Incidental Mutation 'R6157:Smpd4'
| ID |
501884 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smpd4
|
| Ensembl Gene |
ENSMUSG00000005899 |
| Gene Name |
sphingomyelin phosphodiesterase 4 |
| Synonyms |
4122402O22Rik, neutral membrane (neutral sphingomyelinase-3) |
| MMRRC Submission |
044304-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.098)
|
| Stock # |
R6157 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
16 |
| Chromosomal Location |
17437218-17462692 bp(+) (GRCm39) |
| Type of Mutation |
splice site (5 bp from exon) |
| DNA Base Change (assembly) |
G to T
at 17458930 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000156215
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006053]
[ENSMUST00000090159]
[ENSMUST00000163476]
[ENSMUST00000163997]
[ENSMUST00000163997]
[ENSMUST00000165363]
[ENSMUST00000170117]
[ENSMUST00000170273]
[ENSMUST00000170273]
[ENSMUST00000170366]
[ENSMUST00000170366]
[ENSMUST00000170996]
[ENSMUST00000170996]
[ENSMUST00000232021]
[ENSMUST00000232271]
[ENSMUST00000232116]
[ENSMUST00000231627]
[ENSMUST00000231436]
[ENSMUST00000231722]
[ENSMUST00000231792]
|
| 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 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 |
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 |
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 |
|
| 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: 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: 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 |
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 |
probably null
Transcript: ENSMUST00000232021
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000232271
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232116
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232185
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231627
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232270
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000231436
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231722
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232417
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000231378
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000231792
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000232468
|
| Meta Mutation Damage Score |
0.9755 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.6%
- 20x: 93.1%
|
| Validation Efficiency |
93% (40/43) |
| 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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930407I10Rik |
A |
G |
15: 81,947,617 (GRCm39) |
K505E |
possibly damaging |
Het |
| Abcb1b |
A |
T |
5: 8,874,245 (GRCm39) |
N390I |
possibly damaging |
Het |
| Apob |
A |
T |
12: 8,056,077 (GRCm39) |
M1520L |
probably benign |
Het |
| Atg4c |
C |
T |
4: 99,123,400 (GRCm39) |
R396* |
probably null |
Het |
| Atp2a3 |
G |
A |
11: 72,871,442 (GRCm39) |
V648M |
probably damaging |
Het |
| Blm |
T |
C |
7: 80,162,733 (GRCm39) |
D203G |
probably benign |
Het |
| Csrnp3 |
A |
T |
2: 65,779,363 (GRCm39) |
D13V |
probably damaging |
Het |
| Dnajc10 |
A |
T |
2: 80,147,735 (GRCm39) |
|
probably benign |
Het |
| Dst |
A |
G |
1: 34,250,253 (GRCm39) |
Y1729C |
probably damaging |
Het |
| Dynlt2b |
G |
A |
16: 32,238,660 (GRCm39) |
A12T |
possibly damaging |
Het |
| Ecsit |
T |
C |
9: 21,985,987 (GRCm39) |
Y213C |
probably damaging |
Het |
| Fer |
A |
G |
17: 64,385,880 (GRCm39) |
K654R |
probably damaging |
Het |
| Hdac9 |
G |
T |
12: 34,439,428 (GRCm39) |
A383E |
probably damaging |
Het |
| Hltf |
T |
A |
3: 20,130,660 (GRCm39) |
S293T |
probably benign |
Het |
| Hydin |
T |
A |
8: 111,254,648 (GRCm39) |
D2359E |
probably benign |
Het |
| Inf2 |
A |
G |
12: 112,571,222 (GRCm39) |
|
probably benign |
Het |
| Kcns2 |
A |
G |
15: 34,839,504 (GRCm39) |
N289S |
possibly damaging |
Het |
| Meioc |
T |
C |
11: 102,559,227 (GRCm39) |
S50P |
probably damaging |
Het |
| Mocs1 |
G |
T |
17: 49,761,764 (GRCm39) |
E619D |
probably benign |
Het |
| Nfatc2 |
A |
G |
2: 168,361,371 (GRCm39) |
|
probably benign |
Het |
| Or51i1 |
T |
A |
7: 103,671,105 (GRCm39) |
N140I |
possibly damaging |
Het |
| Pag1 |
A |
T |
3: 9,758,896 (GRCm39) |
H407Q |
probably benign |
Het |
| Plaat1 |
A |
G |
16: 29,036,501 (GRCm39) |
I46M |
possibly damaging |
Het |
| Plcb3 |
G |
A |
19: 6,943,533 (GRCm39) |
A122V |
probably damaging |
Het |
| Pld4 |
C |
T |
12: 112,734,535 (GRCm39) |
T432I |
probably damaging |
Het |
| Psd3 |
T |
G |
8: 68,574,179 (GRCm39) |
M1L |
probably benign |
Het |
| Rasgrp2 |
C |
A |
19: 6,452,531 (GRCm39) |
L35I |
probably damaging |
Het |
| Ripor2 |
T |
C |
13: 24,885,052 (GRCm39) |
L390P |
probably damaging |
Het |
| Rpgrip1 |
A |
T |
14: 52,349,631 (GRCm39) |
E6D |
probably benign |
Het |
| Ryr3 |
A |
T |
2: 112,672,244 (GRCm39) |
L1409Q |
probably damaging |
Het |
| Slc6a5 |
A |
G |
7: 49,601,250 (GRCm39) |
T684A |
probably benign |
Het |
| Snx18 |
T |
C |
13: 113,753,725 (GRCm39) |
S403G |
probably damaging |
Het |
| Spsb4 |
G |
T |
9: 96,878,160 (GRCm39) |
H54Q |
probably damaging |
Het |
| Ssrp1 |
A |
G |
2: 84,871,072 (GRCm39) |
Y236C |
probably damaging |
Het |
| Tenm3 |
C |
T |
8: 48,751,843 (GRCm39) |
S982N |
probably damaging |
Het |
| Tet1 |
A |
G |
10: 62,675,749 (GRCm39) |
S776P |
probably damaging |
Het |
| Tln1 |
G |
A |
4: 43,534,744 (GRCm39) |
P2166S |
probably benign |
Het |
| Ufl1 |
T |
A |
4: 25,279,350 (GRCm39) |
Q83L |
possibly damaging |
Het |
| Unc80 |
A |
T |
1: 66,693,188 (GRCm39) |
K2458* |
probably null |
Het |
| Ush2a |
A |
T |
1: 188,460,467 (GRCm39) |
Y2576F |
probably benign |
Het |
| Xrcc6 |
C |
A |
15: 81,913,305 (GRCm39) |
|
probably null |
Het |
| Zbtb48 |
A |
G |
4: 152,106,064 (GRCm39) |
F380L |
probably damaging |
Het |
| Zfp534 |
C |
T |
4: 147,758,947 (GRCm39) |
R574K |
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 |
|
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 |
|
|
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'- TTCTAGGTGAGCAGCTGTTC -3'
(R):5'- TAAGAGTGTCCACCCAGAGG -3'
Sequencing Primer
(F):5'- TGAGCAGCTGTTCCTGGAGC -3'
(R):5'- CCAGAGGGAAAAGGGACATC -3'
|
| Posted On |
2017-12-04 |
Incidental Mutation