Incidental Mutation 'R5046:Scp2'
| ID |
394362 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Scp2
|
| Ensembl Gene |
ENSMUSG00000028603 |
| Gene Name |
sterol carrier protein 2, liver |
| Synonyms |
ns-LTP, SCPx, nonspecific lipid transfer protein, NSL-TP, SCP-2 |
| MMRRC Submission |
042636-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.246)
|
| Stock # |
R5046 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
107901027-108002168 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 107928488 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 401
(T401A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000030340
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030340]
[ENSMUST00000044248]
[ENSMUST00000106701]
|
| AlphaFold |
P32020 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030340
AA Change: T401A
PolyPhen 2
Score 0.068 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000030340
Gene: ENSMUSG00000028603
AA Change: T401A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Thiolase_N
|
14 |
240 |
9.6e-25 |
PFAM |
|
Pfam:Thiolase_C
|
277 |
402 |
2.9e-15 |
PFAM |
|
Pfam:SCP2
|
437 |
539 |
1.5e-32 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000044248
|
| SMART Domains |
Protein: ENSMUSP00000048962
Gene: ENSMUSG00000028600
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
low complexity region
|
40 |
49 |
N/A |
INTRINSIC |
|
LRRNT
|
68 |
101 |
4.34e-5 |
SMART |
|
LRR_TYP
|
120 |
145 |
2.05e-2 |
SMART |
|
LRR
|
146 |
169 |
1.19e1 |
SMART |
|
LRR
|
192 |
216 |
2.84e1 |
SMART |
|
LRR
|
239 |
261 |
6.22e0 |
SMART |
|
LRR
|
262 |
287 |
3.47e0 |
SMART |
|
LRR_TYP
|
288 |
311 |
7.9e-4 |
SMART |
|
LRR
|
333 |
358 |
1.26e1 |
SMART |
|
LRR
|
359 |
382 |
2.82e0 |
SMART |
|
LRR
|
407 |
429 |
1.53e2 |
SMART |
|
LRR_TYP
|
430 |
453 |
7.37e-4 |
SMART |
|
LRR
|
475 |
500 |
1.66e1 |
SMART |
|
LRR
|
501 |
522 |
1.29e1 |
SMART |
|
LRR_TYP
|
523 |
545 |
7.67e-2 |
SMART |
|
low complexity region
|
594 |
609 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000106701
|
| SMART Domains |
Protein: ENSMUSP00000102312
Gene: ENSMUSG00000028603
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Alkyl_sulf_C
|
18 |
140 |
5e-11 |
PFAM |
|
Pfam:SCP2
|
33 |
135 |
4.4e-33 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000122878
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000135379
|
| Meta Mutation Damage Score |
0.3318 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.1%
|
| Validation Efficiency |
100% (52/52) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes two proteins: sterol carrier protein X (SCPx) and sterol carrier protein 2 (SCP2), as a result of transcription initiation from 2 independently regulated promoters. The transcript initiated from the proximal promoter encodes the longer SCPx protein, and the transcript initiated from the distal promoter encodes the shorter SCP2 protein, with the 2 proteins sharing a common C-terminus. Evidence suggests that the SCPx protein is a peroxisome-associated thiolase that is involved in the oxidation of branched chain fatty acids, while the SCP2 protein is thought to be an intracellular lipid transfer protein. This gene is highly expressed in organs involved in lipid metabolism, and may play a role in Zellweger syndrome, in which cells are deficient in peroxisomes and have impaired bile acid synthesis. Alternative splicing of this gene produces multiple transcript variants, some encoding different isoforms.[provided by RefSeq, Aug 2010]
PHENOTYPE: Mice homozygous for disruptions of this gene exhibit altered lipid levels and both males and females are sensitive to phytol-rich diets. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acsm4 |
C |
A |
7: 119,302,597 (GRCm39) |
H241N |
probably damaging |
Het |
| Arhgap32 |
G |
A |
9: 32,168,095 (GRCm39) |
A693T |
probably damaging |
Het |
| B4galnt3 |
G |
T |
6: 120,191,759 (GRCm39) |
A658D |
probably damaging |
Het |
| Car12 |
G |
A |
9: 66,653,895 (GRCm39) |
E84K |
probably benign |
Het |
| Crocc2 |
T |
A |
1: 93,133,624 (GRCm39) |
S969T |
probably damaging |
Het |
| Crym |
A |
G |
7: 119,794,667 (GRCm39) |
V184A |
possibly damaging |
Het |
| Cryzl2 |
T |
C |
1: 157,292,583 (GRCm39) |
C122R |
probably damaging |
Het |
| Defb30 |
T |
C |
14: 63,273,463 (GRCm39) |
E49G |
probably benign |
Het |
| Dnah3 |
A |
G |
7: 119,550,803 (GRCm39) |
L3161P |
probably damaging |
Het |
| Dnajc5g |
A |
G |
5: 31,267,036 (GRCm39) |
N104S |
probably benign |
Het |
| Fcgr1 |
T |
G |
3: 96,194,302 (GRCm39) |
K195T |
probably damaging |
Het |
| Gal |
C |
T |
19: 3,461,167 (GRCm39) |
R89H |
probably damaging |
Het |
| Gcfc2 |
C |
T |
6: 81,925,316 (GRCm39) |
A577V |
probably benign |
Het |
| Gm5116 |
A |
C |
7: 32,195,379 (GRCm39) |
|
noncoding transcript |
Het |
| Golga3 |
A |
T |
5: 110,340,806 (GRCm39) |
Q540L |
probably damaging |
Het |
| Hectd1 |
T |
C |
12: 51,797,171 (GRCm39) |
E2184G |
probably damaging |
Het |
| Hspa12a |
T |
C |
19: 58,787,977 (GRCm39) |
D615G |
probably damaging |
Het |
| Igkv14-130 |
A |
T |
6: 67,768,465 (GRCm39) |
Y107F |
probably damaging |
Het |
| Ldlr |
T |
A |
9: 21,657,203 (GRCm39) |
|
probably null |
Het |
| Lin9 |
T |
A |
1: 180,496,763 (GRCm39) |
L351I |
probably benign |
Het |
| Lrrc37a |
A |
T |
11: 103,389,066 (GRCm39) |
S2120T |
unknown |
Het |
| Mtfmt |
G |
T |
9: 65,346,897 (GRCm39) |
V164F |
probably damaging |
Het |
| Nampt |
T |
C |
12: 32,883,037 (GRCm39) |
V74A |
probably damaging |
Het |
| Ndufc2 |
G |
T |
7: 97,056,871 (GRCm39) |
R120L |
probably damaging |
Het |
| Neo1 |
A |
T |
9: 58,801,194 (GRCm39) |
V1156D |
possibly damaging |
Het |
| Nlrp1b |
G |
A |
11: 71,050,898 (GRCm39) |
P1065S |
possibly damaging |
Het |
| Nop9 |
A |
G |
14: 55,983,397 (GRCm39) |
H56R |
possibly damaging |
Het |
| Or4k41 |
A |
T |
2: 111,279,934 (GRCm39) |
T150S |
probably benign |
Het |
| Or6c75 |
A |
T |
10: 129,337,178 (GRCm39) |
M142L |
possibly damaging |
Het |
| Pign |
A |
T |
1: 105,449,798 (GRCm39) |
N909K |
possibly damaging |
Het |
| Prex1 |
A |
G |
2: 166,414,883 (GRCm39) |
V304A |
probably benign |
Het |
| Racgap1 |
G |
A |
15: 99,526,643 (GRCm39) |
R307W |
probably damaging |
Het |
| Rap1gds1 |
C |
A |
3: 138,661,181 (GRCm39) |
E399* |
probably null |
Het |
| Rwdd4a |
G |
A |
8: 47,995,837 (GRCm39) |
|
probably null |
Het |
| Sanbr |
A |
C |
11: 23,570,354 (GRCm39) |
M182R |
probably benign |
Het |
| Sdha |
A |
G |
13: 74,475,452 (GRCm39) |
F526S |
probably damaging |
Het |
| Shroom1 |
T |
A |
11: 53,354,872 (GRCm39) |
L264Q |
probably benign |
Het |
| Sorl1 |
T |
C |
9: 41,907,590 (GRCm39) |
T1466A |
probably benign |
Het |
| Trpm2 |
C |
T |
10: 77,801,852 (GRCm39) |
C71Y |
probably damaging |
Het |
| Ugt2b34 |
G |
A |
5: 87,052,246 (GRCm39) |
S250L |
probably benign |
Het |
| Vmn2r88 |
A |
G |
14: 51,650,638 (GRCm39) |
D117G |
probably benign |
Het |
| Wdr73 |
A |
T |
7: 80,542,173 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Scp2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01481:Scp2
|
APN |
4 |
107,931,639 (GRCm39) |
splice site |
probably null |
|
|
IGL02190:Scp2
|
APN |
4 |
107,944,325 (GRCm39) |
missense |
probably benign |
0.22 |
|
IGL02615:Scp2
|
APN |
4 |
107,964,828 (GRCm39) |
missense |
probably benign |
0.40 |
|
IGL03006:Scp2
|
APN |
4 |
107,948,477 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL03107:Scp2
|
APN |
4 |
107,955,312 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL03124:Scp2
|
APN |
4 |
107,921,103 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0030:Scp2
|
UTSW |
4 |
107,964,887 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R0030:Scp2
|
UTSW |
4 |
107,964,887 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R0240:Scp2
|
UTSW |
4 |
107,955,275 (GRCm39) |
missense |
probably benign |
0.01 |
|
R0240:Scp2
|
UTSW |
4 |
107,955,275 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1507:Scp2
|
UTSW |
4 |
107,944,209 (GRCm39) |
frame shift |
probably null |
|
|
R1861:Scp2
|
UTSW |
4 |
107,948,518 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2151:Scp2
|
UTSW |
4 |
107,921,141 (GRCm39) |
missense |
probably benign |
|
|
R3013:Scp2
|
UTSW |
4 |
107,928,554 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4127:Scp2
|
UTSW |
4 |
107,921,181 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4271:Scp2
|
UTSW |
4 |
107,942,408 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4385:Scp2
|
UTSW |
4 |
107,928,547 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5345:Scp2
|
UTSW |
4 |
107,912,776 (GRCm39) |
splice site |
probably null |
|
|
R5401:Scp2
|
UTSW |
4 |
108,001,976 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6367:Scp2
|
UTSW |
4 |
107,969,447 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6415:Scp2
|
UTSW |
4 |
107,962,337 (GRCm39) |
missense |
probably benign |
0.22 |
|
R6681:Scp2
|
UTSW |
4 |
107,948,513 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6910:Scp2
|
UTSW |
4 |
107,962,283 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6974:Scp2
|
UTSW |
4 |
107,928,475 (GRCm39) |
start codon destroyed |
probably null |
0.01 |
|
R7206:Scp2
|
UTSW |
4 |
107,931,638 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7342:Scp2
|
UTSW |
4 |
107,948,518 (GRCm39) |
missense |
probably benign |
0.02 |
|
R8935:Scp2
|
UTSW |
4 |
107,950,072 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R9035:Scp2
|
UTSW |
4 |
107,912,717 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9151:Scp2
|
UTSW |
4 |
107,931,603 (GRCm39) |
missense |
possibly damaging |
0.58 |
|
R9536:Scp2
|
UTSW |
4 |
107,928,532 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R9645:Scp2
|
UTSW |
4 |
107,948,519 (GRCm39) |
missense |
probably benign |
0.01 |
|
| Predicted Primers |
PCR Primer
(F):5'- ATTTTCCTAAGGTTGTCTCGGC -3'
(R):5'- CTGTGAATCTTGGGCTTTAAGC -3'
Sequencing Primer
(F):5'- CCTAAGGTTGTCTCGGCTTAAAAAC -3'
(R):5'- GCTTTAAGCTCTGCAGGCG -3'
|
| Posted On |
2016-06-15 |
Incidental Mutation