Incidental Mutation 'R0197:Smpd4'
ID |
23515 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Smpd4
|
Ensembl Gene |
ENSMUSG00000005899 |
Gene Name |
sphingomyelin phosphodiesterase 4 |
Synonyms |
4122402O22Rik, neutral membrane (neutral sphingomyelinase-3) |
MMRRC Submission |
038456-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.098)
|
Stock # |
R0197 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
16 |
Chromosomal Location |
17437218-17462692 bp(+) (GRCm39) |
Type of Mutation |
critical splice donor site (2 bp from exon) |
DNA Base Change (assembly) |
T to A
at 17459461 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Ref Sequence |
ENSEMBL: ENSMUSP00000156215
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006053]
[ENSMUST00000056962]
[ENSMUST00000090159]
[ENSMUST00000163476]
[ENSMUST00000163997]
[ENSMUST00000165363]
[ENSMUST00000170117]
[ENSMUST00000170273]
[ENSMUST00000170366]
[ENSMUST00000170996]
[ENSMUST00000182117]
[ENSMUST00000182368]
[ENSMUST00000232271]
[ENSMUST00000231627]
[ENSMUST00000232021]
[ENSMUST00000231436]
[ENSMUST00000232116]
[ENSMUST00000231792]
[ENSMUST00000231722]
|
AlphaFold |
Q6ZPR5 |
Predicted Effect |
probably null
Transcript: ENSMUST00000006053
|
SMART Domains |
Protein: ENSMUSP00000006053 Gene: ENSMUSG00000005899
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 null
Transcript: ENSMUST00000090159
|
SMART Domains |
Protein: ENSMUSP00000087620 Gene: ENSMUSG00000005899
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 null
Transcript: ENSMUST00000163476
|
SMART Domains |
Protein: ENSMUSP00000131867 Gene: ENSMUSG00000005899
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 null
Transcript: ENSMUST00000163997
|
SMART Domains |
Protein: ENSMUSP00000128595 Gene: ENSMUSG00000005899
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 null
Transcript: ENSMUST00000165363
|
SMART Domains |
Protein: ENSMUSP00000130720 Gene: ENSMUSG00000005899
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 |
|
SMART Domains |
Protein: ENSMUSP00000132279 Gene: ENSMUSG00000005899
Domain | Start | End | E-Value | Type |
Pfam:mit_SMPDase
|
8 |
46 |
2.1e-19 |
PFAM |
|
Predicted Effect |
probably null
Transcript: ENSMUST00000170273
|
SMART Domains |
Protein: ENSMUSP00000129957 Gene: ENSMUSG00000005899
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 null
Transcript: ENSMUST00000170366
|
SMART Domains |
Protein: ENSMUSP00000130990 Gene: ENSMUSG00000005899
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 null
Transcript: ENSMUST00000170996
|
SMART Domains |
Protein: ENSMUSP00000129074 Gene: ENSMUSG00000005899
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: ENSMUST00000170401
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000167362
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000167592
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000182822
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000183101
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000182976
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000231378
|
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 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 null
Transcript: ENSMUST00000232271
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000231627
|
Predicted Effect |
probably null
Transcript: ENSMUST00000232021
|
Predicted Effect |
probably null
Transcript: ENSMUST00000231436
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232185
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232468
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000232116
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232270
|
Predicted Effect |
probably null
Transcript: ENSMUST00000231792
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232417
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000231722
|
Meta Mutation Damage Score |
0.9755 |
Coding Region Coverage |
- 1x: 98.6%
- 3x: 97.3%
- 10x: 92.5%
- 20x: 75.9%
|
Validation Efficiency |
97% (121/125) |
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: 68 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1110002E22Rik |
T |
C |
3: 137,775,632 (GRCm39) |
L1607P |
probably damaging |
Het |
1700016H13Rik |
T |
C |
5: 103,796,687 (GRCm39) |
*118W |
probably null |
Het |
Abcc2 |
A |
T |
19: 43,815,053 (GRCm39) |
R1147* |
probably null |
Het |
Acsbg3 |
A |
T |
17: 57,190,835 (GRCm39) |
N468Y |
probably benign |
Het |
Agap2 |
A |
G |
10: 126,927,571 (GRCm39) |
T1131A |
possibly damaging |
Het |
Aldh9a1 |
A |
G |
1: 167,189,416 (GRCm39) |
D388G |
probably damaging |
Het |
Ap3d1 |
G |
T |
10: 80,565,876 (GRCm39) |
A97E |
probably damaging |
Het |
Arhgef10 |
T |
A |
8: 15,012,636 (GRCm39) |
V320E |
probably damaging |
Het |
Baiap2l1 |
C |
A |
5: 144,202,820 (GRCm39) |
V498L |
probably damaging |
Het |
Bltp2 |
A |
C |
11: 78,160,530 (GRCm39) |
|
probably benign |
Het |
Cdh2 |
T |
C |
18: 16,762,633 (GRCm39) |
N437S |
probably benign |
Het |
Cert1 |
T |
A |
13: 96,685,795 (GRCm39) |
Y63N |
probably benign |
Het |
Cfap119 |
T |
C |
7: 127,184,034 (GRCm39) |
E261G |
probably damaging |
Het |
Cfap20dc |
C |
T |
14: 8,518,695 (GRCm38) |
G254R |
probably damaging |
Het |
Chd1 |
C |
A |
17: 15,945,693 (GRCm39) |
N72K |
probably benign |
Het |
Cstf2t |
A |
T |
19: 31,062,026 (GRCm39) |
M521L |
probably benign |
Het |
Dlx5 |
T |
C |
6: 6,881,619 (GRCm39) |
K90E |
possibly damaging |
Het |
Dmp1 |
A |
G |
5: 104,355,496 (GRCm39) |
E32G |
possibly damaging |
Het |
Espnl |
T |
G |
1: 91,272,211 (GRCm39) |
Y524D |
probably damaging |
Het |
Fam20c |
T |
C |
5: 138,741,479 (GRCm39) |
L30P |
probably damaging |
Het |
Fat1 |
G |
T |
8: 45,479,590 (GRCm39) |
A2879S |
probably benign |
Het |
Gabrg1 |
A |
T |
5: 70,931,732 (GRCm39) |
V337D |
probably damaging |
Het |
Gart |
C |
A |
16: 91,420,291 (GRCm39) |
D851Y |
possibly damaging |
Het |
Gcc1 |
T |
C |
6: 28,420,615 (GRCm39) |
H234R |
probably damaging |
Het |
Gemin6 |
T |
A |
17: 80,535,524 (GRCm39) |
H161Q |
probably damaging |
Het |
Glt6d1 |
A |
G |
2: 25,684,082 (GRCm39) |
I308T |
probably benign |
Het |
Gm10320 |
T |
C |
13: 98,628,491 (GRCm39) |
T7A |
probably benign |
Het |
Gm10912 |
T |
C |
2: 103,896,875 (GRCm39) |
S5P |
probably benign |
Het |
Gmpr2 |
T |
A |
14: 55,910,192 (GRCm39) |
D7E |
possibly damaging |
Het |
Hc |
A |
G |
2: 34,874,762 (GRCm39) |
Y1620H |
probably damaging |
Het |
Hoxa3 |
T |
C |
6: 52,147,123 (GRCm39) |
|
probably benign |
Het |
Ift140 |
A |
G |
17: 25,309,907 (GRCm39) |
T1105A |
probably benign |
Het |
Kdr |
G |
T |
5: 76,129,082 (GRCm39) |
T188N |
possibly damaging |
Het |
Lepr |
A |
T |
4: 101,609,349 (GRCm39) |
D312V |
possibly damaging |
Het |
Mcm3 |
A |
G |
1: 20,880,329 (GRCm39) |
V501A |
probably damaging |
Het |
Mcur1 |
T |
C |
13: 43,699,216 (GRCm39) |
Y267C |
probably damaging |
Het |
Med13 |
T |
A |
11: 86,197,864 (GRCm39) |
T736S |
probably benign |
Het |
Med13l |
T |
C |
5: 118,809,067 (GRCm39) |
|
probably benign |
Het |
Mroh2a |
G |
C |
1: 88,173,764 (GRCm39) |
A871P |
probably damaging |
Het |
Ndrg2 |
T |
A |
14: 52,144,460 (GRCm39) |
|
probably benign |
Het |
Oas3 |
G |
A |
5: 120,894,210 (GRCm39) |
R39C |
probably damaging |
Het |
Onecut2 |
T |
A |
18: 64,474,543 (GRCm39) |
S365T |
possibly damaging |
Het |
Or13c25 |
G |
A |
4: 52,910,849 (GRCm39) |
T315M |
probably benign |
Het |
Or4c10 |
A |
G |
2: 89,760,545 (GRCm39) |
T131A |
probably benign |
Het |
Or4k48 |
C |
T |
2: 111,476,136 (GRCm39) |
V69I |
probably benign |
Het |
Or51e1 |
T |
A |
7: 102,359,202 (GRCm39) |
H245Q |
probably damaging |
Het |
Pds5b |
C |
A |
5: 150,677,896 (GRCm39) |
Q505K |
probably benign |
Het |
Pramel22 |
C |
T |
4: 143,383,010 (GRCm39) |
E70K |
possibly damaging |
Het |
Rfx2 |
T |
C |
17: 57,110,722 (GRCm39) |
Y88C |
probably damaging |
Het |
Rpl6 |
T |
C |
5: 121,346,541 (GRCm39) |
V214A |
probably benign |
Het |
Samd3 |
T |
A |
10: 26,147,752 (GRCm39) |
C476S |
possibly damaging |
Het |
Sfi1 |
TCGC |
TC |
11: 3,096,254 (GRCm39) |
|
probably null |
Het |
Shank1 |
C |
T |
7: 44,001,718 (GRCm39) |
R1146W |
unknown |
Het |
Smcr8 |
T |
C |
11: 60,668,941 (GRCm39) |
Y30H |
probably damaging |
Het |
Strip1 |
C |
A |
3: 107,521,929 (GRCm39) |
D750Y |
probably damaging |
Het |
Svep1 |
T |
C |
4: 58,070,851 (GRCm39) |
K2312E |
possibly damaging |
Het |
Taf1c |
A |
T |
8: 120,326,722 (GRCm39) |
I438N |
probably damaging |
Het |
Tnfaip1 |
A |
T |
11: 78,420,840 (GRCm39) |
|
probably benign |
Het |
Unc45b |
T |
A |
11: 82,831,031 (GRCm39) |
L797Q |
possibly damaging |
Het |
Usp24 |
T |
A |
4: 106,264,330 (GRCm39) |
W1754R |
probably damaging |
Het |
Utp20 |
G |
A |
10: 88,613,378 (GRCm39) |
P1301L |
probably benign |
Het |
Vmn2r115 |
T |
A |
17: 23,578,755 (GRCm39) |
S743T |
probably damaging |
Het |
Vps41 |
T |
G |
13: 19,038,833 (GRCm39) |
|
probably null |
Het |
Vps72 |
G |
T |
3: 95,029,894 (GRCm39) |
L304F |
probably damaging |
Het |
Wiz |
A |
T |
17: 32,575,415 (GRCm39) |
I907N |
probably damaging |
Het |
Zfp521 |
T |
C |
18: 13,978,119 (GRCm39) |
T765A |
probably benign |
Het |
Zfp616 |
A |
T |
11: 73,976,500 (GRCm39) |
H923L |
probably damaging |
Het |
Zp2 |
A |
T |
7: 119,742,799 (GRCm39) |
|
probably benign |
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 |
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 |
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'- TTGCTCAGCTCATCACACAGGC -3'
(R):5'- TGAGAAACGACAGCTCATGCGAC -3'
Sequencing Primer
(F):5'- AGACTGCCAAGTCCATCTCTG -3'
(R):5'- CAATGCAATCTGGGAGCTGC -3'
|
Posted On |
2013-04-16 |