Incidental Mutation 'R2849:Smpd4'
| ID |
252023 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smpd4
|
| Ensembl Gene |
ENSMUSG00000005899 |
| Gene Name |
sphingomyelin phosphodiesterase 4 |
| Synonyms |
4122402O22Rik, neutral membrane (neutral sphingomyelinase-3) |
| MMRRC Submission |
040442-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.098)
|
| Stock # |
R2849 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
16 |
| Chromosomal Location |
17437218-17462692 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 17460076 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 436
(D436G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000156362
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006053]
[ENSMUST00000056962]
[ENSMUST00000090159]
[ENSMUST00000163476]
[ENSMUST00000163997]
[ENSMUST00000165363]
[ENSMUST00000170996]
[ENSMUST00000170273]
[ENSMUST00000182368]
[ENSMUST00000182344]
[ENSMUST00000182117]
[ENSMUST00000232271]
[ENSMUST00000231792]
[ENSMUST00000232021]
[ENSMUST00000231722]
[ENSMUST00000231436]
[ENSMUST00000231627]
[ENSMUST00000232116]
|
| AlphaFold |
Q6ZPR5 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000006053
AA Change: D686G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899
AA Change: D686G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:mit_SMPDase
|
8 |
768 |
N/A |
PFAM |
|
transmembrane domain
|
769 |
791 |
N/A |
INTRINSIC |
|
transmembrane domain
|
798 |
815 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000056962
|
| SMART Domains |
Protein: ENSMUSP00000049541
Gene: ENSMUSG00000041617
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
12 |
34 |
N/A |
INTRINSIC |
|
Pfam:CCDC92
|
50 |
105 |
4.1e-24 |
PFAM |
|
low complexity region
|
154 |
164 |
N/A |
INTRINSIC |
|
Pfam:CCDC74_C
|
209 |
326 |
1.4e-49 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000090159
AA Change: D670G
PolyPhen 2
Score 0.971 (Sensitivity: 0.77; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000087620
Gene: ENSMUSG00000005899
AA Change: D670G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:mit_SMPDase
|
8 |
288 |
7.4e-177 |
PFAM |
|
Pfam:mit_SMPDase
|
287 |
752 |
9.4e-259 |
PFAM |
|
transmembrane domain
|
753 |
775 |
N/A |
INTRINSIC |
|
transmembrane domain
|
782 |
799 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000163476
AA Change: D657G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000131867
Gene: ENSMUSG00000005899
AA Change: D657G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:mit_SMPDase
|
8 |
289 |
6.2e-177 |
PFAM |
|
Pfam:mit_SMPDase
|
285 |
739 |
9.8e-266 |
PFAM |
|
transmembrane domain
|
740 |
762 |
N/A |
INTRINSIC |
|
transmembrane domain
|
769 |
786 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000163997
AA Change: D436G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000128595
Gene: ENSMUSG00000005899
AA Change: D436G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:mit_SMPDase
|
8 |
43 |
2.1e-17 |
PFAM |
|
Pfam:mit_SMPDase
|
42 |
68 |
2.5e-13 |
PFAM |
|
Pfam:mit_SMPDase
|
65 |
518 |
4.9e-266 |
PFAM |
|
transmembrane domain
|
519 |
541 |
N/A |
INTRINSIC |
|
transmembrane domain
|
548 |
565 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000164292
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000165363
AA Change: D656G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000130720
Gene: ENSMUSG00000005899
AA Change: D656G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:mit_SMPDase
|
8 |
289 |
6.2e-177 |
PFAM |
|
Pfam:mit_SMPDase
|
285 |
738 |
4.1e-262 |
PFAM |
|
transmembrane domain
|
739 |
761 |
N/A |
INTRINSIC |
|
transmembrane domain
|
768 |
785 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000170996
AA Change: D362G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000129074
Gene: ENSMUSG00000005899
AA Change: D362G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:mit_SMPDase
|
26 |
444 |
4.4e-234 |
PFAM |
|
transmembrane domain
|
445 |
467 |
N/A |
INTRINSIC |
|
transmembrane domain
|
474 |
491 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000170273
AA Change: D584G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000129957
Gene: ENSMUSG00000005899
AA Change: D584G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:mit_SMPDase
|
8 |
43 |
2.6e-17 |
PFAM |
|
Pfam:mit_SMPDase
|
41 |
215 |
4.1e-103 |
PFAM |
|
Pfam:mit_SMPDase
|
214 |
666 |
1.3e-265 |
PFAM |
|
transmembrane domain
|
667 |
689 |
N/A |
INTRINSIC |
|
transmembrane domain
|
696 |
713 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170401
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000182822
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000166091
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000167362
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000167592
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000183101
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000182526
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000182368
|
| SMART Domains |
Protein: ENSMUSP00000138262
Gene: ENSMUSG00000041617
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
12 |
34 |
N/A |
INTRINSIC |
|
Pfam:CCDC92
|
49 |
110 |
2.9e-26 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000182671
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000182344
|
| SMART Domains |
Protein: ENSMUSP00000138131
Gene: ENSMUSG00000041617
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:CCDC92
|
18 |
79 |
1.4e-26 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000182976
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000182117
|
| SMART Domains |
Protein: ENSMUSP00000138657
Gene: ENSMUSG00000041617
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
1 |
21 |
N/A |
INTRINSIC |
|
Pfam:CCDC92
|
36 |
97 |
2e-26 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000232271
AA Change: D362G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000231792
AA Change: D436G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000232021
AA Change: D584G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000231378
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231722
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231436
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232270
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232417
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000183279
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231627
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232116
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232468
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232185
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.8%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Sphingomyelinases (EC 3.1.4.12), such as SMPD4, catalyze the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide (Krut et al., 2006 [PubMed 16517606]).[supplied by OMIM, Mar 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca17 |
G |
C |
17: 24,508,481 (GRCm39) |
T1018R |
probably damaging |
Het |
| Abca8a |
T |
C |
11: 109,932,931 (GRCm39) |
D1231G |
probably damaging |
Het |
| Adcy7 |
A |
G |
8: 89,054,021 (GRCm39) |
I1017V |
probably benign |
Het |
| Agpat2 |
A |
G |
2: 26,487,251 (GRCm39) |
I109T |
probably damaging |
Het |
| Aldh9a1 |
G |
A |
1: 167,180,197 (GRCm39) |
R97H |
probably damaging |
Het |
| Als2 |
G |
A |
1: 59,245,697 (GRCm39) |
T593M |
probably damaging |
Het |
| Ap3d1 |
G |
C |
10: 80,577,742 (GRCm39) |
H28Q |
possibly damaging |
Het |
| Atxn1 |
A |
T |
13: 45,720,175 (GRCm39) |
D573E |
probably damaging |
Het |
| Begain |
T |
A |
12: 108,999,044 (GRCm39) |
M576L |
probably benign |
Het |
| Bod1l |
T |
C |
5: 41,995,419 (GRCm39) |
N109S |
probably damaging |
Het |
| Boll |
A |
G |
1: 55,385,532 (GRCm39) |
M131T |
possibly damaging |
Het |
| Celf2 |
T |
C |
2: 6,608,936 (GRCm39) |
R282G |
probably damaging |
Het |
| Cers2 |
T |
C |
3: 95,229,770 (GRCm39) |
F330L |
probably benign |
Het |
| Chst13 |
T |
C |
6: 90,286,140 (GRCm39) |
D274G |
probably benign |
Het |
| Cimap1a |
A |
G |
7: 140,429,182 (GRCm39) |
T156A |
probably benign |
Het |
| Cstdc5 |
T |
A |
16: 36,187,814 (GRCm39) |
Q17L |
probably damaging |
Het |
| Dclk2 |
A |
G |
3: 86,700,530 (GRCm39) |
V649A |
probably damaging |
Het |
| Deaf1 |
T |
C |
7: 140,894,367 (GRCm39) |
*54W |
probably null |
Het |
| Fbf1 |
C |
T |
11: 116,048,514 (GRCm39) |
|
probably null |
Het |
| Fbxo32 |
C |
T |
15: 58,071,368 (GRCm39) |
S71N |
probably benign |
Het |
| Fbxo42 |
T |
A |
4: 140,927,821 (GRCm39) |
N700K |
probably damaging |
Het |
| Fis1 |
T |
C |
5: 136,991,971 (GRCm39) |
I55T |
possibly damaging |
Het |
| Fyco1 |
A |
T |
9: 123,663,891 (GRCm39) |
L121* |
probably null |
Het |
| Gm2381 |
G |
A |
7: 42,469,831 (GRCm39) |
P98S |
probably damaging |
Het |
| Grm7 |
G |
T |
6: 110,623,309 (GRCm39) |
V161F |
probably damaging |
Het |
| Gtf2ird1 |
G |
A |
5: 134,387,861 (GRCm39) |
T946I |
probably damaging |
Het |
| Hmcn1 |
G |
T |
1: 150,439,350 (GRCm39) |
Y5494* |
probably null |
Het |
| Josd2 |
A |
G |
7: 44,118,397 (GRCm39) |
|
probably null |
Het |
| Lfng |
T |
A |
5: 140,597,622 (GRCm39) |
D149E |
probably damaging |
Het |
| Lrp1 |
C |
T |
10: 127,378,165 (GRCm39) |
A4052T |
probably damaging |
Het |
| Lrrtm3 |
T |
C |
10: 63,924,810 (GRCm39) |
N119S |
probably damaging |
Het |
| Lypd6 |
C |
T |
2: 50,055,664 (GRCm39) |
P38L |
probably damaging |
Het |
| Msl3l2 |
T |
C |
10: 55,991,538 (GRCm39) |
C88R |
probably benign |
Het |
| Nsd1 |
A |
G |
13: 55,361,505 (GRCm39) |
T158A |
probably damaging |
Het |
| Nudt22 |
A |
T |
19: 6,970,852 (GRCm39) |
S239R |
probably benign |
Het |
| Or4g7 |
T |
C |
2: 111,309,699 (GRCm39) |
M190T |
probably benign |
Het |
| Or52r1c |
A |
T |
7: 102,735,319 (GRCm39) |
D193V |
probably damaging |
Het |
| Osbpl8 |
T |
A |
10: 111,105,297 (GRCm39) |
S251T |
probably benign |
Het |
| Otop3 |
T |
C |
11: 115,235,384 (GRCm39) |
F339L |
probably damaging |
Het |
| Pcdhga10 |
T |
A |
18: 37,881,253 (GRCm39) |
V338E |
possibly damaging |
Het |
| Pcnx2 |
A |
G |
8: 126,487,666 (GRCm39) |
F1779S |
probably damaging |
Het |
| Plxna4 |
T |
C |
6: 32,162,467 (GRCm39) |
K1349E |
probably damaging |
Het |
| Poteg |
A |
T |
8: 27,971,704 (GRCm39) |
N406I |
probably benign |
Het |
| Ppp4r4 |
T |
C |
12: 103,573,192 (GRCm39) |
V697A |
probably benign |
Het |
| Ptpra |
C |
A |
2: 130,386,919 (GRCm39) |
H603Q |
probably benign |
Het |
| Rnf10 |
T |
C |
5: 115,387,171 (GRCm39) |
D439G |
probably benign |
Het |
| Rnf43 |
T |
A |
11: 87,623,093 (GRCm39) |
N731K |
probably benign |
Het |
| Slc2a4 |
T |
A |
11: 69,836,997 (GRCm39) |
N116Y |
probably damaging |
Het |
| Slc6a15 |
C |
A |
10: 103,240,552 (GRCm39) |
H392N |
probably benign |
Het |
| Slco6d1 |
C |
T |
1: 98,394,441 (GRCm39) |
T375I |
probably benign |
Het |
| Spata22 |
G |
A |
11: 73,244,571 (GRCm39) |
W311* |
probably null |
Het |
| Syt3 |
G |
A |
7: 44,042,866 (GRCm39) |
V383I |
probably benign |
Het |
| Tle6 |
T |
A |
10: 81,430,235 (GRCm39) |
I306F |
probably damaging |
Het |
| Tox3 |
G |
A |
8: 90,975,018 (GRCm39) |
Q538* |
probably null |
Het |
| Trim24 |
T |
A |
6: 37,933,388 (GRCm39) |
S656T |
probably damaging |
Het |
| Trnau1ap |
C |
A |
4: 132,049,045 (GRCm39) |
V119F |
possibly damaging |
Het |
| Vmn1r181 |
G |
T |
7: 23,683,943 (GRCm39) |
S136I |
possibly damaging |
Het |
| Vmn1r82 |
T |
C |
7: 12,039,333 (GRCm39) |
V202A |
probably damaging |
Het |
| Zfp607b |
G |
A |
7: 27,401,819 (GRCm39) |
V92I |
probably benign |
Het |
| Zfp964 |
G |
C |
8: 70,116,504 (GRCm39) |
C368S |
unknown |
Het |
| Zw10 |
A |
G |
9: 48,968,941 (GRCm39) |
|
probably null |
Het |
|
| Other mutations in Smpd4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00944:Smpd4
|
APN |
16 |
17,460,621 (GRCm39) |
missense |
probably benign |
0.04 |
|
IGL01461:Smpd4
|
APN |
16 |
17,439,370 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02051:Smpd4
|
APN |
16 |
17,444,382 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02492:Smpd4
|
APN |
16 |
17,457,215 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03181:Smpd4
|
APN |
16 |
17,443,671 (GRCm39) |
nonsense |
probably null |
|
|
Victim
|
UTSW |
16 |
17,458,835 (GRCm39) |
missense |
probably damaging |
1.00 |
|
weakling
|
UTSW |
16 |
17,456,350 (GRCm39) |
intron |
probably benign |
|
|
G1citation:Smpd4
|
UTSW |
16 |
17,458,097 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0197:Smpd4
|
UTSW |
16 |
17,459,461 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0549:Smpd4
|
UTSW |
16 |
17,457,176 (GRCm39) |
missense |
probably benign |
0.15 |
|
R0789:Smpd4
|
UTSW |
16 |
17,443,690 (GRCm39) |
missense |
probably benign |
0.14 |
|
R1077:Smpd4
|
UTSW |
16 |
17,441,833 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1120:Smpd4
|
UTSW |
16 |
17,456,350 (GRCm39) |
intron |
probably benign |
|
|
R1716:Smpd4
|
UTSW |
16 |
17,460,365 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1758:Smpd4
|
UTSW |
16 |
17,458,744 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1758:Smpd4
|
UTSW |
16 |
17,443,872 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1838:Smpd4
|
UTSW |
16 |
17,460,166 (GRCm39) |
splice site |
probably null |
|
|
R2115:Smpd4
|
UTSW |
16 |
17,444,729 (GRCm39) |
missense |
probably benign |
0.33 |
|
R4654:Smpd4
|
UTSW |
16 |
17,459,992 (GRCm39) |
intron |
probably benign |
|
|
R6157:Smpd4
|
UTSW |
16 |
17,458,930 (GRCm39) |
splice site |
probably null |
|
|
R6190:Smpd4
|
UTSW |
16 |
17,449,877 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6822:Smpd4
|
UTSW |
16 |
17,458,097 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7062:Smpd4
|
UTSW |
16 |
17,458,835 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7305:Smpd4
|
UTSW |
16 |
17,459,647 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7759:Smpd4
|
UTSW |
16 |
17,456,497 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7853:Smpd4
|
UTSW |
16 |
17,460,605 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8187:Smpd4
|
UTSW |
16 |
17,446,999 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8303:Smpd4
|
UTSW |
16 |
17,457,195 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8518:Smpd4
|
UTSW |
16 |
17,458,884 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R8735:Smpd4
|
UTSW |
16 |
17,453,410 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R9075:Smpd4
|
UTSW |
16 |
17,457,849 (GRCm39) |
missense |
unknown |
|
|
R9439:Smpd4
|
UTSW |
16 |
17,459,451 (GRCm39) |
missense |
probably benign |
|
|
Z1176:Smpd4
|
UTSW |
16 |
17,437,450 (GRCm39) |
intron |
probably benign |
|
|
Z1177:Smpd4
|
UTSW |
16 |
17,439,305 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- ATCCAAATGCTGGCATTGTCC -3'
(R):5'- CTCTGGGACCAAGTGATTCTC -3'
Sequencing Primer
(F):5'- GGCATTGTCCAGAAAATTTTAACAGG -3'
(R):5'- TGATTCTCACGCAGGGCC -3'
|
| Posted On |
2014-12-04 |
Incidental Mutation