Incidental Mutation 'R8303:Smpd4'
ID |
639351 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Smpd4
|
Ensembl Gene |
ENSMUSG00000005899 |
Gene Name |
sphingomyelin phosphodiesterase 4 |
Synonyms |
4122402O22Rik, neutral membrane (neutral sphingomyelinase-3) |
MMRRC Submission |
067715-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.098)
|
Stock # |
R8303 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
16 |
Chromosomal Location |
17437218-17462692 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 17457195 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Phenylalanine to Leucine
at position 384
(F384L)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000006053
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006053]
[ENSMUST00000090159]
[ENSMUST00000163476]
[ENSMUST00000163997]
[ENSMUST00000165363]
[ENSMUST00000167217]
[ENSMUST00000170117]
[ENSMUST00000170273]
[ENSMUST00000170366]
[ENSMUST00000170996]
|
AlphaFold |
Q6ZPR5 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000006053
AA Change: F384L
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000006053 Gene: ENSMUSG00000005899 AA Change: F384L
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 damaging
Transcript: ENSMUST00000090159
AA Change: F355L
PolyPhen 2
Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000087620 Gene: ENSMUSG00000005899 AA Change: F355L
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 |
possibly damaging
Transcript: ENSMUST00000163476
AA Change: F355L
PolyPhen 2
Score 0.816 (Sensitivity: 0.84; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000131867 Gene: ENSMUSG00000005899 AA Change: F355L
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 |
noncoding transcript
Transcript: ENSMUST00000163997
AA Change: F134L
|
SMART Domains |
Protein: ENSMUSP00000128595 Gene: ENSMUSG00000005899 AA Change: F134L
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 damaging
Transcript: ENSMUST00000165363
AA Change: F355L
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000130720 Gene: ENSMUSG00000005899 AA Change: F355L
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: ENSMUST00000167217
|
SMART Domains |
Protein: ENSMUSP00000130570 Gene: ENSMUSG00000005899
Domain | Start | End | E-Value | Type |
Pfam:mit_SMPDase
|
8 |
92 |
3.4e-51 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170117
|
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: ENSMUST00000170273
AA Change: F282L
|
SMART Domains |
Protein: ENSMUSP00000129957 Gene: ENSMUSG00000005899 AA Change: F282L
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: ENSMUST00000170366
AA Change: F355L
|
SMART Domains |
Protein: ENSMUSP00000130990 Gene: ENSMUSG00000005899 AA Change: F355L
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: ENSMUST00000170996
AA Change: F60L
|
SMART Domains |
Protein: ENSMUSP00000129074 Gene: ENSMUSG00000005899 AA Change: F60L
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 |
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.7%
|
Validation Efficiency |
100% (65/65) |
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: 65 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
2810021J22Rik |
T |
A |
11: 58,770,966 (GRCm39) |
D149E |
probably benign |
Het |
Aars2 |
T |
C |
17: 45,818,523 (GRCm39) |
C103R |
probably damaging |
Het |
Aass |
T |
C |
6: 23,092,367 (GRCm39) |
D591G |
probably benign |
Het |
Arhgap32 |
A |
G |
9: 32,172,205 (GRCm39) |
T1662A |
probably benign |
Het |
Arhgap42 |
A |
T |
9: 9,009,327 (GRCm39) |
I520N |
probably damaging |
Het |
Arhgef3 |
T |
C |
14: 27,116,095 (GRCm39) |
I279T |
probably damaging |
Het |
Arid4b |
A |
G |
13: 14,294,808 (GRCm39) |
K30R |
probably damaging |
Het |
Asxl3 |
C |
T |
18: 22,657,473 (GRCm39) |
R1828W |
probably benign |
Het |
Bid |
T |
C |
6: 120,877,200 (GRCm39) |
Y47C |
probably benign |
Het |
Card6 |
T |
C |
15: 5,134,847 (GRCm39) |
T119A |
probably benign |
Het |
Cbr1 |
T |
C |
16: 93,406,905 (GRCm39) |
I207T |
probably damaging |
Het |
Cep135 |
T |
C |
5: 76,759,575 (GRCm39) |
L443P |
probably damaging |
Het |
Cfap251 |
T |
A |
5: 123,460,650 (GRCm39) |
V1204E |
probably damaging |
Het |
Cfap43 |
T |
A |
19: 47,754,274 (GRCm39) |
R1017* |
probably null |
Het |
Cfap52 |
T |
A |
11: 67,830,621 (GRCm39) |
S280C |
probably benign |
Het |
Cntnap5b |
T |
C |
1: 100,069,022 (GRCm39) |
F81L |
probably damaging |
Het |
Cyp4a12a |
A |
G |
4: 115,186,130 (GRCm39) |
D430G |
probably damaging |
Het |
Cyp4f37 |
G |
A |
17: 32,853,152 (GRCm39) |
|
probably null |
Het |
Dclre1a |
A |
G |
19: 56,531,121 (GRCm39) |
S742P |
probably damaging |
Het |
Ddx54 |
T |
C |
5: 120,759,855 (GRCm39) |
F414S |
probably damaging |
Het |
Dsp |
A |
G |
13: 38,381,319 (GRCm39) |
N2688S |
probably benign |
Het |
Elovl4 |
A |
T |
9: 83,670,320 (GRCm39) |
|
probably null |
Het |
Erbin |
A |
C |
13: 103,966,694 (GRCm39) |
|
probably null |
Het |
Fsip2 |
A |
G |
2: 82,818,724 (GRCm39) |
D4819G |
probably benign |
Het |
Gapvd1 |
G |
A |
2: 34,602,212 (GRCm39) |
P645L |
probably damaging |
Het |
Gbp9 |
T |
C |
5: 105,229,171 (GRCm39) |
E492G |
possibly damaging |
Het |
Gpc5 |
T |
A |
14: 115,665,667 (GRCm39) |
I497K |
probably benign |
Het |
Hlx |
A |
G |
1: 184,459,905 (GRCm39) |
L411P |
probably damaging |
Het |
Hmmr |
G |
A |
11: 40,612,499 (GRCm39) |
S206F |
probably damaging |
Het |
Ice1 |
A |
T |
13: 70,754,526 (GRCm39) |
I520N |
probably benign |
Het |
Ist1 |
T |
C |
8: 110,410,412 (GRCm39) |
|
probably null |
Het |
Itga3 |
T |
C |
11: 94,953,466 (GRCm39) |
D292G |
probably benign |
Het |
Kif21a |
T |
C |
15: 90,855,399 (GRCm39) |
N655S |
probably damaging |
Het |
Lrrtm1 |
A |
G |
6: 77,221,662 (GRCm39) |
H373R |
probably benign |
Het |
Ngdn |
A |
T |
14: 55,260,602 (GRCm39) |
H270L |
probably benign |
Het |
Nol4 |
G |
A |
18: 23,173,231 (GRCm39) |
|
probably benign |
Het |
Nup50l |
T |
C |
6: 96,142,702 (GRCm39) |
E114G |
probably benign |
Het |
Nxpe5 |
G |
A |
5: 138,239,264 (GRCm39) |
|
probably benign |
Het |
Or1j18 |
A |
G |
2: 36,624,467 (GRCm39) |
I45V |
probably damaging |
Het |
Or4c11c |
G |
A |
2: 88,661,633 (GRCm39) |
M57I |
possibly damaging |
Het |
Or8d1 |
A |
C |
9: 38,766,837 (GRCm39) |
T160P |
probably damaging |
Het |
Or8g30 |
A |
C |
9: 39,230,689 (GRCm39) |
S74A |
probably damaging |
Het |
Pask |
C |
A |
1: 93,248,286 (GRCm39) |
R1005L |
probably benign |
Het |
Pcm1 |
A |
G |
8: 41,736,758 (GRCm39) |
T875A |
probably damaging |
Het |
Pdrg1 |
A |
T |
2: 152,851,587 (GRCm39) |
I130N |
probably damaging |
Het |
Plec |
A |
T |
15: 76,073,466 (GRCm39) |
M448K |
unknown |
Het |
R3hdml |
T |
G |
2: 163,341,832 (GRCm39) |
V204G |
probably damaging |
Het |
Rasa4 |
G |
A |
5: 136,118,235 (GRCm39) |
V32M |
possibly damaging |
Het |
Scaf8 |
T |
C |
17: 3,198,827 (GRCm39) |
V44A |
unknown |
Het |
Smad3 |
G |
T |
9: 63,574,760 (GRCm39) |
P177T |
probably benign |
Het |
Sycp2l |
G |
C |
13: 41,283,275 (GRCm39) |
L170F |
probably damaging |
Het |
Tas2r107 |
T |
C |
6: 131,636,585 (GRCm39) |
S155G |
probably benign |
Het |
Tmem143 |
T |
A |
7: 45,565,994 (GRCm39) |
M439K |
probably benign |
Het |
Ttc41 |
A |
T |
10: 86,555,494 (GRCm39) |
T317S |
probably benign |
Het |
Umps |
A |
G |
16: 33,784,240 (GRCm39) |
V71A |
possibly damaging |
Het |
Usp17lc |
G |
A |
7: 103,067,389 (GRCm39) |
G228D |
possibly damaging |
Het |
Usp17ld |
C |
T |
7: 102,900,023 (GRCm39) |
C303Y |
probably damaging |
Het |
Vmn2r65 |
C |
A |
7: 84,589,391 (GRCm39) |
E842* |
probably null |
Het |
Vmn2r94 |
A |
G |
17: 18,464,433 (GRCm39) |
F619S |
probably damaging |
Het |
Vps13a |
T |
C |
19: 16,594,270 (GRCm39) |
T3154A |
probably benign |
Het |
Vps13b |
C |
T |
15: 35,640,063 (GRCm39) |
T1311I |
probably damaging |
Het |
Xpot |
A |
T |
10: 121,447,405 (GRCm39) |
Y353* |
probably null |
Het |
Zfp319 |
A |
T |
8: 96,055,765 (GRCm39) |
L146Q |
probably damaging |
Het |
Zfp422 |
T |
A |
6: 116,603,612 (GRCm39) |
H129L |
probably damaging |
Het |
Zzef1 |
T |
C |
11: 72,808,015 (GRCm39) |
F2709L |
probably 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 |
|
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 |
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'- GGTTTCTTCTGGAGAATCAGGC -3'
(R):5'- GCTGAGTATGGCCAACAGAAC -3'
Sequencing Primer
(F):5'- CAAATCTTACCTCAGGGAGTGTG -3'
(R):5'- TATGGCCAACAGAACGACAAG -3'
|
Posted On |
2020-07-28 |