Mutagenetix > Incidental Mutation

Incidental Mutation 'R6931:Ptcd1'

540017

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: 0.140) question?

Stock #

R6931 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

145147514-145167108 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 145155075 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 405 (T405A)

Ref Sequence

ENSEMBL: ENSMUSP00000031628 (fasta)

Gene Model

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

AlphaFold

Q8C2E4

Predicted Effect

probably benign
Transcript: ENSMUST00000031628
AA Change: T405A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000031628
Gene: ENSMUSG00000029624
AA Change: T405A

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: 99.4%
20x: 98.0%

Validation Efficiency

99% (77/78)

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700123L14Rik	T	C	6: 96,165,548	T172A	possibly damaging	Het
2310003L06Rik	T	A	5: 87,970,702	I15N	probably damaging	Het
2900092C05Rik	T	A	7: 12,512,596	S6R	unknown	Het
Abca6	T	A	11: 110,244,328	L210F	probably benign	Het
Abcc4	T	C	14: 118,527,988	Q919R	probably damaging	Het
Adcy1	A	G	11: 7,150,884	D811G	possibly damaging	Het
Akna	A	G	4: 63,387,102	S476P	probably benign	Het
Ankrd49	T	C	9: 14,782,826	N15S	probably benign	Het
Apcdd1	A	G	18: 62,933,908	D31G	probably damaging	Het
Aplp1	G	T	7: 30,443,200	R106S	probably damaging	Het
Arhgap40	T	C	2: 158,531,218	L132S	probably benign	Het
Atp8b5	G	T	4: 43,364,108		probably null	Het
Axl	T	C	7: 25,761,433	D717G	probably damaging	Het
Bub1	T	A	2: 127,801,382	D1014V	probably damaging	Het
Cacna2d4	T	A	6: 119,282,234	V603E	possibly damaging	Het
Cnot11	G	C	1: 39,539,921	C289S	probably damaging	Het
Coasy	A	G	11: 101,083,581	H191R	probably benign	Het
Cyp11a1	A	T	9: 58,025,120	N341Y	possibly damaging	Het
Cyp1a2	T	C	9: 57,682,156	N125S	probably benign	Het
Cyp2j8	A	T	4: 96,444,781		probably null	Het
Dnah9	A	T	11: 66,117,626	I791K	possibly damaging	Het
Ecm2	A	T	13: 49,529,011	Q505H	probably benign	Het
Fam135a	T	A	1: 24,085,487	M1L	probably damaging	Het
Fam171a2	A	G	11: 102,438,434	S500P	possibly damaging	Het
Fat3	A	G	9: 15,959,942	S3718P	possibly damaging	Het
Frem1	G	A	4: 82,970,677	P1085S	probably damaging	Het
Gcfc2	A	G	6: 81,942,985	I390V	probably benign	Het
Gemin4	A	G	11: 76,210,956	L993P	probably damaging	Het
Ggnbp2	T	A	11: 84,833,167	D647V	probably damaging	Het
Gm7534	A	T	4: 134,193,153	M567K	probably benign	Het
Gpr84	A	C	15: 103,309,014	L212R	probably damaging	Het
Hnrnpu	T	C	1: 178,331,432		probably benign	Het
Hspg2	G	T	4: 137,540,720	C2116F	probably damaging	Het
Icam4	T	A	9: 21,030,451	V249E	probably damaging	Het
Itga1	T	C	13: 115,001,563	N429D	probably benign	Het
Kcns1	T	C	2: 164,164,838	T402A	probably damaging	Het
Ky	T	A	9: 102,537,627	V246E	probably damaging	Het
March1	A	G	8: 66,468,492	T529A	probably benign	Het
Med18	C	G	4: 132,459,883	V102L	probably damaging	Het
Mlst8	T	C	17: 24,477,275	D160G	probably damaging	Het
Mthfd1	T	C	12: 76,303,698	I470T	probably benign	Het
Muc1	C	T	3: 89,229,159		probably benign	Het
Mup8	G	A	4: 60,220,322	L137F	probably damaging	Het
Mybpc1	A	T	10: 88,542,330	L341*	probably null	Het
Nacad	A	G	11: 6,601,877	F438S	probably benign	Het
Necap2	C	A	4: 141,078,212		probably null	Het
Nifk	T	C	1: 118,332,348	L163S	possibly damaging	Het
Npsr1	A	G	9: 24,289,997	I73V	probably benign	Het
Olfr1179	G	A	2: 88,402,064	T290I	probably benign	Het
Olfr1186	T	A	2: 88,526,194	C204S	possibly damaging	Het
Olfr142	A	T	2: 90,252,777	C70*	probably null	Het
Olfr715	A	G	7: 107,128,901	L164P	probably damaging	Het
Oog3	C	T	4: 144,159,353	C225Y	probably benign	Het
Plagl2	C	A	2: 153,235,943	K39N	probably benign	Het
Plcg2	T	A	8: 117,557,319	D118E	probably benign	Het
Ppp4r3b	A	T	11: 29,211,786	K720I	possibly damaging	Het
Prmt3	A	T	7: 49,829,016	T442S	probably benign	Het
Prr14l	G	A	5: 32,830,691	H487Y	probably damaging	Het
Psmb3	G	A	11: 97,703,971	V63I	probably benign	Het
Psmc6	T	A	14: 45,343,725	I326K	possibly damaging	Het
Rbm33	G	A	5: 28,410,745	V29M	probably damaging	Het
Rsrc1	C	T	3: 66,994,649	P44L	unknown	Het
Scarb1	T	A	5: 125,284,719	I107F	probably damaging	Het
Slc39a12	A	G	2: 14,389,375	S19G	probably benign	Het
Slc44a5	T	C	3: 154,258,506	V503A	probably benign	Het
Slc9a9	T	C	9: 94,670,086	S9P	possibly damaging	Het
Snrnp35	A	C	5: 124,490,701	R192S	possibly damaging	Het
Tbx15	T	C	3: 99,352,151	L446P	probably damaging	Het
Tlnrd1	A	G	7: 83,882,597	F209L	probably benign	Het
Tmprss12	C	T	15: 100,285,268	R164C	probably damaging	Het
Tnfsf4	T	A	1: 161,417,073	F111Y	possibly damaging	Het
Trib2	A	T	12: 15,793,639	M198K	probably benign	Het
Ttll8	A	G	15: 88,914,304	S743P	possibly damaging	Het
Ush2a	A	T	1: 188,728,383	N2614Y	probably benign	Het
Usp6nl	G	A	2: 6,430,458	V343I	possibly damaging	Het
Vrtn	C	A	12: 84,650,242	Q589K	probably benign	Het
Zbed5	T	A	5: 129,903,329	Y706*	probably null	Het
Zc3h10	A	G	10: 128,544,684	V268A	probably damaging	Het
Zfp442	C	T	2: 150,410,940		probably null	Het

Other mutations in Ptcd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00858:Ptcd1	APN	5	145151282	unclassified	probably benign
IGL00984:Ptcd1	APN	5	145165429	missense	probably benign
IGL01120:Ptcd1	APN	5	145152243	unclassified	probably benign
IGL01545:Ptcd1	APN	5	145159536	missense	probably damaging	1.00
IGL01861:Ptcd1	APN	5	145158777	missense	possibly damaging	0.81
IGL02543:Ptcd1	APN	5	145154687	missense	possibly damaging	0.66
IGL02835:Ptcd1	UTSW	5	145154690	missense	possibly damaging	0.78
PIT4366001:Ptcd1	UTSW	5	145151335	missense	probably benign	0.01
PIT4494001:Ptcd1	UTSW	5	145155358	missense	probably benign	0.01
R3001:Ptcd1	UTSW	5	145159576	missense	probably damaging	0.98
R3002:Ptcd1	UTSW	5	145159576	missense	probably damaging	0.98
R4460:Ptcd1	UTSW	5	145159506	missense	probably benign	0.25
R4587:Ptcd1	UTSW	5	145154721	missense	possibly damaging	0.47
R4652:Ptcd1	UTSW	5	145155175	missense	probably benign	0.01
R5059:Ptcd1	UTSW	5	145152224	missense	probably benign	0.07
R5364:Ptcd1	UTSW	5	145151431	missense	probably damaging	0.99
R5367:Ptcd1	UTSW	5	145147905	utr 3 prime	probably benign
R5733:Ptcd1	UTSW	5	145154861	missense	probably damaging	1.00
R5800:Ptcd1	UTSW	5	145159665	missense	probably damaging	0.99
R6281:Ptcd1	UTSW	5	145165071	missense	probably benign	0.10
R7472:Ptcd1	UTSW	5	145154730	missense	possibly damaging	0.94
R7723:Ptcd1	UTSW	5	145154829	missense	probably damaging	1.00
R7731:Ptcd1	UTSW	5	145151364	missense	probably benign	0.07
R8048:Ptcd1	UTSW	5	145155077	missense	probably benign
R8090:Ptcd1	UTSW	5	145159535	missense	possibly damaging	0.91
R8774:Ptcd1	UTSW	5	145155365	missense	probably damaging	1.00
R8774-TAIL:Ptcd1	UTSW	5	145155365	missense	probably damaging	1.00
R8952:Ptcd1	UTSW	5	145155134	missense	probably damaging	1.00
R8990:Ptcd1	UTSW	5	145165237	missense	probably damaging	1.00
R9072:Ptcd1	UTSW	5	145154715	missense	probably benign	0.36
R9073:Ptcd1	UTSW	5	145154715	missense	probably benign	0.36
R9602:Ptcd1	UTSW	5	145159638	missense	probably benign	0.00
R9740:Ptcd1	UTSW	5	145159484	missense	probably benign
Z1177:Ptcd1	UTSW	5	145165435	missense	probably benign	0.04

Predicted Primers

PCR Primer
(F):5'- CCAGCAGAGTGAGGGTTTTG -3'
(R):5'- AGAGACCATCTTGCTCCCAC -3'

Sequencing Primer
(F):5'- TTCGGTCATCTTGCCCAGGAAG -3'
(R):5'- TTGCTCCCACCCCCAAAGG -3'

Posted On

2018-11-06