Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02835:Ptcd1'

391967

Institutional Source

Beutler Lab

Gene Symbol

Ptcd1

Ensembl Gene

ENSMUSG00000029624

Gene Name

pentatricopeptide repeat domain 1

Synonyms

1110069M14Rik

Accession Numbers

Essential gene?

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

Stock #

IGL02835 (G1)

Quality Score

126

Status

Validated

Chromosome

Chromosomal Location

145084324-145103918 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 145091500 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 533 (D533G)

Ref Sequence

ENSEMBL: ENSMUSP00000031628 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031628]

AlphaFold

Q8C2E4

Predicted Effect

possibly damaging
Transcript: ENSMUST00000031628
AA Change: D533G

PolyPhen 2 Score 0.778 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000031628
Gene: ENSMUSG00000029624
AA Change: D533G

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

Meta Mutation Damage Score

0.4260

Coding Region Coverage

1x: 0.0%
3x: 0.0%
10x: 0.0%
20x: 0.0%

Validation Efficiency

98% (57/58)

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700011L22Rik	T	A	8: 79,937,284 (GRCm39)	K208*	probably null	Het
A530016L24Rik	A	C	12: 112,461,420 (GRCm39)		probably null	Het
A830018L16Rik	A	C	1: 12,042,279 (GRCm39)	D433A	possibly damaging	Het
Abca13	T	A	11: 9,401,515 (GRCm39)	I3985N	probably damaging	Het
Abhd17c	C	T	7: 83,800,731 (GRCm39)	D108N	probably benign	Het
Adam29	C	T	8: 56,326,173 (GRCm39)	D94N	probably damaging	Het
Agr2	A	G	12: 36,045,903 (GRCm39)	D50G	probably benign	Het
Angptl1	A	G	1: 156,686,090 (GRCm39)	D392G	probably benign	Het
Apob	A	G	12: 8,065,097 (GRCm39)	N3989S	possibly damaging	Het
AU018091	T	C	7: 3,218,897 (GRCm39)	D12G	unknown	Het
Cyfip2	A	T	11: 46,140,598 (GRCm39)	S742T	probably benign	Het
Dlc1	C	T	8: 37,051,055 (GRCm39)	S892N	probably damaging	Het
Dsg1b	A	G	18: 20,525,071 (GRCm39)	N169S	possibly damaging	Het
Egfem1	T	C	3: 29,711,390 (GRCm39)	L323P	probably damaging	Het
Emilin3	G	A	2: 160,750,649 (GRCm39)	Q320*	probably null	Het
Fjx1	G	A	2: 102,281,092 (GRCm39)	A281V	possibly damaging	Het
Fmn2	T	A	1: 174,409,625 (GRCm39)	D619E	unknown	Het
Gm4795	A	C	10: 44,882,254 (GRCm39)		noncoding transcript	Het
Gm5117	T	C	8: 32,227,198 (GRCm39)		noncoding transcript	Het
Gm5250	T	C	1: 13,132,418 (GRCm39)		noncoding transcript	Het
Gtdc1	A	T	2: 44,646,324 (GRCm39)	Y101*	probably null	Het
Herc6	T	C	6: 57,623,146 (GRCm39)	I583T	possibly damaging	Het
Hyal4	G	A	6: 24,765,714 (GRCm39)	R356H	probably benign	Het
Il22ra2	C	A	10: 19,502,424 (GRCm39)	T81K	probably benign	Het
Iqcm	T	A	8: 76,281,511 (GRCm39)		probably benign	Het
Izumo4	G	A	10: 80,540,959 (GRCm39)	V220I	probably benign	Het
Kif16b	A	T	2: 142,554,133 (GRCm39)	D899E	probably benign	Het
Lrp2	A	T	2: 69,335,648 (GRCm39)	N1358K	probably damaging	Het
Lrrk2	A	G	15: 91,698,863 (GRCm39)		probably null	Het
Lyst	C	T	13: 13,835,685 (GRCm39)	T1789M	possibly damaging	Het
Map4k4	A	G	1: 40,049,760 (GRCm39)	T732A	probably damaging	Het
Mdh1b	A	T	1: 63,757,816 (GRCm39)	I305N	probably damaging	Het
Mettl13	A	G	1: 162,373,585 (GRCm39)	I222T	probably damaging	Het
Mtcl2	G	A	2: 156,883,854 (GRCm39)	T363I	possibly damaging	Het
Muc4	T	C	16: 32,584,319 (GRCm39)	F2583L	probably benign	Het
Nbea	C	T	3: 55,625,290 (GRCm39)	R2267Q	possibly damaging	Het
Ndfip1	T	C	18: 38,589,144 (GRCm39)	Y178H	probably damaging	Het
Nin	A	T	12: 70,103,512 (GRCm39)	F243I	probably damaging	Het
Nlrp10	A	T	7: 108,523,869 (GRCm39)	I537K	possibly damaging	Het
Nup155	T	C	15: 8,172,614 (GRCm39)	Y867H	probably damaging	Het
Pakap	C	G	4: 57,883,044 (GRCm39)	P837A	probably damaging	Het
Pik3r4	A	C	9: 105,549,905 (GRCm39)	I999L	probably benign	Het
Pitpnm3	G	A	11: 71,952,292 (GRCm39)		probably benign	Het
Pkd1l2	G	A	8: 117,792,484 (GRCm39)	T436I	probably benign	Het
Polg2	A	T	11: 106,666,266 (GRCm39)	V293E	probably benign	Het
Pramel22	T	A	4: 143,380,817 (GRCm39)	Y402F	probably damaging	Het
Prok1	T	C	3: 107,144,531 (GRCm39)		probably null	Het
Ptpn13	T	C	5: 103,707,891 (GRCm39)	V1484A	probably damaging	Het
Rapgef2	A	T	3: 79,000,293 (GRCm39)		probably benign	Het
Serpinb8	T	G	1: 107,530,586 (GRCm39)	F121L	probably damaging	Het
Sh3rf1	T	A	8: 61,679,081 (GRCm39)	V41E	probably damaging	Het
Snx13	A	G	12: 35,182,126 (GRCm39)	N725S	possibly damaging	Het
Stab1	A	T	14: 30,867,981 (GRCm39)		probably null	Het
Themis	A	T	10: 28,637,616 (GRCm39)		probably benign	Het
Trim68	T	A	7: 102,327,780 (GRCm39)	Y391F	probably benign	Het
Trmt1	T	G	8: 85,423,589 (GRCm39)	V327G	probably null	Het
Vill	C	T	9: 118,896,513 (GRCm39)	T120M	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
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
R5367:Ptcd1	UTSW	5	145,084,715 (GRCm39)	utr 3 prime	probably benign
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'- CGTGAATGCCCTTCATACCC -3'
(R):5'- TCTCATTTGGGACAGTGGC -3'

Sequencing Primer
(F):5'- CTTCCGCTGGGTGGTAGGAC -3'
(R):5'- AGGCTTCCTGGGCAAGATGAC -3'

Posted On

2016-06-08