Mutagenetix > Incidental Mutation

Incidental Mutation 'R5367:Ptcd1'

429405

Institutional Source

Beutler Lab

Gene Symbol

Ptcd1

Ensembl Gene

ENSMUSG00000029624

Gene Name

pentatricopeptide repeat domain 1

Synonyms

1110069M14Rik

MMRRC Submission

042945-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.114) question?

Stock #

R5367 (G1)

Quality Score

161

Status

Validated

Chromosome

Chromosomal Location

145084324-145103918 bp(-) (GRCm39)

Type of Mutation

utr 3 prime

DNA Base Change (assembly)

T to A at 145084715 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000125738 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031628] [ENSMUST00000159018] [ENSMUST00000160075] [ENSMUST00000162308] [ENSMUST00000162594]

AlphaFold

Q8C2E4

Predicted Effect

probably benign
Transcript: ENSMUST00000031628

SMART Domains

Protein: ENSMUSP00000031628
Gene: ENSMUSG00000029624

Domain	Start	End	E-Value	Type
low complexity region	48	58	N/A	INTRINSIC
low complexity region	64	74	N/A	INTRINSIC
low complexity region	110	123	N/A	INTRINSIC
Pfam:PPR_2	169	218	1.2e-16	PFAM
Pfam:PPR	172	202	1.1e-9	PFAM
Pfam:PPR_3	173	204	2.5e-5	PFAM
Pfam:PPR_3	245	278	3.2e-5	PFAM
Pfam:PPR	246	276	6.5e-4	PFAM
internal_repeat_1	437	595	1.57e-9	PROSPERO

Predicted Effect

probably benign
Transcript: ENSMUST00000159018

SMART Domains

Protein: ENSMUSP00000124999
Gene: ENSMUSG00000038722

Domain	Start	End	E-Value	Type
Pfam:G10	1	144	2.2e-69	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000160075

SMART Domains

Protein: ENSMUSP00000125564
Gene: ENSMUSG00000038722

Domain	Start	End	E-Value	Type
Pfam:G10	1	144	2.2e-71	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160840

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161974

Predicted Effect

probably benign
Transcript: ENSMUST00000162308

SMART Domains

Protein: ENSMUSP00000125590
Gene: ENSMUSG00000038722

Domain	Start	End	E-Value	Type
Pfam:G10	29	103	9.4e-36	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162594

SMART Domains

Protein: ENSMUSP00000125738
Gene: ENSMUSG00000038722

Domain	Start	End	E-Value	Type
Pfam:G10	1	144	2.2e-69	PFAM

Meta Mutation Damage Score

0.0846

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.5%

Validation Efficiency

97% (70/72)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This locus represents naturally occurring read-through transcription between the ATP5J2 (ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2) and PTCD1 (pentatricopeptide repeat domain 1) genes on chromosome 7. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]
PHENOTYPE: Knockout affects mitochondrial protein synthesis and RNA metabolism. Homozygous KO is embryonic lethal. Heterozygous KO causes adult onset obesity, liver fibrosis and cardiac hypertrophy. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadac	T	C	3: 59,947,057 (GRCm39)	Y252H	probably damaging	Het
Aadat	T	C	8: 60,979,630 (GRCm39)	I164T	probably damaging	Het
Adam11	A	G	11: 102,664,479 (GRCm39)	H389R	probably benign	Het
Alkbh5	G	T	11: 60,429,529 (GRCm39)	R94L	possibly damaging	Het
Ampd3	A	G	7: 110,407,078 (GRCm39)	K644R	possibly damaging	Het
Ankhd1	T	A	18: 36,722,461 (GRCm39)	L328H	probably damaging	Het
Ankrd55	G	T	13: 112,455,036 (GRCm39)	V45F	probably damaging	Het
Apol7c	C	A	15: 77,410,347 (GRCm39)	V200F	probably damaging	Het
Arap1	G	A	7: 101,058,337 (GRCm39)	V721M	probably damaging	Het
Arhgef40	A	G	14: 52,227,156 (GRCm39)	D400G	probably damaging	Het
Bmp4	G	T	14: 46,621,950 (GRCm39)	T198K	possibly damaging	Het
Cblb	T	A	16: 52,025,016 (GRCm39)	F970L	probably damaging	Het
Celf5	A	G	10: 81,303,098 (GRCm39)	S148P	probably damaging	Het
Ckap5	T	A	2: 91,445,486 (GRCm39)	C1708S	possibly damaging	Het
Clec2l	T	C	6: 38,654,459 (GRCm39)	F147L	possibly damaging	Het
Cnksr1	T	A	4: 133,957,525 (GRCm39)	I465F	possibly damaging	Het
Coq10b	A	G	1: 55,092,143 (GRCm39)	D37G	probably benign	Het
Cpq	T	G	15: 33,213,250 (GRCm39)	Y90D	possibly damaging	Het
Depdc1a	G	A	3: 159,229,591 (GRCm39)		probably null	Het
Eif2ak4	T	A	2: 118,266,639 (GRCm39)		probably null	Het
Eif3e	C	T	15: 43,115,700 (GRCm39)	M355I	probably damaging	Het
Eif4e1b	G	A	13: 54,934,757 (GRCm39)	V181M	probably damaging	Het
Erap1	A	G	13: 74,794,680 (GRCm39)	E113G	probably damaging	Het
Fads2	A	G	19: 10,041,649 (GRCm39)	L438P	probably damaging	Het
Fbl	T	A	7: 27,874,475 (GRCm39)	V67E	probably damaging	Het
Gde1	A	G	7: 118,304,629 (GRCm39)	L82P	probably damaging	Het
Gm10226	T	C	17: 21,910,884 (GRCm39)	S40P	possibly damaging	Het
Gm10717	T	G	9: 3,026,317 (GRCm39)	F205C	probably damaging	Het
Gm1988	T	A	7: 38,823,204 (GRCm39)		noncoding transcript	Het
Gm6728	T	C	6: 136,463,502 (GRCm39)		noncoding transcript	Het
Grb14	C	T	2: 64,747,653 (GRCm39)	V369I	probably benign	Het
Jag1	T	A	2: 136,927,014 (GRCm39)	Q915L	possibly damaging	Het
Kdm5d	G	A	Y: 941,645 (GRCm39)	G1282D	probably benign	Het
Krt87	A	T	15: 101,384,875 (GRCm39)	L407Q	probably damaging	Het
Mlf1	A	T	3: 67,301,296 (GRCm39)	H118L	probably damaging	Het
Mmp10	G	T	9: 7,505,603 (GRCm39)	C289F	probably damaging	Het
Mroh2a	A	T	1: 88,182,687 (GRCm39)	N1205I	possibly damaging	Het
Myo9a	T	A	9: 59,807,732 (GRCm39)	S2029T	probably damaging	Het
Nap1l4	A	C	7: 143,088,035 (GRCm39)	S174R	probably damaging	Het
Nos3	A	G	5: 24,576,942 (GRCm39)	T490A	probably benign	Het
Or12d2	T	A	17: 37,625,147 (GRCm39)	I43F	probably damaging	Het
Or4k35	T	A	2: 111,100,235 (GRCm39)	Q159L	possibly damaging	Het
Or5a1	A	G	19: 12,097,800 (GRCm39)	V80A	possibly damaging	Het
Or5b106	G	A	19: 13,123,865 (GRCm39)	L53F	probably damaging	Het
Or5g23	A	T	2: 85,438,718 (GRCm39)	C179S	probably damaging	Het
Pdlim7	G	C	13: 55,653,975 (GRCm39)	T214S	probably benign	Het
Piezo2	T	C	18: 63,197,802 (GRCm39)	E1578G	probably damaging	Het
Sart3	C	T	5: 113,897,277 (GRCm39)		probably null	Het
Scara5	CG	C	14: 65,997,111 (GRCm39)		probably null	Het
Scrn2	A	G	11: 96,923,953 (GRCm39)	D279G	possibly damaging	Het
Sh2d3c	A	G	2: 32,635,914 (GRCm39)	D94G	probably damaging	Het
Slc12a4	A	T	8: 106,678,266 (GRCm39)	V309E	probably damaging	Het
Slc1a6	A	G	10: 78,623,637 (GRCm39)	E12G	probably damaging	Het
Smarcal1	T	C	1: 72,635,135 (GRCm39)		probably null	Het
Smr3a	T	C	5: 88,155,897 (GRCm39)		probably benign	Het
Stox2	A	G	8: 47,656,260 (GRCm39)	I72T	probably damaging	Het
Tmem234	G	T	4: 129,494,500 (GRCm39)		probably benign	Het
Tmem35b	A	G	4: 127,018,266 (GRCm39)	Q20R	possibly damaging	Het
Tom1l2	G	A	11: 60,132,634 (GRCm39)	H430Y	probably benign	Het
Tpo	T	C	12: 30,153,289 (GRCm39)	Y355C	probably damaging	Het
Tulp2	A	G	7: 45,166,075 (GRCm39)	N122S	possibly damaging	Het
Washc2	T	A	6: 116,236,111 (GRCm39)	L1194H	probably damaging	Het
Xbp1	T	C	11: 5,471,910 (GRCm39)	V12A	probably benign	Het

Other mutations in Ptcd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00858:Ptcd1	APN	5	145,088,092 (GRCm39)	unclassified	probably benign
IGL00984:Ptcd1	APN	5	145,102,239 (GRCm39)	missense	probably benign
IGL01120:Ptcd1	APN	5	145,089,053 (GRCm39)	unclassified	probably benign
IGL01545:Ptcd1	APN	5	145,096,346 (GRCm39)	missense	probably damaging	1.00
IGL01861:Ptcd1	APN	5	145,095,587 (GRCm39)	missense	possibly damaging	0.81
IGL02543:Ptcd1	APN	5	145,091,497 (GRCm39)	missense	possibly damaging	0.66
IGL02835:Ptcd1	UTSW	5	145,091,500 (GRCm39)	missense	possibly damaging	0.78
PIT4366001:Ptcd1	UTSW	5	145,088,145 (GRCm39)	missense	probably benign	0.01
PIT4494001:Ptcd1	UTSW	5	145,092,168 (GRCm39)	missense	probably benign	0.01
R3001:Ptcd1	UTSW	5	145,096,386 (GRCm39)	missense	probably damaging	0.98
R3002:Ptcd1	UTSW	5	145,096,386 (GRCm39)	missense	probably damaging	0.98
R4460:Ptcd1	UTSW	5	145,096,316 (GRCm39)	missense	probably benign	0.25
R4587:Ptcd1	UTSW	5	145,091,531 (GRCm39)	missense	possibly damaging	0.47
R4652:Ptcd1	UTSW	5	145,091,985 (GRCm39)	missense	probably benign	0.01
R5059:Ptcd1	UTSW	5	145,089,034 (GRCm39)	missense	probably benign	0.07
R5364:Ptcd1	UTSW	5	145,088,241 (GRCm39)	missense	probably damaging	0.99
R5733:Ptcd1	UTSW	5	145,091,671 (GRCm39)	missense	probably damaging	1.00
R5800:Ptcd1	UTSW	5	145,096,475 (GRCm39)	missense	probably damaging	0.99
R6281:Ptcd1	UTSW	5	145,101,881 (GRCm39)	missense	probably benign	0.10
R6931:Ptcd1	UTSW	5	145,091,885 (GRCm39)	missense	probably benign	0.00
R7472:Ptcd1	UTSW	5	145,091,540 (GRCm39)	missense	possibly damaging	0.94
R7723:Ptcd1	UTSW	5	145,091,639 (GRCm39)	missense	probably damaging	1.00
R7731:Ptcd1	UTSW	5	145,088,174 (GRCm39)	missense	probably benign	0.07
R8048:Ptcd1	UTSW	5	145,091,887 (GRCm39)	missense	probably benign
R8090:Ptcd1	UTSW	5	145,096,345 (GRCm39)	missense	possibly damaging	0.91
R8774:Ptcd1	UTSW	5	145,092,175 (GRCm39)	missense	probably damaging	1.00
R8774-TAIL:Ptcd1	UTSW	5	145,092,175 (GRCm39)	missense	probably damaging	1.00
R8952:Ptcd1	UTSW	5	145,091,944 (GRCm39)	missense	probably damaging	1.00
R8990:Ptcd1	UTSW	5	145,102,047 (GRCm39)	missense	probably damaging	1.00
R9072:Ptcd1	UTSW	5	145,091,525 (GRCm39)	missense	probably benign	0.36
R9073:Ptcd1	UTSW	5	145,091,525 (GRCm39)	missense	probably benign	0.36
R9602:Ptcd1	UTSW	5	145,096,448 (GRCm39)	missense	probably benign	0.00
R9740:Ptcd1	UTSW	5	145,096,294 (GRCm39)	missense	probably benign
Z1177:Ptcd1	UTSW	5	145,102,245 (GRCm39)	missense	probably benign	0.04

Predicted Primers

PCR Primer
(F):5'- TTCCGCCTGGTAGTAACTGTTC -3'
(R):5'- CATCCCCTGGCACTCTTAAAAG -3'

Sequencing Primer
(F):5'- GTAGTAACTGTTCCACGTCACAAAGG -3'
(R):5'- CCTGGCACTCTTAAAAGAAAGAATG -3'

Posted On

2016-09-06