Incidental Mutation 'R6822:Smpd4'
| ID |
537692 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smpd4
|
| Ensembl Gene |
ENSMUSG00000005899 |
| Gene Name |
sphingomyelin phosphodiesterase 4 |
| Synonyms |
4122402O22Rik, neutral membrane (neutral sphingomyelinase-3) |
| MMRRC Submission |
044934-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.098)
|
| Stock # |
R6822 (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 C
at 17458097 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 465
(V465A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000006053
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006053]
[ENSMUST00000090159]
[ENSMUST00000163476]
[ENSMUST00000165363]
[ENSMUST00000231436]
[ENSMUST00000231627]
[ENSMUST00000231722]
[ENSMUST00000231792]
[ENSMUST00000232021]
[ENSMUST00000232116]
[ENSMUST00000232271]
|
| AlphaFold |
Q6ZPR5 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000006053
AA Change: V465A
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899
AA Change: V465A
| 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 |
possibly damaging
Transcript: ENSMUST00000090159
AA Change: V449A
PolyPhen 2
Score 0.915 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000087620
Gene: ENSMUSG00000005899
AA Change: V449A
| 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 damaging
Transcript: ENSMUST00000163476
AA Change: V436A
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000131867
Gene: ENSMUSG00000005899
AA Change: V436A
| 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 damaging
Transcript: ENSMUST00000165363
AA Change: V435A
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000130720
Gene: ENSMUSG00000005899
AA Change: V435A
| 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 |
probably damaging
Transcript: ENSMUST00000231436
AA Change: V436A
PolyPhen 2
Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231627
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231722
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000231792
AA Change: V215A
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000232021
AA Change: V363A
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000232116
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000232271
AA Change: V141A
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.7%
|
| Validation Efficiency |
94% (46/49) |
| 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 |
|---|
| Adam11 |
G |
A |
11: 102,667,501 (GRCm39) |
R687Q |
possibly damaging |
Het |
| AI987944 |
A |
G |
7: 41,024,232 (GRCm39) |
L249P |
probably damaging |
Het |
| Ankrd28 |
T |
A |
14: 31,458,797 (GRCm39) |
|
probably null |
Het |
| Bahcc1 |
T |
C |
11: 120,178,547 (GRCm39) |
S2369P |
probably damaging |
Het |
| Birc6 |
T |
C |
17: 74,887,377 (GRCm39) |
S902P |
possibly damaging |
Het |
| Birc6 |
A |
T |
17: 74,905,039 (GRCm39) |
K1277N |
probably damaging |
Het |
| Brwd1 |
T |
C |
16: 95,842,474 (GRCm39) |
E821G |
probably benign |
Het |
| Cct8l1 |
T |
C |
5: 25,722,937 (GRCm39) |
S551P |
possibly damaging |
Het |
| Cmtm1 |
TCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGG |
TCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGG |
8: 105,036,334 (GRCm39) |
|
probably null |
Het |
| Cyp2c39 |
A |
T |
19: 39,525,261 (GRCm39) |
D188V |
probably damaging |
Het |
| Dclk3 |
G |
T |
9: 111,268,405 (GRCm39) |
A25S |
probably benign |
Het |
| Dpep2 |
A |
T |
8: 106,711,873 (GRCm39) |
M518K |
probably benign |
Het |
| Dst |
T |
C |
1: 34,314,755 (GRCm39) |
V6462A |
probably damaging |
Het |
| Entpd3 |
T |
C |
9: 120,391,104 (GRCm39) |
|
probably null |
Het |
| Epm2aip1 |
T |
C |
9: 111,101,624 (GRCm39) |
V199A |
probably damaging |
Het |
| Fam193b |
A |
G |
13: 55,689,504 (GRCm39) |
|
probably benign |
Het |
| Fam50b |
G |
A |
13: 34,931,084 (GRCm39) |
E187K |
possibly damaging |
Het |
| Fat1 |
A |
G |
8: 45,479,441 (GRCm39) |
D2829G |
probably damaging |
Het |
| Fcgbp |
T |
A |
7: 27,806,781 (GRCm39) |
Y2250N |
probably damaging |
Het |
| Gm40460 |
ACCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG |
ACCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG |
7: 141,794,450 (GRCm39) |
|
probably benign |
Het |
| Grik5 |
C |
T |
7: 24,745,780 (GRCm39) |
R431Q |
possibly damaging |
Het |
| H2-Aa |
C |
T |
17: 34,506,651 (GRCm39) |
|
probably null |
Het |
| Igsf9 |
T |
A |
1: 172,324,730 (GRCm39) |
S883T |
possibly damaging |
Het |
| Kcnh7 |
T |
G |
2: 62,618,248 (GRCm39) |
I414L |
probably damaging |
Het |
| Kcnma1 |
T |
C |
14: 24,053,812 (GRCm39) |
|
probably null |
Het |
| Kcnmb1 |
T |
C |
11: 33,914,686 (GRCm39) |
|
probably benign |
Het |
| Kmt2d |
A |
G |
15: 98,747,340 (GRCm39) |
|
probably benign |
Het |
| Krt9 |
TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC |
TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC |
11: 100,079,903 (GRCm39) |
|
probably benign |
Het |
| Map3k13 |
G |
A |
16: 21,741,013 (GRCm39) |
S780N |
probably benign |
Het |
| Nlgn1 |
T |
C |
3: 26,187,796 (GRCm39) |
T30A |
probably benign |
Het |
| Nucb1 |
A |
G |
7: 45,148,289 (GRCm39) |
F175L |
probably damaging |
Het |
| Pax6 |
T |
A |
2: 105,516,268 (GRCm39) |
V182E |
probably benign |
Het |
| Ptger1 |
A |
G |
8: 84,395,279 (GRCm39) |
D252G |
probably benign |
Het |
| Rexo4 |
T |
C |
2: 26,850,283 (GRCm39) |
D275G |
probably damaging |
Het |
| Ripk4 |
T |
C |
16: 97,547,236 (GRCm39) |
D342G |
probably damaging |
Het |
| Rpl10l |
A |
T |
12: 66,330,987 (GRCm39) |
C49S |
possibly damaging |
Het |
| Sema7a |
T |
C |
9: 57,867,619 (GRCm39) |
F457S |
probably damaging |
Het |
| Shank3 |
G |
A |
15: 89,415,830 (GRCm39) |
D155N |
probably damaging |
Het |
| Smpd3 |
G |
A |
8: 106,992,596 (GRCm39) |
|
probably benign |
Het |
| Sohlh2 |
T |
C |
3: 55,115,107 (GRCm39) |
V364A |
probably damaging |
Het |
| Sos2 |
C |
T |
12: 69,697,423 (GRCm39) |
R99Q |
probably damaging |
Het |
| Spry2 |
G |
A |
14: 106,130,791 (GRCm39) |
Q132* |
probably null |
Het |
| Tbx19 |
G |
T |
1: 164,967,709 (GRCm39) |
P346Q |
probably damaging |
Het |
| Tdrd6 |
A |
G |
17: 43,938,106 (GRCm39) |
Y981H |
probably damaging |
Het |
| Tinag |
T |
C |
9: 76,938,984 (GRCm39) |
K165E |
probably benign |
Het |
| Tubb4a |
A |
T |
17: 57,387,904 (GRCm39) |
I374N |
probably damaging |
Het |
| Umodl1 |
C |
T |
17: 31,205,528 (GRCm39) |
Q708* |
probably null |
Het |
| Vmn2r3 |
A |
T |
3: 64,194,876 (GRCm39) |
V14E |
probably benign |
Het |
| Zfp82 |
G |
A |
7: 29,755,712 (GRCm39) |
L457F |
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 |
|
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'- TGCCTCCTATAAGGGGTCTACAC -3'
(R):5'- CACTAGGAAGGGGACATTAGCC -3'
Sequencing Primer
(F):5'- CCTATAAGGGGTCTACACGGTGG -3'
(R):5'- GGGGACATTAGCCAAACTTTTAC -3'
|
| Posted On |
2018-10-18 |
Incidental Mutation