Incidental Mutation 'R5409:Smpd5'
| ID |
426465 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smpd5
|
| Ensembl Gene |
ENSMUSG00000071724 |
| Gene Name |
sphingomyelin phosphodiesterase 5 |
| Synonyms |
Gm10345 |
| MMRRC Submission |
042978-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.144)
|
| Stock # |
R5409 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
15 |
| Chromosomal Location |
76178548-76181096 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 76179914 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Lysine
at position 321
(T321K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000134687
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000023222]
[ENSMUST00000074173]
[ENSMUST00000163991]
[ENSMUST00000230221]
[ENSMUST00000171340]
[ENSMUST00000171192]
|
| AlphaFold |
D6MZJ6 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000023222
|
| SMART Domains |
Protein: ENSMUSP00000023222
Gene: ENSMUSG00000022562
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Hydant_A_N
|
9 |
212 |
1.5e-63 |
PFAM |
|
Pfam:Hydantoinase_A
|
231 |
531 |
6.4e-109 |
PFAM |
|
low complexity region
|
629 |
637 |
N/A |
INTRINSIC |
|
Pfam:Hydantoinase_B
|
734 |
1256 |
5.2e-225 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000074173
|
| SMART Domains |
Protein: ENSMUSP00000073805
Gene: ENSMUSG00000049653
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Speriolin_N
|
1 |
176 |
5.1e-67 |
PFAM |
|
Pfam:Speriolin_N
|
172 |
262 |
1.2e-25 |
PFAM |
|
Pfam:Speriolin_C
|
334 |
480 |
1.5e-66 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000096370
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000163991
AA Change: T321K
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000134687
Gene: ENSMUSG00000071724
AA Change: T321K
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
77 |
99 |
N/A |
INTRINSIC |
|
Pfam:Exo_endo_phos
|
176 |
471 |
4.1e-11 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000167433
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000169664
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170063
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175428
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170261
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000230221
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000171340
|
| SMART Domains |
Protein: ENSMUSP00000129100
Gene: ENSMUSG00000022562
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Hydant_A_N
|
9 |
212 |
2.8e-60 |
PFAM |
|
Pfam:Hydantoinase_A
|
231 |
531 |
6.6e-102 |
PFAM |
|
low complexity region
|
629 |
637 |
N/A |
INTRINSIC |
|
Pfam:Hydantoinase_B
|
733 |
1260 |
8.2e-190 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000230735
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000171192
|
| SMART Domains |
Protein: ENSMUSP00000133693
Gene: ENSMUSG00000071724
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
35 |
46 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 94.8%
|
| Validation Efficiency |
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca7 |
T |
C |
10: 79,850,154 (GRCm39) |
L2002P |
probably damaging |
Het |
| Acot11 |
C |
T |
4: 106,617,327 (GRCm39) |
G240R |
probably damaging |
Het |
| Adgrl1 |
A |
G |
8: 84,656,371 (GRCm39) |
T230A |
probably damaging |
Het |
| Anapc4 |
A |
G |
5: 53,005,941 (GRCm39) |
E316G |
probably damaging |
Het |
| Asic1 |
GCACC |
GCACCACC |
15: 99,596,684 (GRCm39) |
|
probably benign |
Het |
| Aurka |
T |
G |
2: 172,209,036 (GRCm39) |
Q33P |
possibly damaging |
Het |
| Ccn5 |
G |
A |
2: 163,667,158 (GRCm39) |
C53Y |
probably damaging |
Het |
| Cenpm |
T |
C |
15: 82,118,564 (GRCm39) |
T153A |
probably benign |
Het |
| Clca4b |
T |
A |
3: 144,622,452 (GRCm39) |
K538* |
probably null |
Het |
| Clip2 |
G |
A |
5: 134,551,645 (GRCm39) |
T159M |
possibly damaging |
Het |
| Col5a1 |
C |
T |
2: 27,850,457 (GRCm39) |
T518I |
unknown |
Het |
| Dis3 |
A |
T |
14: 99,323,368 (GRCm39) |
M566K |
possibly damaging |
Het |
| Dnah1 |
C |
T |
14: 30,985,212 (GRCm39) |
R3869H |
probably damaging |
Het |
| Gm4775 |
A |
T |
14: 106,338,386 (GRCm39) |
|
noncoding transcript |
Het |
| Hipk2 |
C |
T |
6: 38,706,977 (GRCm39) |
G637D |
probably damaging |
Het |
| Igkv4-61 |
T |
C |
6: 69,394,111 (GRCm39) |
K18E |
possibly damaging |
Het |
| Kcnk4 |
A |
G |
19: 6,903,578 (GRCm39) |
S324P |
probably benign |
Het |
| Larp4 |
T |
C |
15: 99,883,945 (GRCm39) |
C61R |
probably damaging |
Het |
| Nid2 |
T |
C |
14: 19,856,030 (GRCm39) |
F986L |
probably damaging |
Het |
| Or5ac16 |
A |
G |
16: 59,021,920 (GRCm39) |
Y290H |
probably damaging |
Het |
| Or5aq1b |
T |
C |
2: 86,902,214 (GRCm39) |
E88G |
possibly damaging |
Het |
| Or5h22 |
C |
T |
16: 58,894,559 (GRCm39) |
V295I |
possibly damaging |
Het |
| Pgbd5 |
T |
A |
8: 125,098,619 (GRCm39) |
I359F |
probably damaging |
Het |
| Plekhh2 |
T |
C |
17: 84,893,906 (GRCm39) |
|
probably null |
Het |
| Pomgnt2 |
A |
T |
9: 121,811,303 (GRCm39) |
S493T |
possibly damaging |
Het |
| Rnf7l |
A |
T |
10: 63,257,403 (GRCm39) |
M39K |
possibly damaging |
Het |
| Rp1l1 |
T |
C |
14: 64,268,070 (GRCm39) |
S1219P |
probably benign |
Het |
| Rprd1b |
T |
A |
2: 157,916,987 (GRCm39) |
F322L |
probably damaging |
Het |
| Sh3rf1 |
G |
A |
8: 61,827,279 (GRCm39) |
V678M |
probably benign |
Het |
| Spag8 |
T |
A |
4: 43,653,134 (GRCm39) |
|
probably benign |
Het |
| Tanc2 |
T |
C |
11: 105,758,311 (GRCm39) |
C691R |
possibly damaging |
Het |
| Tnc |
A |
C |
4: 63,884,773 (GRCm39) |
M1834R |
probably damaging |
Het |
| Tnc |
A |
T |
4: 63,925,654 (GRCm39) |
Y961N |
probably damaging |
Het |
| Ttn |
T |
C |
2: 76,700,893 (GRCm39) |
|
probably benign |
Het |
| Ufl1 |
A |
G |
4: 25,280,706 (GRCm39) |
V47A |
probably damaging |
Het |
| Unc13c |
T |
A |
9: 73,485,672 (GRCm39) |
D1676V |
possibly damaging |
Het |
| Vmn1r65 |
T |
C |
7: 6,012,012 (GRCm39) |
N74S |
possibly damaging |
Het |
| Vmn2r30 |
A |
G |
7: 7,315,547 (GRCm39) |
F762S |
probably damaging |
Het |
|
| Other mutations in Smpd5 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
R4411:Smpd5
|
UTSW |
15 |
76,179,112 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R4475:Smpd5
|
UTSW |
15 |
76,178,926 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4715:Smpd5
|
UTSW |
15 |
76,179,893 (GRCm39) |
missense |
probably benign |
0.04 |
|
R4745:Smpd5
|
UTSW |
15 |
76,179,008 (GRCm39) |
missense |
probably benign |
0.04 |
|
R4879:Smpd5
|
UTSW |
15 |
76,179,070 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
R5533:Smpd5
|
UTSW |
15 |
76,178,757 (GRCm39) |
missense |
possibly damaging |
0.47 |
|
R5579:Smpd5
|
UTSW |
15 |
76,179,325 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R6076:Smpd5
|
UTSW |
15 |
76,179,092 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7531:Smpd5
|
UTSW |
15 |
76,180,539 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7826:Smpd5
|
UTSW |
15 |
76,180,496 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8184:Smpd5
|
UTSW |
15 |
76,179,926 (GRCm39) |
missense |
probably benign |
0.00 |
|
Z1177:Smpd5
|
UTSW |
15 |
76,180,501 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
Z1177:Smpd5
|
UTSW |
15 |
76,180,451 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCTCCTTCGAAGGCAGTAGG -3'
(R):5'- GCTCCTTGGCATGATCTGTG -3'
Sequencing Primer
(F):5'- TTCGAAGGCAGTAGGTCCCTTAAC -3'
(R):5'- CATGATCTGTGGAGAAAAGCCGTTTC -3'
|
| Posted On |
2016-09-01 |
Incidental Mutation