Mutagenetix > Incidental Mutation

Incidental Mutation 'R7827:Pmpca'

602222

Institutional Source

Beutler Lab

Gene Symbol

Pmpca

Ensembl Gene

ENSMUSG00000026926

Gene Name

peptidase (mitochondrial processing) alpha

Synonyms

4933435E07Rik, INPP5E, Alpha-MPP

MMRRC Submission

045881-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.959) question?

Stock #

R7827 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

26279351-26287134 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 26280144 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 89 (V89I)

Ref Sequence

ENSEMBL: ENSMUSP00000109727 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028293] [ENSMUST00000076431] [ENSMUST00000077983] [ENSMUST00000114093] [ENSMUST00000114100] [ENSMUST00000114102] [ENSMUST00000139738]

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: V89I

PolyPhen 2 Score 0.438 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000075762
Gene: ENSMUSG00000026926
AA Change: V89I

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

possibly damaging
Transcript: ENSMUST00000114093
AA Change: V89I

PolyPhen 2 Score 0.514 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000109727
Gene: ENSMUSG00000026926
AA Change: V89I

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: ENSMUST00000139738

SMART Domains

Protein: ENSMUSP00000121256
Gene: ENSMUSG00000026927

Domain	Start	End	E-Value	Type
low complexity region	1	15	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl2fm2	A	G	3: 59,651,112 (GRCm39)	N78S	probably damaging	Het
Abca12	G	A	1: 71,453,837 (GRCm39)		probably benign	Het
Abcb1b	T	C	5: 8,887,747 (GRCm39)	S878P	probably damaging	Het
Adamts20	T	C	15: 94,223,814 (GRCm39)	R1305G	probably damaging	Het
Adcy2	A	T	13: 68,837,400 (GRCm39)	C650S	probably damaging	Het
Ahnak	A	T	19: 8,982,708 (GRCm39)	K1331*	probably null	Het
Alpk1	A	T	3: 127,473,700 (GRCm39)	S768T	probably benign	Het
Ap4b1	T	G	3: 103,722,398 (GRCm39)	L124R	probably damaging	Het
Arrdc2	A	T	8: 71,292,038 (GRCm39)	F3Y	probably damaging	Het
Atp9a	A	G	2: 168,547,114 (GRCm39)	V155A	probably benign	Het
Bptf	A	G	11: 106,938,013 (GRCm39)	S87P	probably benign	Het
Carmil1	A	T	13: 24,220,421 (GRCm39)	M697K	probably benign	Het
Ccdc42	G	A	11: 68,485,022 (GRCm39)	V32M	probably benign	Het
Cert1	A	G	13: 96,753,563 (GRCm39)	H391R	probably damaging	Het
Ces1d	A	G	8: 93,924,294 (GRCm39)		probably null	Het
Dcpp2	T	G	17: 24,119,566 (GRCm39)	Y127D	probably damaging	Het
Def8	C	A	8: 124,174,060 (GRCm39)	T7K	probably benign	Het
Dnah8	CGTGTCTTCAATATTTTGTTCCCTTTCCCGTAGGTGCCGTCCTTTGACTTTCCTGTGTCTTCAATATTTTGTTCCCTTTCCCGTAGGTGCCGTCCTTTGACTTTCCTGTGTCTTCAATATTTTGTTCCCTTTCCCGTAGGTGCCGTCCTT	CGTGTCTTCAATATTTTGTTCCCTTTCCCGTAGGTGCCGTCCTTTGACTTTCCTGTGTCTTCAATATTTTGTTCCCTTTCCCGTAGGTGCCGTCCTT	17: 30,979,841 (GRCm39)		probably null	Het
En2	G	A	5: 28,371,594 (GRCm39)	G24S	probably benign	Het
Evi2a	T	C	11: 79,418,688 (GRCm39)		probably benign	Het
Fam117b	A	T	1: 59,952,837 (GRCm39)	H172L	possibly damaging	Het
Fam169b	A	G	7: 67,954,338 (GRCm39)	I67M	probably benign	Het
Fbxo40	T	A	16: 36,789,861 (GRCm39)	E416D	probably damaging	Het
Gja8	T	A	3: 96,827,635 (GRCm39)	N9I	possibly damaging	Het
Gsg1l2	T	A	11: 67,676,097 (GRCm39)	C154S	probably benign	Het
Hdhd3	C	A	4: 62,418,232 (GRCm39)		probably benign	Het
Hunk	C	T	16: 90,278,214 (GRCm39)	P341L	possibly damaging	Het
Ighv8-5	T	C	12: 115,031,258 (GRCm39)	T94A	possibly damaging	Het
Ints3	T	C	3: 90,331,319 (GRCm39)	N75D	probably benign	Het
Krt39	T	C	11: 99,409,901 (GRCm39)	E212G	probably damaging	Het
Ldlrad4	A	G	18: 68,387,495 (GRCm39)	H269R	probably damaging	Het
Lrrc2	T	A	9: 110,790,049 (GRCm39)	V102E	possibly damaging	Het
Ltbp2	T	A	12: 84,836,655 (GRCm39)	I1292L	probably benign	Het
Mad2l1bp	A	T	17: 46,458,993 (GRCm39)	V179E	possibly damaging	Het
Map3k1	A	G	13: 111,892,663 (GRCm39)	V864A	probably benign	Het
Mapk8ip2	T	G	15: 89,342,322 (GRCm39)	V511G	probably damaging	Het
Mknk2	A	C	10: 80,503,021 (GRCm39)	S434A	probably benign	Het
Mllt11	A	G	3: 95,127,548 (GRCm39)	F74S	probably damaging	Het
Muc16	G	T	9: 18,506,519 (GRCm39)	T6412K	possibly damaging	Het
Nek5	C	A	8: 22,573,403 (GRCm39)	A518S	possibly damaging	Het
Npy1r	T	C	8: 67,156,864 (GRCm39)	F95L	possibly damaging	Het
Nup98	G	A	7: 101,773,569 (GRCm39)	T1586I	probably benign	Het
Olig3	A	T	10: 19,232,518 (GRCm39)	M48L	probably benign	Het
Or13n4	A	G	7: 106,422,932 (GRCm39)	M267T	probably benign	Het
Or14j7	T	A	17: 38,234,568 (GRCm39)	L37*	probably null	Het
Or5b120	T	G	19: 13,480,587 (GRCm39)	N293K	probably damaging	Het
Or6aa1	T	A	7: 86,043,765 (GRCm39)	K314*	probably null	Het
Pcdhb16	A	G	18: 37,611,904 (GRCm39)	D288G	possibly damaging	Het
Peg10	GC	GCTCC	6: 4,756,452 (GRCm39)		probably benign	Het
Phip	T	C	9: 82,790,886 (GRCm39)	I687V	probably benign	Het
Piezo1	G	A	8: 123,209,659 (GRCm39)	T2348M	probably damaging	Het
Plod3	A	G	5: 137,018,835 (GRCm39)	T291A	probably benign	Het
Polr1b	C	A	2: 128,967,464 (GRCm39)	F952L	probably damaging	Het
Pou6f2	C	A	13: 18,553,092 (GRCm39)	A81S		Het
Ppl	T	A	16: 4,905,828 (GRCm39)	E1489V	probably damaging	Het
Ptpdc1	A	G	13: 48,733,264 (GRCm39)	F792S	probably damaging	Het
Pus1	A	G	5: 110,927,582 (GRCm39)	Y58H	probably damaging	Het
Rex2	C	A	4: 147,142,547 (GRCm39)	T345N	possibly damaging	Het
Rnf144a	T	C	12: 26,389,439 (GRCm39)	M1V	probably null	Het
Siglec15	A	T	18: 78,100,445 (GRCm39)	C13*	probably null	Het
Skint10	G	A	4: 112,632,003 (GRCm39)	Q6*	probably null	Het
Slc5a1	T	C	5: 33,304,057 (GRCm39)	W291R	probably damaging	Het
Snx27	A	G	3: 94,426,366 (GRCm39)	F378L	probably benign	Het
Strip2	A	T	6: 29,923,928 (GRCm39)	T81S	probably benign	Het
Tas2r143	A	G	6: 42,377,656 (GRCm39)	N162S	probably damaging	Het
Tatdn1	T	C	15: 58,776,607 (GRCm39)	D256G	probably benign	Het
Tbc1d5	A	G	17: 51,089,291 (GRCm39)	S630P	probably damaging	Het
Tlr11	A	G	14: 50,598,611 (GRCm39)	D199G	probably benign	Het
Tmed8	C	A	12: 87,246,991 (GRCm39)		probably benign	Het
Ttll3	CAAAGTAA	CAAAGTAAAGTAA	6: 113,376,118 (GRCm39)		probably null	Het
Ttll3	TAA	TAAAGCAA	6: 113,376,123 (GRCm39)		probably null	Het
U2af2	T	C	7: 5,077,661 (GRCm39)		probably null	Het
Ywhag	C	T	5: 135,940,394 (GRCm39)	E67K	probably damaging	Het
Zfp105	A	G	9: 122,759,808 (GRCm39)	H493R	probably damaging	Het
Zfp426	A	T	9: 20,381,446 (GRCm39)	C514S	probably damaging	Het
Zfp536	T	A	7: 37,269,113 (GRCm39)	D101V	probably damaging	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
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
R9600:Pmpca	UTSW	2	26,282,598 (GRCm39)	missense	probably benign	0.03
R9621:Pmpca	UTSW	2	26,279,988 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- ACACAGACGGTTCAGCAGTG -3'
(R):5'- TGAGCACCAACTTCATATTCAGATC -3'

Sequencing Primer
(F):5'- TGGTGCCACCTACCCCAAC -3'
(R):5'- CTGACCGAAAATGCCAATTTTTCC -3'

Posted On

2019-12-03