Incidental Mutation 'R1120:Smpd4'
| ID |
95556 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smpd4
|
| Ensembl Gene |
ENSMUSG00000005899 |
| Gene Name |
sphingomyelin phosphodiesterase 4 |
| Synonyms |
4122402O22Rik, neutral membrane (neutral sphingomyelinase-3) |
| MMRRC Submission |
039193-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.098)
|
| Stock # |
R1120 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
16 |
| Chromosomal Location |
17437218-17462692 bp(+) (GRCm39) |
| Type of Mutation |
intron |
| DNA Base Change (assembly) |
T to C
at 17456350 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000156215
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006053]
[ENSMUST00000090159]
[ENSMUST00000163476]
[ENSMUST00000163997]
[ENSMUST00000165363]
[ENSMUST00000167217]
[ENSMUST00000170366]
[ENSMUST00000170117]
[ENSMUST00000170273]
[ENSMUST00000231436]
[ENSMUST00000231722]
[ENSMUST00000231627]
[ENSMUST00000232116]
[ENSMUST00000231792]
[ENSMUST00000232021]
[ENSMUST00000232271]
|
| AlphaFold |
Q6ZPR5 |
| Predicted Effect |
probably benign
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: 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 benign
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 |
|
| 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 benign
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: ENSMUSP00000130570
Gene: ENSMUSG00000005899
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:mit_SMPDase
|
8 |
92 |
3.4e-51 |
PFAM |
|
| Predicted Effect |
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000167362
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000170401
|
| Predicted Effect |
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000167592
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231436
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231722
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231627
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232116
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231792
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232021
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000231378
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232271
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232270
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232185
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232417
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232468
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.2%
|
| Validation Efficiency |
100% (40/40) |
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb8 |
T |
G |
5: 24,613,818 (GRCm39) |
|
probably null |
Het |
| Akp3 |
A |
T |
1: 87,053,159 (GRCm39) |
Q77L |
probably damaging |
Het |
| Blm |
A |
G |
7: 80,131,214 (GRCm39) |
L878S |
probably damaging |
Het |
| Cabin1 |
A |
G |
10: 75,561,550 (GRCm39) |
Y984H |
probably damaging |
Het |
| Cadps2 |
T |
C |
6: 23,838,793 (GRCm39) |
Q86R |
probably damaging |
Het |
| Cd2 |
C |
T |
3: 101,194,804 (GRCm39) |
D95N |
probably damaging |
Het |
| Cd36 |
A |
G |
5: 17,990,826 (GRCm39) |
I438T |
possibly damaging |
Het |
| Crhbp |
G |
T |
13: 95,578,593 (GRCm39) |
T176K |
probably benign |
Het |
| D630045J12Rik |
G |
T |
6: 38,171,705 (GRCm39) |
T821K |
probably damaging |
Het |
| Disp1 |
T |
C |
1: 182,880,139 (GRCm39) |
D288G |
probably benign |
Het |
| Dsc3 |
A |
G |
18: 20,120,034 (GRCm39) |
V208A |
probably benign |
Het |
| Eef1e1 |
A |
T |
13: 38,842,910 (GRCm39) |
N20K |
probably damaging |
Het |
| Ercc5 |
A |
G |
1: 44,201,001 (GRCm39) |
D187G |
probably damaging |
Het |
| Etl4 |
T |
A |
2: 20,811,514 (GRCm39) |
M1199K |
probably benign |
Het |
| Fnbp1 |
A |
T |
2: 30,926,606 (GRCm39) |
Y433N |
probably damaging |
Het |
| Fxyd3 |
A |
G |
7: 30,770,803 (GRCm39) |
|
probably benign |
Het |
| Hfm1 |
A |
T |
5: 107,052,084 (GRCm39) |
|
probably benign |
Het |
| Irak2 |
T |
A |
6: 113,652,720 (GRCm39) |
|
probably benign |
Het |
| Jpt2 |
T |
C |
17: 25,179,585 (GRCm39) |
M1V |
probably null |
Het |
| Knl1 |
A |
G |
2: 118,892,856 (GRCm39) |
R51G |
probably damaging |
Het |
| Krtap8-1 |
A |
G |
16: 89,284,753 (GRCm39) |
Y15H |
probably benign |
Het |
| Lrba |
A |
T |
3: 86,202,499 (GRCm39) |
D250V |
probably damaging |
Het |
| Mgat4a |
A |
G |
1: 37,491,662 (GRCm39) |
S357P |
probably damaging |
Het |
| Nup98 |
T |
A |
7: 101,809,923 (GRCm39) |
T536S |
probably damaging |
Het |
| Or4a27 |
A |
G |
2: 88,559,281 (GRCm39) |
Y221H |
probably damaging |
Het |
| Or4c109 |
A |
G |
2: 88,818,423 (GRCm39) |
M41T |
possibly damaging |
Het |
| Or9k2 |
A |
G |
10: 129,998,406 (GRCm39) |
L263P |
probably damaging |
Het |
| Parp14 |
G |
A |
16: 35,677,130 (GRCm39) |
A946V |
probably benign |
Het |
| Pnpla8 |
A |
G |
12: 44,351,730 (GRCm39) |
T568A |
possibly damaging |
Het |
| Ptprn |
A |
G |
1: 75,234,825 (GRCm39) |
I254T |
probably benign |
Het |
| Rab5b |
A |
C |
10: 128,515,483 (GRCm39) |
N188K |
probably benign |
Het |
| Samd5 |
A |
G |
10: 9,504,792 (GRCm39) |
V154A |
possibly damaging |
Het |
| Smarcb1 |
A |
G |
10: 75,757,157 (GRCm39) |
F25L |
probably benign |
Het |
| Smchd1 |
A |
T |
17: 71,665,141 (GRCm39) |
Y1847* |
probably null |
Het |
| Tex14 |
T |
A |
11: 87,429,502 (GRCm39) |
|
probably benign |
Het |
| Tnfrsf26 |
G |
A |
7: 143,171,651 (GRCm39) |
R101C |
probably damaging |
Het |
| Trmu |
A |
G |
15: 85,774,486 (GRCm39) |
K37E |
possibly damaging |
Het |
| Tsen54 |
C |
T |
11: 115,705,839 (GRCm39) |
A52V |
probably damaging |
Het |
| Ubb |
T |
C |
11: 62,443,009 (GRCm39) |
I13T |
possibly damaging |
Het |
| Vmn2r101 |
A |
T |
17: 19,797,723 (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 |
|
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 |
|
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'- ACTTGAGCAAGGTGAGTCCTGGTG -3'
(R):5'- TTGAATTCCTCCAGCGGACTGGTG -3'
Sequencing Primer
(F):5'- GGGTATAAATTGCTCTTCGCAGAC -3'
(R):5'- GGCATGGGAGTGTGCAG -3'
|
| Posted On |
2014-01-05 |
Incidental Mutation