Mutagenetix > Incidental Mutation

Incidental Mutation 'R9602:Ptcd1'

723724

Institutional Source

Beutler Lab

Gene Symbol

Ptcd1

Ensembl Gene

ENSMUSG00000029624

Gene Name

pentatricopeptide repeat domain 1

Synonyms

1110069M14Rik

MMRRC Submission

Accession Numbers

Essential gene?

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

Stock #

R9602 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

145084324-145103918 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 145096448 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 215 (V215A)

Ref Sequence

ENSEMBL: ENSMUSP00000031628 (fasta)

Gene Model

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

AlphaFold

Q8C2E4

Predicted Effect

probably benign
Transcript: ENSMUST00000031628
AA Change: V215A

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000031628
Gene: ENSMUSG00000029624
AA Change: V215A

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

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
4930563M21Rik	G	A	9: 55,910,261 (GRCm39)	S125L	possibly damaging	Het
Abca3	T	C	17: 24,617,378 (GRCm39)	V1025A	probably benign	Het
Adam5	T	C	8: 25,303,402 (GRCm39)	K175R	probably damaging	Het
Arhgap39	A	C	15: 76,610,954 (GRCm39)	S885R	probably damaging	Het
Arhgef12	A	G	9: 42,895,676 (GRCm39)	Y951H	probably damaging	Het
Bbs1	G	A	19: 4,941,083 (GRCm39)	L544F	probably damaging	Het
Bcar1	C	T	8: 112,440,498 (GRCm39)	E499K	probably benign	Het
Brinp3	C	T	1: 146,622,234 (GRCm39)	T212I	probably damaging	Het
Cdh20	A	T	1: 104,868,823 (GRCm39)	I105F	probably benign	Het
Cenpp	T	C	13: 49,801,049 (GRCm39)	E123G	probably damaging	Het
Col14a1	C	A	15: 55,351,345 (GRCm39)	D1557E	unknown	Het
Col6a3	A	T	1: 90,731,497 (GRCm39)	N1585K	probably benign	Het
Cox6a1	G	A	5: 115,486,934 (GRCm39)	P26S	unknown	Het
Epb41l1	G	T	2: 156,367,068 (GRCm39)	D646Y	probably damaging	Het
Fbxw10	G	T	11: 62,750,782 (GRCm39)	R455L	possibly damaging	Het
Fmnl2	T	C	2: 53,013,587 (GRCm39)		probably null	Het
Gata3	T	A	2: 9,863,297 (GRCm39)	I406F	possibly damaging	Het
Gm14406	C	T	2: 177,261,028 (GRCm39)	G417D	probably damaging	Het
Gpr31b	C	T	17: 13,270,771 (GRCm39)	G133S	possibly damaging	Het
Gtf2h1	T	A	7: 46,456,219 (GRCm39)	D196E	possibly damaging	Het
Hcn2	A	G	10: 79,562,128 (GRCm39)	I375V	probably benign	Het
Kctd20	T	C	17: 29,180,442 (GRCm39)	M72T	probably benign	Het
Klhl2	A	T	8: 65,205,696 (GRCm39)	F408L	probably damaging	Het
Mllt10	T	C	2: 18,211,850 (GRCm39)	V921A	probably damaging	Het
Mn1	A	T	5: 111,565,449 (GRCm39)		probably benign	Het
Mov10	A	T	3: 104,708,284 (GRCm39)	D488E	probably benign	Het
Muc5b	G	T	7: 141,417,211 (GRCm39)	D3386Y	probably benign	Het
Myo15b	G	A	11: 115,769,269 (GRCm39)		probably null	Het
Nudt7	T	C	8: 114,878,499 (GRCm39)	F176L	probably damaging	Het
Obscn	A	G	11: 58,981,385 (GRCm39)	Y1878H	probably damaging	Het
Or6c5b	A	T	10: 129,245,802 (GRCm39)	D189V	probably damaging	Het
Pabpn1l	T	A	8: 123,347,101 (GRCm39)	T250S	probably benign	Het
Prr11	C	T	11: 86,987,998 (GRCm39)	D302N	possibly damaging	Het
Prx	T	A	7: 27,218,445 (GRCm39)	V1121D	possibly damaging	Het
Rasa3	T	C	8: 13,681,844 (GRCm39)	D35G	probably benign	Het
Rbm5	A	G	9: 107,629,152 (GRCm39)	S348P	probably benign	Het
Rmdn2	G	A	17: 79,975,440 (GRCm39)	G310R	probably damaging	Het
Rnf114	T	A	2: 167,353,162 (GRCm39)	C144*	probably null	Het
Rreb1	T	C	13: 38,114,477 (GRCm39)	I612T	probably damaging	Het
Sdk1	A	T	5: 142,071,353 (GRCm39)	D1181V	probably damaging	Het
Secisbp2l	A	T	2: 125,609,356 (GRCm39)	M324K	probably benign	Het
Slc14a1	C	A	18: 78,152,807 (GRCm39)	A367S	probably damaging	Het
Slc22a6	G	T	19: 8,598,560 (GRCm39)	E206*	probably null	Het
Smg5	T	C	3: 88,250,214 (GRCm39)	C109R	probably damaging	Het
Socs7	A	G	11: 97,267,837 (GRCm39)	T323A	probably benign	Het
Spen	T	C	4: 141,205,183 (GRCm39)	N1148S	unknown	Het
Tek	C	G	4: 94,715,968 (GRCm39)	I463M	possibly damaging	Het
Ttn	C	T	2: 76,715,357 (GRCm39)	E7912K	unknown	Het
Ugt2b34	T	C	5: 87,054,163 (GRCm39)	D206G	probably damaging	Het
Upk3a	C	T	15: 84,905,464 (GRCm39)	P191L	probably benign	Het
Vmn2r101	T	A	17: 19,831,780 (GRCm39)	L592*	probably null	Het
Vmn2r82	A	G	10: 79,214,880 (GRCm39)	I288V	probably benign	Het
Vmn2r88	T	A	14: 51,651,189 (GRCm39)	S168T		Het
Wnt5a	C	A	14: 28,240,295 (GRCm39)	N148K	probably benign	Het
Yipf5	T	C	18: 40,345,134 (GRCm39)	Y82C	probably damaging	Het
Zfp655	T	A	5: 145,181,473 (GRCm39)	C444S	probably benign	Het
Zpr1	A	G	9: 46,184,663 (GRCm39)	N57D	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
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
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'- CCACCCGACTGACTTTGAAG -3'
(R):5'- TTGGATACTGTATACGAGGTGCC -3'

Sequencing Primer
(F):5'- CCCGACTGACTTTGAAGGCAAG -3'
(R):5'- ATACTGTATACGAGGTGCCACTTG -3'

Posted On

2022-09-12