations in Smyd3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02044:Smyd3
|
APN |
1 |
178,799,844 (GRCm39) |
missense |
probably benign |
|
|
IGL03088:Smyd3
|
APN |
1 |
178,921,898 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0165:Smyd3
|
UTSW |
1 |
178,871,437 (GRCm39) |
missense |
probably benign |
|
|
R0230:Smyd3
|
UTSW |
1 |
179,250,993 (GRCm39) |
splice site |
probably benign |
|
|
R0390:Smyd3
|
UTSW |
1 |
178,785,138 (GRCm39) |
splice site |
probably benign |
|
|
R1651:Smyd3
|
UTSW |
1 |
178,871,441 (GRCm39) |
missense |
probably benign |
|
|
R4651:Smyd3
|
UTSW |
1 |
178,871,306 (GRCm39) |
missense |
probably benign |
0.08 |
|
R4771:Smyd3
|
UTSW |
1 |
178,921,961 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5326:Smyd3
|
UTSW |
1 |
179,238,024 (GRCm39) |
missense |
probably benign |
|
|
R5542:Smyd3
|
UTSW |
1 |
179,238,024 (GRCm39) |
missense |
probably benign |
|
|
R5697:Smyd3
|
UTSW |
1 |
179,239,247 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5850:Smyd3
|
UTSW |
1 |
178,871,420 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6732:Smyd3
|
UTSW |
1 |
179,223,395 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7782:Smyd3
|
UTSW |
1 |
178,799,859 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R8065:Smyd3
|
UTSW |
1 |
179,238,028 (GRCm39) |
missense |
possibly damaging |
0.60 |
|
R8067:Smyd3
|
UTSW |
1 |
179,238,028 (GRCm39) |
missense |
possibly damaging |
0.60 |
|
R8236:Smyd3
|
UTSW |
1 |
179,233,205 (GRCm39) |
splice site |
probably null |
|
|
R8735:Smyd3
|
UTSW |
1 |
178,920,482 (GRCm39) |
missense |
probably benign |
0.12 |
|
R9146:Smyd3
|
UTSW |
1 |
178,920,529 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9185:Smyd3
|
UTSW |
1 |
178,877,854 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9200:Smyd3
|
UTSW |
1 |
179,232,963 (GRCm39) |
missense |
probably benign |
0.04 |
|
R9372:Smyd3
|
UTSW |
1 |
178,871,470 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
X0024:Smyd3
|
UTSW |
1 |
178,877,854 (GRCm39) |
critical splice donor site |
probably null |
|
|
| Nature of Mutation |
.gif) DNA sequencing using the SOLiD technique identified a T to C transition at position 767 of the Smyd3 transcript. Multiple transcripts of the Smyd3 gene are displayed on Ensembl. The mutation causes a tyrosine to histidine change at amino acid 239 of the encoded protein using Ensembl record ENSMUSP00000117410. The mutation has been confirmed by DNA sequencing using the Sanger method (Figure 1).
|
| Protein Function and Prediction |
The Smyd3 gene encodes a 428 amino acid histone methyltransferase that plays an important role in transcriptional activation. SMYD3 contains a MYND-type zinc finger at amino acids 49-87 and a SET domain at amino acids 126-246 (Uniprot Q9CWR2).
The Y239H change is located in the SET domain in a conserved amino acid implicated in mediating methylation activity, and is predicted to be probably damaging by the PolyPhen program. |
| Posted On |
2010-03-11 |
Incidental Mutation