Incidental Mutation 'PIT4498001:Smyd1'
| ID |
556062 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smyd1
|
| Ensembl Gene |
ENSMUSG00000055027 |
| Gene Name |
SET and MYND domain containing 1 |
| Synonyms |
Bop, 4632404M21Rik |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
PIT4498001 (G1)
|
| Quality Score |
206.009 |
|
Status
|
Not validated
|
| Chromosome |
6 |
| Chromosomal Location |
71190924-71239265 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 71196272 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Arginine
at position 372
(H372R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000073911
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000074301]
[ENSMUST00000114186]
[ENSMUST00000114188]
[ENSMUST00000173730]
|
| AlphaFold |
P97443 |
| PDB Structure |
Crystal structure of cardiac specific histone methyltransferase SmyD1 [X-RAY DIFFRACTION]
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000074301
AA Change: H372R
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000073911
Gene: ENSMUSG00000055027
AA Change: H372R
| Domain | Start | End | E-Value | Type |
|---|
|
SET
|
7 |
259 |
2.79e-21 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000114186
AA Change: H359R
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000109824
Gene: ENSMUSG00000055027
AA Change: H359R
| Domain | Start | End | E-Value | Type |
|---|
|
SET
|
7 |
246 |
2.45e-17 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000114188
AA Change: H338R
PolyPhen 2
Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
|
| SMART Domains |
Protein: ENSMUSP00000109826
Gene: ENSMUSG00000055027
AA Change: H338R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:zf-MYND
|
18 |
56 |
5.4e-11 |
PFAM |
|
SET
|
76 |
225 |
1.53e-9 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000173730
|
| SMART Domains |
Protein: ENSMUSP00000134399
Gene: ENSMUSG00000055027
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:3N71|A
|
5 |
58 |
3e-30 |
PDB |
|
| Coding Region Coverage |
- 1x: 93.2%
- 3x: 91.0%
- 10x: 86.1%
- 20x: 75.4%
|
| Validation Efficiency |
|
| MGI Phenotype |
PHENOTYPE: Homozygous mutation of this gene results in embryonic lethality at E10.5. Mutant embryos exhibit an enlarged heart and developmental abnormalities of the right ventricle. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aldh18a1 |
T |
C |
19: 40,562,800 (GRCm39) |
N191S |
probably benign |
Het |
| Cacnb2 |
T |
A |
2: 14,879,630 (GRCm39) |
L84* |
probably null |
Het |
| Cdhr2 |
C |
T |
13: 54,866,052 (GRCm39) |
T284M |
possibly damaging |
Het |
| Defb45 |
T |
C |
2: 152,438,394 (GRCm39) |
|
probably benign |
Het |
| Dkk3 |
C |
T |
7: 111,718,679 (GRCm39) |
V236M |
probably benign |
Het |
| Dscc1 |
A |
T |
15: 54,945,711 (GRCm39) |
V328D |
probably benign |
Het |
| Epha3 |
T |
C |
16: 63,372,889 (GRCm39) |
Y938C |
probably damaging |
Het |
| Erc1 |
A |
T |
6: 119,756,452 (GRCm39) |
F435I |
possibly damaging |
Het |
| Fbxl5 |
T |
C |
5: 43,908,323 (GRCm39) |
Y626C |
possibly damaging |
Het |
| Fmn2 |
A |
G |
1: 174,440,170 (GRCm39) |
R1196G |
probably damaging |
Het |
| Gabrr1 |
C |
T |
4: 33,160,225 (GRCm39) |
S303F |
probably damaging |
Het |
| Ggt1 |
T |
C |
10: 75,414,689 (GRCm39) |
V169A |
possibly damaging |
Het |
| Gm10800 |
CAAGAAAACTGAAAATCAAAGAAAACTGAAAATCA |
CAAGAAAACTGAAAATCA |
2: 98,497,361 (GRCm39) |
|
probably null |
Het |
| Gm3182 |
T |
A |
14: 4,481,832 (GRCm38) |
C9S |
probably damaging |
Het |
| Gpr88 |
A |
C |
3: 116,046,264 (GRCm39) |
S16A |
unknown |
Het |
| Kalrn |
A |
T |
16: 33,851,952 (GRCm39) |
M2076K |
possibly damaging |
Het |
| Katnip |
A |
G |
7: 125,412,768 (GRCm39) |
T371A |
probably benign |
Het |
| Kcnd3 |
T |
C |
3: 105,566,025 (GRCm39) |
I402T |
probably damaging |
Het |
| Mink1 |
A |
G |
11: 70,489,714 (GRCm39) |
D57G |
probably benign |
Het |
| Ncl |
T |
C |
1: 86,279,162 (GRCm39) |
T584A |
possibly damaging |
Het |
| Nfx1 |
A |
T |
4: 40,977,244 (GRCm39) |
Q306L |
probably benign |
Het |
| Ogdh |
A |
T |
11: 6,290,504 (GRCm39) |
D374V |
probably benign |
Het |
| Or5d39 |
T |
A |
2: 87,980,259 (GRCm39) |
T35S |
probably benign |
Het |
| Pak5 |
T |
A |
2: 135,925,211 (GRCm39) |
H697L |
probably damaging |
Het |
| Pappa |
T |
C |
4: 65,234,469 (GRCm39) |
C1425R |
probably damaging |
Het |
| Pramel26 |
T |
C |
4: 143,539,406 (GRCm39) |
E29G |
possibly damaging |
Het |
| Rab3gap2 |
T |
A |
1: 185,013,882 (GRCm39) |
I1196N |
probably damaging |
Het |
| Ralyl |
A |
T |
3: 14,172,299 (GRCm39) |
D56V |
probably damaging |
Het |
| Scin |
C |
T |
12: 40,119,446 (GRCm39) |
|
probably null |
Het |
| Slc25a19 |
T |
C |
11: 115,514,781 (GRCm39) |
I69V |
possibly damaging |
Het |
| Slc8a1 |
G |
T |
17: 81,956,269 (GRCm39) |
Y256* |
probably null |
Het |
| St8sia1 |
T |
C |
6: 142,859,848 (GRCm39) |
T94A |
probably damaging |
Het |
| Stard9 |
T |
A |
2: 120,527,916 (GRCm39) |
M1391K |
possibly damaging |
Het |
| Tlr9 |
G |
A |
9: 106,100,721 (GRCm39) |
R4H |
probably benign |
Het |
| Trim50 |
A |
G |
5: 135,382,331 (GRCm39) |
D61G |
probably damaging |
Het |
| Ttn |
G |
A |
2: 76,597,295 (GRCm39) |
P19873S |
probably damaging |
Het |
| Vmn1r228 |
G |
T |
17: 20,996,772 (GRCm39) |
H249N |
probably benign |
Het |
| Vmn2r108 |
C |
T |
17: 20,683,279 (GRCm39) |
G642S |
probably damaging |
Het |
| Wdr27 |
A |
G |
17: 15,154,831 (GRCm39) |
S29P |
probably benign |
Het |
| Zan |
A |
G |
5: 137,415,298 (GRCm39) |
|
probably null |
Het |
|
| Other mutations in Smyd1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02869:Smyd1
|
APN |
6 |
71,198,007 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02901:Smyd1
|
APN |
6 |
71,215,614 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0134:Smyd1
|
UTSW |
6 |
71,193,749 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1344:Smyd1
|
UTSW |
6 |
71,239,151 (GRCm39) |
missense |
probably benign |
0.36 |
|
R1418:Smyd1
|
UTSW |
6 |
71,239,151 (GRCm39) |
missense |
probably benign |
0.36 |
|
R1737:Smyd1
|
UTSW |
6 |
71,193,875 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1909:Smyd1
|
UTSW |
6 |
71,216,563 (GRCm39) |
missense |
probably benign |
0.34 |
|
R1978:Smyd1
|
UTSW |
6 |
71,289,703 (GRCm39) |
splice site |
probably null |
|
|
R2281:Smyd1
|
UTSW |
6 |
71,215,660 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2418:Smyd1
|
UTSW |
6 |
71,216,537 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4914:Smyd1
|
UTSW |
6 |
71,196,321 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5395:Smyd1
|
UTSW |
6 |
71,196,374 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R5589:Smyd1
|
UTSW |
6 |
71,239,164 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5663:Smyd1
|
UTSW |
6 |
71,216,705 (GRCm39) |
missense |
probably benign |
|
|
R6572:Smyd1
|
UTSW |
6 |
71,202,396 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7014:Smyd1
|
UTSW |
6 |
71,215,611 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7074:Smyd1
|
UTSW |
6 |
71,214,359 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8478:Smyd1
|
UTSW |
6 |
71,193,811 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8724:Smyd1
|
UTSW |
6 |
71,193,767 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8816:Smyd1
|
UTSW |
6 |
71,192,868 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R9484:Smyd1
|
UTSW |
6 |
71,202,450 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9623:Smyd1
|
UTSW |
6 |
71,192,808 (GRCm39) |
missense |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GAGAAGCCTGACCATGACCATG -3'
(R):5'- CAGGTTTCAAAGAGTGAGTCTAGTG -3'
Sequencing Primer
(F):5'- CATGACCATGGCCTGTGG -3'
(R):5'- TCCACGTGTCGGTTAAGAC -3'
|
| Posted On |
2019-06-07 |
Incidental Mutation