Incidental Mutation 'R9600:Pmpca'
| ID |
723645 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pmpca
|
| Ensembl Gene |
ENSMUSG00000026926 |
| Gene Name |
peptidase (mitochondrial processing) alpha |
| Synonyms |
4933435E07Rik, INPP5E, Alpha-MPP |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.956)
|
| Stock # |
R9600 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
2 |
| Chromosomal Location |
26279351-26287134 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 26282598 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 269
(Y269H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000075762
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028293]
[ENSMUST00000076431]
[ENSMUST00000077983]
[ENSMUST00000114090]
[ENSMUST00000114093]
[ENSMUST00000114100]
[ENSMUST00000114102]
[ENSMUST00000139738]
[ENSMUST00000145701]
|
| AlphaFold |
Q9DC61 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000028293
|
| SMART Domains |
Protein: ENSMUSP00000028293
Gene: ENSMUSG00000026927
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
209 |
321 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000076431
AA Change: Y269H
PolyPhen 2
Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000075762
Gene: ENSMUSG00000026926
AA Change: Y269H
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Peptidase_M16
|
76 |
226 |
4.5e-47 |
PFAM |
|
Pfam:Peptidase_M16_C
|
231 |
430 |
4.1e-43 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000077983
|
| SMART Domains |
Protein: ENSMUSP00000077133
Gene: ENSMUSG00000026927
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
186 |
298 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000114090
|
| SMART Domains |
Protein: ENSMUSP00000109724
Gene: ENSMUSG00000026925
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
277 |
294 |
N/A |
INTRINSIC |
|
IPPc
|
300 |
602 |
1.27e-62 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000114093
AA Change: Y269H
PolyPhen 2
Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
|
| SMART Domains |
Protein: ENSMUSP00000109727
Gene: ENSMUSG00000026926
AA Change: Y269H
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Peptidase_M16
|
76 |
226 |
1.6e-47 |
PFAM |
|
Pfam:Peptidase_M16_C
|
231 |
420 |
9.6e-39 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000114100
|
| SMART Domains |
Protein: ENSMUSP00000109735
Gene: ENSMUSG00000026927
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
236 |
348 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000114102
|
| SMART Domains |
Protein: ENSMUSP00000109737
Gene: ENSMUSG00000026927
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
259 |
371 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000131109
|
| SMART Domains |
Protein: ENSMUSP00000118739
Gene: ENSMUSG00000026925
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Exo_endo_phos
|
4 |
88 |
6.4e-9 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000139738
|
| SMART Domains |
Protein: ENSMUSP00000121256
Gene: ENSMUSG00000026927
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
1 |
15 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000145701
|
| SMART Domains |
Protein: ENSMUSP00000119485
Gene: ENSMUSG00000026925
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
277 |
294 |
N/A |
INTRINSIC |
|
IPPc
|
300 |
602 |
1.27e-62 |
SMART |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is found in the mitochondrion, where it represents the alpha subunit of a proteolytic heterodimer. This heterodimer is responsible for cleaving the transit peptide from nuclear-encoded mitochondrial proteins. Defects in this gene are a cause of spinocerebellar ataxia, autosomal recessive 2. [provided by RefSeq, Mar 2016]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 64 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5730455P16Rik |
A |
G |
11: 80,261,197 (GRCm39) |
V210A |
probably damaging |
Het |
| Abcc9 |
G |
A |
6: 142,536,102 (GRCm39) |
A1544V |
possibly damaging |
Het |
| Akap6 |
A |
G |
12: 52,933,341 (GRCm39) |
T278A |
probably benign |
Het |
| Arfgef1 |
T |
A |
1: 10,233,977 (GRCm39) |
I1106F |
probably benign |
Het |
| Armc7 |
T |
C |
11: 115,367,038 (GRCm39) |
L61S |
probably damaging |
Het |
| Atp1a3 |
G |
A |
7: 24,700,027 (GRCm39) |
T111M |
probably benign |
Het |
| Bltp1 |
A |
T |
3: 37,095,565 (GRCm39) |
K1103* |
probably null |
Het |
| Cacna2d4 |
T |
A |
6: 119,322,023 (GRCm39) |
S962R |
probably benign |
Het |
| Camsap2 |
T |
C |
1: 136,204,936 (GRCm39) |
T526A |
|
Het |
| Casq2 |
A |
T |
3: 102,052,622 (GRCm39) |
D378V |
unknown |
Het |
| Chst8 |
C |
T |
7: 34,374,646 (GRCm39) |
D398N |
possibly damaging |
Het |
| Cmya5 |
C |
T |
13: 93,226,604 (GRCm39) |
G2828D |
probably damaging |
Het |
| Cntnap2 |
T |
A |
6: 45,969,009 (GRCm39) |
N250K |
probably damaging |
Het |
| Cpne5 |
T |
C |
17: 29,380,520 (GRCm39) |
N401D |
probably damaging |
Het |
| Cse1l |
A |
G |
2: 166,757,119 (GRCm39) |
N7S |
probably damaging |
Het |
| Cyp4f39 |
G |
A |
17: 32,705,920 (GRCm39) |
G337D |
probably damaging |
Het |
| Dera |
C |
T |
6: 137,814,135 (GRCm39) |
R308C |
probably benign |
Het |
| Drd5 |
T |
A |
5: 38,478,174 (GRCm39) |
I389N |
possibly damaging |
Het |
| F830016B08Rik |
A |
G |
18: 60,433,237 (GRCm39) |
T107A |
probably damaging |
Het |
| Fbxw22 |
C |
A |
9: 109,212,986 (GRCm39) |
L320F |
probably damaging |
Het |
| Fndc3b |
G |
T |
3: 27,552,941 (GRCm39) |
T352K |
probably damaging |
Het |
| Gm36864 |
T |
A |
7: 43,886,275 (GRCm39) |
I169K |
unknown |
Het |
| Hdac4 |
A |
T |
1: 91,889,277 (GRCm39) |
D749E |
probably damaging |
Het |
| Herc1 |
C |
T |
9: 66,304,594 (GRCm39) |
A805V |
possibly damaging |
Het |
| Hrh1 |
A |
G |
6: 114,457,453 (GRCm39) |
K245E |
probably benign |
Het |
| Khdc1a |
A |
G |
1: 21,421,204 (GRCm39) |
T130A |
probably benign |
Het |
| Lrp5 |
C |
G |
19: 3,641,712 (GRCm39) |
A1417P |
probably benign |
Het |
| Macf1 |
T |
C |
4: 123,365,002 (GRCm39) |
Q3253R |
possibly damaging |
Het |
| Mdn1 |
T |
A |
4: 32,684,723 (GRCm39) |
L811* |
probably null |
Het |
| Mettl8 |
T |
C |
2: 70,812,383 (GRCm39) |
D84G |
possibly damaging |
Het |
| Miga1 |
T |
G |
3: 151,993,186 (GRCm39) |
T412P |
probably benign |
Het |
| Mtor |
G |
T |
4: 148,632,092 (GRCm39) |
R2322L |
possibly damaging |
Het |
| Muc16 |
T |
C |
9: 18,567,147 (GRCm39) |
N1791D |
unknown |
Het |
| Myo9b |
C |
G |
8: 71,743,075 (GRCm39) |
S45R |
possibly damaging |
Het |
| Nup50l |
A |
T |
6: 96,142,156 (GRCm39) |
L296Q |
possibly damaging |
Het |
| Olfm4 |
T |
C |
14: 80,243,747 (GRCm39) |
F105S |
probably damaging |
Het |
| Or5af2 |
A |
T |
11: 58,708,370 (GRCm39) |
I179F |
possibly damaging |
Het |
| Osbpl1a |
T |
C |
18: 13,015,277 (GRCm39) |
I384V |
probably benign |
Het |
| Pcnx1 |
T |
C |
12: 82,030,435 (GRCm39) |
L1131P |
|
Het |
| Pex6 |
T |
A |
17: 47,035,322 (GRCm39) |
V827E |
probably damaging |
Het |
| Plek |
A |
C |
11: 16,940,119 (GRCm39) |
S197A |
probably benign |
Het |
| Pop1 |
T |
C |
15: 34,512,881 (GRCm39) |
I493T |
probably benign |
Het |
| Rap1gap2 |
T |
C |
11: 74,283,954 (GRCm39) |
N615D |
probably benign |
Het |
| Rtp3 |
T |
C |
9: 110,815,198 (GRCm39) |
Y389C |
unknown |
Het |
| Rusf1 |
T |
A |
7: 127,875,676 (GRCm39) |
D253V |
possibly damaging |
Het |
| Sardh |
T |
C |
2: 27,120,513 (GRCm39) |
Q423R |
probably benign |
Het |
| Slc11a1 |
T |
C |
1: 74,422,688 (GRCm39) |
|
probably null |
Het |
| Slc5a4b |
T |
C |
10: 75,896,239 (GRCm39) |
D572G |
probably damaging |
Het |
| Slco1a8 |
T |
G |
6: 141,949,234 (GRCm39) |
|
probably null |
Het |
| Slfn14 |
A |
G |
11: 83,170,048 (GRCm39) |
V532A |
probably benign |
Het |
| Spmip10 |
T |
C |
18: 56,725,450 (GRCm39) |
W37R |
probably benign |
Het |
| Stxbp1 |
T |
C |
2: 32,701,120 (GRCm39) |
Y264C |
possibly damaging |
Het |
| Syce1l |
T |
C |
8: 114,381,750 (GRCm39) |
I230T |
unknown |
Het |
| Taf5l |
T |
C |
8: 124,730,173 (GRCm39) |
Y172C |
|
Het |
| Trpc4 |
A |
T |
3: 54,102,248 (GRCm39) |
K49* |
probably null |
Het |
| Ttc13 |
A |
G |
8: 125,415,284 (GRCm39) |
V285A |
probably benign |
Het |
| Ttc17 |
A |
T |
2: 94,204,890 (GRCm39) |
L344Q |
probably damaging |
Het |
| Unc79 |
A |
G |
12: 103,135,972 (GRCm39) |
H2469R |
probably benign |
Het |
| Xkr7 |
A |
G |
2: 152,896,393 (GRCm39) |
I416V |
probably benign |
Het |
| Zeb2 |
C |
A |
2: 44,987,180 (GRCm39) |
D35Y |
unknown |
Het |
| Zfp28 |
A |
G |
7: 6,397,917 (GRCm39) |
H784R |
probably benign |
Het |
| Zfp644 |
A |
C |
5: 106,783,909 (GRCm39) |
S848R |
probably benign |
Het |
| Zfp809 |
G |
A |
9: 22,150,384 (GRCm39) |
E294K |
possibly damaging |
Het |
| Zfp820 |
A |
G |
17: 22,038,861 (GRCm39) |
Y156H |
probably benign |
Het |
|
| Other mutations in Pmpca |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02164:Pmpca
|
APN |
2 |
26,285,581 (GRCm39) |
missense |
probably benign |
|
|
R0064:Pmpca
|
UTSW |
2 |
26,285,519 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0064:Pmpca
|
UTSW |
2 |
26,285,519 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0690:Pmpca
|
UTSW |
2 |
26,281,109 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0864:Pmpca
|
UTSW |
2 |
26,283,221 (GRCm39) |
splice site |
probably null |
|
|
R0893:Pmpca
|
UTSW |
2 |
26,283,230 (GRCm39) |
unclassified |
probably benign |
|
|
R1386:Pmpca
|
UTSW |
2 |
26,282,530 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4541:Pmpca
|
UTSW |
2 |
26,280,201 (GRCm39) |
unclassified |
probably benign |
|
|
R4580:Pmpca
|
UTSW |
2 |
26,283,347 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4967:Pmpca
|
UTSW |
2 |
26,280,320 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4970:Pmpca
|
UTSW |
2 |
26,285,178 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5112:Pmpca
|
UTSW |
2 |
26,285,178 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5161:Pmpca
|
UTSW |
2 |
26,285,183 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5567:Pmpca
|
UTSW |
2 |
26,280,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5570:Pmpca
|
UTSW |
2 |
26,280,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6456:Pmpca
|
UTSW |
2 |
26,285,179 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7203:Pmpca
|
UTSW |
2 |
26,285,046 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R7249:Pmpca
|
UTSW |
2 |
26,285,046 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R7251:Pmpca
|
UTSW |
2 |
26,285,046 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R7252:Pmpca
|
UTSW |
2 |
26,285,046 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R7827:Pmpca
|
UTSW |
2 |
26,280,144 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R7971:Pmpca
|
UTSW |
2 |
26,283,164 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8461:Pmpca
|
UTSW |
2 |
26,285,046 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R8558:Pmpca
|
UTSW |
2 |
26,285,046 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R8671:Pmpca
|
UTSW |
2 |
26,285,046 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R8674:Pmpca
|
UTSW |
2 |
26,285,046 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R8717:Pmpca
|
UTSW |
2 |
26,281,893 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8737:Pmpca
|
UTSW |
2 |
26,283,531 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9042:Pmpca
|
UTSW |
2 |
26,283,581 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9181:Pmpca
|
UTSW |
2 |
26,283,365 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9621:Pmpca
|
UTSW |
2 |
26,279,988 (GRCm39) |
missense |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GGCTGCTTTTAGGGAGAACAC -3'
(R):5'- CCTCTTGCTTTGAACAGGGG -3'
Sequencing Primer
(F):5'- CTTTTAGGGAGAACACAGTGGGTC -3'
(R):5'- CATAGTGCTGGATTGTACACTAAGG -3'
|
| Posted On |
2022-09-12 |
Incidental Mutation