Incidental Mutation 'R0549:Smpd4'
| ID |
45043 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smpd4
|
| Ensembl Gene |
ENSMUSG00000005899 |
| Gene Name |
sphingomyelin phosphodiesterase 4 |
| Synonyms |
4122402O22Rik, neutral membrane (neutral sphingomyelinase-3) |
| MMRRC Submission |
038741-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.098)
|
| Stock # |
R0549 (G1)
|
| Quality Score |
107 |
|
Status
|
Validated
|
| Chromosome |
16 |
| Chromosomal Location |
17437218-17462692 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 17457176 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 378
(V378A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000006053
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006053]
[ENSMUST00000090159]
[ENSMUST00000163476]
[ENSMUST00000163997]
[ENSMUST00000165363]
[ENSMUST00000170366]
[ENSMUST00000170273]
[ENSMUST00000170996]
[ENSMUST00000231792]
[ENSMUST00000232021]
[ENSMUST00000231436]
[ENSMUST00000231627]
[ENSMUST00000232116]
[ENSMUST00000231722]
[ENSMUST00000232271]
|
| AlphaFold |
Q6ZPR5 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000006053
AA Change: V378A
PolyPhen 2
Score 0.154 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899
AA Change: V378A
| 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: ENSMUST00000090159
AA Change: V349A
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000087620
Gene: ENSMUSG00000005899
AA Change: V349A
| 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 benign
Transcript: ENSMUST00000163476
AA Change: V349A
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000131867
Gene: ENSMUSG00000005899
AA Change: V349A
| 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 benign
Transcript: ENSMUST00000163997
AA Change: V128A
PolyPhen 2
Score 0.072 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000128595
Gene: ENSMUSG00000005899
AA Change: V128A
| 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 benign
Transcript: ENSMUST00000165363
AA Change: V349A
PolyPhen 2
Score 0.049 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000130720
Gene: ENSMUSG00000005899
AA Change: V349A
| 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 |
noncoding transcript
Transcript: ENSMUST00000166091
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000170366
AA Change: V349A
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000130990
Gene: ENSMUSG00000005899
AA Change: V349A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:mit_SMPDase
|
8 |
288 |
7.1e-177 |
PFAM |
|
Pfam:mit_SMPDase
|
286 |
643 |
1.8e-214 |
PFAM |
|
Pfam:mit_SMPDase
|
642 |
696 |
8.6e-18 |
PFAM |
|
transmembrane domain
|
697 |
719 |
N/A |
INTRINSIC |
|
transmembrane domain
|
726 |
743 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000170273
AA Change: V276A
PolyPhen 2
Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
|
| SMART Domains |
Protein: ENSMUSP00000129957
Gene: ENSMUSG00000005899
AA Change: V276A
| 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 |
probably benign
Transcript: ENSMUST00000170996
AA Change: V54A
PolyPhen 2
Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000129074
Gene: ENSMUSG00000005899
AA Change: V54A
| 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 |
noncoding transcript
Transcript: ENSMUST00000167592
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000167362
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170401
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231792
AA Change: V128A
PolyPhen 2
Score 0.059 (Sensitivity: 0.94; Specificity: 0.84)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232021
AA Change: V276A
PolyPhen 2
Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231436
AA Change: V349A
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231627
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232116
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000231378
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232185
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231722
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232271
AA Change: V54A
PolyPhen 2
Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232270
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232417
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232468
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 96.9%
- 20x: 94.3%
|
| Validation Efficiency |
96% (48/50) |
| 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: 49 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc10 |
A |
G |
17: 46,633,216 (GRCm39) |
F498L |
probably damaging |
Het |
| Adamts6 |
A |
T |
13: 104,433,763 (GRCm39) |
D64V |
possibly damaging |
Het |
| Agbl2 |
T |
C |
2: 90,620,187 (GRCm39) |
|
probably benign |
Het |
| Angptl3 |
A |
G |
4: 98,919,692 (GRCm39) |
S151G |
probably benign |
Het |
| Arhgap39 |
C |
T |
15: 76,619,086 (GRCm39) |
D833N |
probably damaging |
Het |
| C4b |
G |
T |
17: 34,954,389 (GRCm39) |
L927I |
probably damaging |
Het |
| Ccl3 |
T |
C |
11: 83,539,162 (GRCm39) |
T66A |
probably damaging |
Het |
| Cdh20 |
T |
C |
1: 110,036,674 (GRCm39) |
L618P |
probably damaging |
Het |
| Cfap65 |
T |
C |
1: 74,957,603 (GRCm39) |
T989A |
probably benign |
Het |
| Cfhr4 |
A |
T |
1: 139,667,226 (GRCm39) |
D377E |
probably damaging |
Het |
| Cnpy4 |
T |
C |
5: 138,185,899 (GRCm39) |
F18S |
possibly damaging |
Het |
| Col6a5 |
A |
G |
9: 105,781,778 (GRCm39) |
|
probably benign |
Het |
| Dppa2 |
G |
A |
16: 48,139,034 (GRCm39) |
R289H |
probably benign |
Het |
| Evx2 |
T |
C |
2: 74,489,478 (GRCm39) |
T96A |
probably benign |
Het |
| Frmd4a |
A |
G |
2: 4,608,778 (GRCm39) |
E577G |
possibly damaging |
Het |
| Gcgr |
G |
A |
11: 120,427,387 (GRCm39) |
G166S |
probably benign |
Het |
| Gm5316 |
T |
C |
6: 122,877,150 (GRCm39) |
|
noncoding transcript |
Het |
| Gria1 |
G |
A |
11: 57,119,799 (GRCm39) |
R292Q |
probably damaging |
Het |
| Hars2 |
T |
A |
18: 36,919,261 (GRCm39) |
|
probably null |
Het |
| Hkdc1 |
T |
A |
10: 62,236,019 (GRCm39) |
T508S |
probably benign |
Het |
| Kif2b |
A |
T |
11: 91,467,410 (GRCm39) |
I291N |
probably damaging |
Het |
| Lmbrd1 |
A |
T |
1: 24,784,001 (GRCm39) |
T377S |
probably benign |
Het |
| Lrrc28 |
A |
G |
7: 67,278,090 (GRCm39) |
|
probably benign |
Het |
| Mmp3 |
A |
T |
9: 7,455,638 (GRCm39) |
N463I |
probably benign |
Het |
| Myh6 |
A |
G |
14: 55,196,065 (GRCm39) |
F578S |
probably damaging |
Het |
| Ncbp1 |
T |
A |
4: 46,168,476 (GRCm39) |
M608K |
possibly damaging |
Het |
| Nf1 |
T |
C |
11: 79,359,597 (GRCm39) |
F1412L |
probably damaging |
Het |
| Nlrp5 |
T |
A |
7: 23,141,227 (GRCm39) |
W1083R |
probably damaging |
Het |
| Nrsn1 |
T |
C |
13: 25,446,241 (GRCm39) |
Y45C |
probably benign |
Het |
| Or3a1b |
T |
G |
11: 74,012,301 (GRCm39) |
M62R |
probably damaging |
Het |
| Osbpl7 |
G |
T |
11: 96,958,368 (GRCm39) |
R881L |
probably damaging |
Het |
| Papss1 |
A |
G |
3: 131,324,974 (GRCm39) |
E456G |
possibly damaging |
Het |
| Pbxip1 |
T |
A |
3: 89,350,899 (GRCm39) |
|
probably benign |
Het |
| Pcca |
A |
G |
14: 122,875,789 (GRCm39) |
|
probably benign |
Het |
| Pde1a |
T |
A |
2: 79,695,414 (GRCm39) |
N511I |
probably damaging |
Het |
| Prpf39 |
A |
T |
12: 65,103,030 (GRCm39) |
I435F |
probably benign |
Het |
| Rnf213 |
C |
T |
11: 119,355,908 (GRCm39) |
T4117M |
probably damaging |
Het |
| Sel1l2 |
A |
T |
2: 140,107,802 (GRCm39) |
M216K |
probably damaging |
Het |
| Sidt2 |
A |
G |
9: 45,864,417 (GRCm39) |
|
probably null |
Het |
| Sirt3 |
A |
T |
7: 140,449,400 (GRCm39) |
|
probably null |
Het |
| Svil |
T |
A |
18: 5,064,566 (GRCm39) |
S642T |
possibly damaging |
Het |
| Tcp10a |
A |
G |
17: 7,593,950 (GRCm39) |
K92E |
probably benign |
Het |
| Tmem144 |
T |
C |
3: 79,730,051 (GRCm39) |
D233G |
probably damaging |
Het |
| Tnfrsf21 |
C |
T |
17: 43,349,104 (GRCm39) |
H239Y |
probably benign |
Het |
| Tnik |
T |
C |
3: 28,625,069 (GRCm39) |
S335P |
possibly damaging |
Het |
| Ush2a |
T |
C |
1: 188,679,150 (GRCm39) |
L4786P |
probably damaging |
Het |
| Utp11 |
A |
T |
4: 124,579,872 (GRCm39) |
|
probably benign |
Het |
| Vmn1r67 |
A |
G |
7: 10,181,641 (GRCm39) |
N241D |
probably damaging |
Het |
| Vmn2r11 |
A |
T |
5: 109,199,963 (GRCm39) |
C497S |
possibly damaging |
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 |
|
|
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 |
|
R2849:Smpd4
|
UTSW |
16 |
17,460,076 (GRCm39) |
missense |
probably damaging |
1.00 |
|
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'- GCTGCCACTGACTTCAAAGGCAAC -3'
(R):5'- TCAGCGTAGATGCCAATGAGTGAAC -3'
Sequencing Primer
(F):5'- AGGCAACTTACACACTGTGTTC -3'
(R):5'- ATGAGTGAACAAGTCTTCCTCC -3'
|
| Posted On |
2013-06-11 |
Incidental Mutation