Incidental Mutation 'R4033:Smyd4'
| ID |
313593 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smyd4
|
| Ensembl Gene |
ENSMUSG00000018809 |
| Gene Name |
SET and MYND domain containing 4 |
| Synonyms |
G430029E23Rik |
| MMRRC Submission |
040961-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4033 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
75239259-75296531 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 75240580 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 25
(D25G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000047505
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000000767]
[ENSMUST00000044530]
[ENSMUST00000092907]
|
| AlphaFold |
Q8BTK5 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000000767
|
| SMART Domains |
Protein: ENSMUSP00000000767
Gene: ENSMUSG00000000751
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Rep-A_N
|
5 |
93 |
7.2e-30 |
PFAM |
|
low complexity region
|
145 |
175 |
N/A |
INTRINSIC |
|
Pfam:tRNA_anti-codon
|
227 |
316 |
5e-13 |
PFAM |
|
Pfam:REPA_OB_2
|
335 |
432 |
5e-37 |
PFAM |
|
Pfam:Rep_fac-A_C
|
491 |
636 |
4.5e-57 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000044530
AA Change: D25G
PolyPhen 2
Score 0.059 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000047505
Gene: ENSMUSG00000018809
AA Change: D25G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:TPR_11
|
65 |
132 |
2.4e-10 |
PFAM |
|
SET
|
231 |
576 |
4.85e-1 |
SMART |
|
Blast:TPR
|
694 |
726 |
1e-6 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000092907
|
| SMART Domains |
Protein: ENSMUSP00000090585
Gene: ENSMUSG00000000751
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Rep-A_N
|
5 |
104 |
4.3e-35 |
PFAM |
|
low complexity region
|
124 |
154 |
N/A |
INTRINSIC |
|
Pfam:tRNA_anti-codon
|
206 |
295 |
8.4e-13 |
PFAM |
|
SCOP:d1fgua2
|
308 |
435 |
8e-46 |
SMART |
|
Pfam:Rep_fac-A_C
|
470 |
615 |
9.2e-56 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149365
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000154894
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000157055
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.2%
|
| Validation Efficiency |
100% (47/47) |
| MGI Phenotype |
PHENOTYPE: Mice homozygous for a knock-out allele exhibit testicular degeneration and atrophy. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam34l |
C |
G |
8: 44,079,710 (GRCm39) |
M171I |
probably benign |
Het |
| Als2 |
G |
T |
1: 59,235,400 (GRCm39) |
S761R |
probably benign |
Het |
| Ankrd63 |
C |
A |
2: 118,533,412 (GRCm39) |
|
probably benign |
Het |
| Brf1 |
G |
A |
12: 112,943,352 (GRCm39) |
T166M |
probably damaging |
Het |
| Car9 |
T |
C |
4: 43,508,624 (GRCm39) |
V131A |
possibly damaging |
Het |
| Cerk |
T |
G |
15: 86,039,228 (GRCm39) |
H221P |
possibly damaging |
Het |
| Cfap69 |
A |
T |
5: 5,654,389 (GRCm39) |
I458N |
possibly damaging |
Het |
| Chil4 |
T |
C |
3: 106,121,765 (GRCm39) |
Y28C |
probably damaging |
Het |
| Cracd |
A |
G |
5: 77,006,312 (GRCm39) |
N891S |
unknown |
Het |
| Dmxl1 |
A |
G |
18: 49,984,498 (GRCm39) |
T165A |
possibly damaging |
Het |
| Erich6b |
A |
T |
14: 75,896,207 (GRCm39) |
N31I |
probably benign |
Het |
| Fgf17 |
G |
T |
14: 70,878,966 (GRCm39) |
|
probably benign |
Het |
| Fhit |
A |
T |
14: 10,751,671 (GRCm38) |
|
probably benign |
Het |
| Fnip1 |
A |
T |
11: 54,393,297 (GRCm39) |
I578L |
probably benign |
Het |
| Gm17641 |
C |
T |
3: 68,777,146 (GRCm39) |
R36W |
probably damaging |
Het |
| Gprin2 |
A |
T |
14: 33,916,635 (GRCm39) |
D378E |
probably benign |
Het |
| Grhl3 |
T |
A |
4: 135,300,735 (GRCm39) |
M1L |
probably benign |
Het |
| Hsp90aa1 |
T |
A |
12: 110,662,114 (GRCm39) |
M1L |
possibly damaging |
Het |
| Hsp90aa1 |
C |
A |
12: 110,662,115 (GRCm39) |
|
probably null |
Het |
| Ifih1 |
G |
A |
2: 62,465,534 (GRCm39) |
S212L |
probably benign |
Het |
| Iqck |
T |
C |
7: 118,540,827 (GRCm39) |
I242T |
probably damaging |
Het |
| Kalrn |
C |
T |
16: 33,810,180 (GRCm39) |
D2525N |
possibly damaging |
Het |
| Lsm14b |
A |
G |
2: 179,673,309 (GRCm39) |
K195E |
probably benign |
Het |
| Mical1 |
G |
A |
10: 41,357,172 (GRCm39) |
V326I |
probably benign |
Het |
| Mtnr1b |
A |
T |
9: 15,774,830 (GRCm39) |
N76K |
probably damaging |
Het |
| Nalcn |
T |
C |
14: 123,837,401 (GRCm39) |
|
probably benign |
Het |
| Nop14 |
T |
C |
5: 34,807,861 (GRCm39) |
D367G |
probably benign |
Het |
| Nrxn3 |
T |
C |
12: 89,499,771 (GRCm39) |
C721R |
probably damaging |
Het |
| Or51e1 |
C |
T |
7: 102,358,697 (GRCm39) |
T77I |
probably damaging |
Het |
| Prr27 |
G |
T |
5: 87,991,164 (GRCm39) |
E259* |
probably null |
Het |
| Psmg3 |
G |
A |
5: 139,812,086 (GRCm39) |
P5S |
probably damaging |
Het |
| Pxdn |
A |
G |
12: 30,053,224 (GRCm39) |
T1134A |
probably benign |
Het |
| Rbm28 |
T |
C |
6: 29,159,668 (GRCm39) |
N120S |
probably damaging |
Het |
| Reg3b |
A |
T |
6: 78,350,192 (GRCm39) |
K157N |
possibly damaging |
Het |
| Rlf |
T |
G |
4: 121,004,540 (GRCm39) |
Q1480P |
probably damaging |
Het |
| Slc16a12 |
A |
T |
19: 34,652,567 (GRCm39) |
L193Q |
probably damaging |
Het |
| Smo |
G |
A |
6: 29,759,917 (GRCm39) |
R672H |
probably damaging |
Het |
| Sorbs2 |
C |
G |
8: 46,228,632 (GRCm39) |
D264E |
probably damaging |
Het |
| Tctn3 |
G |
T |
19: 40,585,767 (GRCm39) |
Q593K |
probably benign |
Het |
| Tdrd9 |
A |
T |
12: 111,958,973 (GRCm39) |
I136L |
possibly damaging |
Het |
| Tshz3 |
G |
A |
7: 36,470,009 (GRCm39) |
S666N |
possibly damaging |
Het |
| Ubn1 |
C |
T |
16: 4,882,475 (GRCm39) |
T69M |
probably damaging |
Het |
| Unk |
A |
T |
11: 115,944,353 (GRCm39) |
H368L |
probably benign |
Het |
| Zan |
A |
T |
5: 137,436,122 (GRCm39) |
L2051* |
probably null |
Het |
|
| Other mutations in Smyd4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00777:Smyd4
|
APN |
11 |
75,281,634 (GRCm39) |
missense |
probably benign |
|
|
IGL02372:Smyd4
|
APN |
11 |
75,281,111 (GRCm39) |
nonsense |
probably null |
|
|
IGL02390:Smyd4
|
APN |
11 |
75,278,332 (GRCm39) |
splice site |
probably null |
|
|
IGL02492:Smyd4
|
APN |
11 |
75,294,252 (GRCm39) |
missense |
probably benign |
|
|
IGL02504:Smyd4
|
APN |
11 |
75,281,507 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02623:Smyd4
|
APN |
11 |
75,280,890 (GRCm39) |
splice site |
probably benign |
|
|
IGL02661:Smyd4
|
APN |
11 |
75,281,767 (GRCm39) |
nonsense |
probably null |
|
|
IGL03084:Smyd4
|
APN |
11 |
75,281,433 (GRCm39) |
missense |
probably benign |
0.00 |
|
PIT4431001:Smyd4
|
UTSW |
11 |
75,294,339 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0507:Smyd4
|
UTSW |
11 |
75,290,534 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R0834:Smyd4
|
UTSW |
11 |
75,281,958 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R1075:Smyd4
|
UTSW |
11 |
75,291,164 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1215:Smyd4
|
UTSW |
11 |
75,281,121 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
R1759:Smyd4
|
UTSW |
11 |
75,273,192 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2496:Smyd4
|
UTSW |
11 |
75,281,927 (GRCm39) |
missense |
probably benign |
0.03 |
|
R2862:Smyd4
|
UTSW |
11 |
75,280,962 (GRCm39) |
missense |
probably benign |
0.12 |
|
R4655:Smyd4
|
UTSW |
11 |
75,281,558 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4775:Smyd4
|
UTSW |
11 |
75,282,018 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4801:Smyd4
|
UTSW |
11 |
75,294,010 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4802:Smyd4
|
UTSW |
11 |
75,294,010 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4963:Smyd4
|
UTSW |
11 |
75,273,120 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5306:Smyd4
|
UTSW |
11 |
75,292,984 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5327:Smyd4
|
UTSW |
11 |
75,281,765 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5386:Smyd4
|
UTSW |
11 |
75,280,982 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5578:Smyd4
|
UTSW |
11 |
75,295,602 (GRCm39) |
missense |
probably benign |
0.03 |
|
R7038:Smyd4
|
UTSW |
11 |
75,281,340 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7271:Smyd4
|
UTSW |
11 |
75,281,325 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R7312:Smyd4
|
UTSW |
11 |
75,281,082 (GRCm39) |
missense |
probably benign |
0.18 |
|
R7576:Smyd4
|
UTSW |
11 |
75,281,032 (GRCm39) |
missense |
probably benign |
0.03 |
|
R7904:Smyd4
|
UTSW |
11 |
75,240,613 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
R8387:Smyd4
|
UTSW |
11 |
75,292,984 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8816:Smyd4
|
UTSW |
11 |
75,281,232 (GRCm39) |
missense |
probably benign |
0.24 |
|
R9235:Smyd4
|
UTSW |
11 |
75,295,689 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9436:Smyd4
|
UTSW |
11 |
75,293,017 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9786:Smyd4
|
UTSW |
11 |
75,281,625 (GRCm39) |
missense |
probably benign |
0.06 |
|
Z1176:Smyd4
|
UTSW |
11 |
75,290,440 (GRCm39) |
missense |
probably benign |
0.03 |
|
| Predicted Primers |
PCR Primer
(F):5'- CTGGGTGAATTGGTACCACAC -3'
(R):5'- GTAACTGCTAAATGCCCCATAC -3'
Sequencing Primer
(F):5'- CCCCAGAAGAAATGATTTTGGTTGC -3'
(R):5'- GCAGAACATTTTCCAGACC -3'
|
| Posted On |
2015-04-30 |
Incidental Mutation