Mutagenetix > Incidental Mutation

Incidental Mutation 'PIT4366001:Ptcd1'

554757

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 #

PIT4366001 (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 145088145 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 622 (V622A)

Ref Sequence

ENSEMBL: ENSMUSP00000031628 (fasta)

Gene Model

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

AlphaFold

Q8C2E4

Predicted Effect

probably benign
Transcript: ENSMUST00000031628
AA Change: V622A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000031628
Gene: ENSMUSG00000029624
AA Change: V622A

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

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

Coding Region Coverage

1x: 93.0%
3x: 90.7%
10x: 85.5%
20x: 73.8%

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aatk	C	A	11: 119,901,786 (GRCm39)	S870I	possibly damaging	Het
Abca13	T	C	11: 9,244,962 (GRCm39)	V2275A	probably benign	Het
Abcb5	T	C	12: 118,899,833 (GRCm39)	K278R	probably damaging	Het
Adcy2	TA	TAA	13: 68,858,109 (GRCm39)		probably benign	Het
Add3	C	T	19: 53,205,298 (GRCm39)	P16L	unknown	Het
Akap9	T	A	5: 4,096,221 (GRCm39)	D2365E	probably benign	Het
Asah1	A	G	8: 41,796,783 (GRCm39)	S300P	possibly damaging	Het
Astn1	A	T	1: 158,424,779 (GRCm39)	H655L	probably benign	Het
Astn1	A	T	1: 158,424,781 (GRCm39)	I656F	probably benign	Het
Bmpr1b	T	A	3: 141,586,224 (GRCm39)	T13S	probably benign	Het
Camsap2	A	G	1: 136,208,055 (GRCm39)	F478L		Het
Card10	G	A	15: 78,671,631 (GRCm39)	S611L	probably benign	Het
Cep68	T	C	11: 20,190,007 (GRCm39)	N335S	probably benign	Het
Chac1	T	C	2: 119,181,986 (GRCm39)	W35R	probably damaging	Het
Cntn6	T	C	6: 104,809,498 (GRCm39)	V511A	probably benign	Het
Cpne9	G	T	6: 113,271,707 (GRCm39)	G356W	probably damaging	Het
Dnah10	C	A	5: 124,852,588 (GRCm39)	T1939K	possibly damaging	Het
Dock10	T	C	1: 80,573,438 (GRCm39)	N239D	probably benign	Het
Dock5	T	C	14: 68,062,123 (GRCm39)	K415R	possibly damaging	Het
Dtd2	C	A	12: 52,046,582 (GRCm39)	D86Y	probably damaging	Het
Efcab9	A	G	11: 32,473,608 (GRCm39)	F127S	probably damaging	Het
Ermp1	T	C	19: 29,606,189 (GRCm39)	H375R	probably benign	Het
Frem2	A	T	3: 53,560,622 (GRCm39)	M1295K	probably damaging	Het
Gbp7	T	G	3: 142,248,712 (GRCm39)	I325R	probably benign	Het
Gpr179	T	C	11: 97,227,677 (GRCm39)	K1493E	probably benign	Het
Gucy2g	T	A	19: 55,226,214 (GRCm39)	E234V	probably null	Het
Itpr1	T	A	6: 108,470,718 (GRCm39)	C2215*	probably null	Het
Ltn1	G	A	16: 87,177,728 (GRCm39)	R1634*	probably null	Het
Lynx1	A	T	15: 74,623,258 (GRCm39)	M58K	possibly damaging	Het
Macc1	T	C	12: 119,410,684 (GRCm39)	V484A	probably benign	Het
Map3k9	C	T	12: 81,819,535 (GRCm39)	V240M	possibly damaging	Het
Mars1	A	G	10: 127,135,267 (GRCm39)	M608T	possibly damaging	Het
Mc2r	T	C	18: 68,540,826 (GRCm39)	M156V	probably benign	Het
Mchr1	G	T	15: 81,121,417 (GRCm39)	V56L	probably benign	Het
Mlxip	C	T	5: 123,533,173 (GRCm39)	P61S	probably benign	Het
Mtarc1	A	G	1: 184,539,383 (GRCm39)	F96S	probably benign	Het
Muc4	A	G	16: 32,575,542 (GRCm39)	T1557A	unknown	Het
Myt1	T	C	2: 181,467,731 (GRCm39)	V1135A	probably damaging	Het
Ndufaf6	A	T	4: 11,073,215 (GRCm39)	S76T	probably benign	Het
Ntrk2	A	G	13: 59,208,149 (GRCm39)	Y665C	probably damaging	Het
Oaz3	T	G	3: 94,340,901 (GRCm39)	R215S	unknown	Het
Or10x1	T	C	1: 174,196,656 (GRCm39)	Y58H	probably damaging	Het
Or5m10b	T	C	2: 85,699,226 (GRCm39)	C97R	probably damaging	Het
Or5m8	A	T	2: 85,822,385 (GRCm39)	N75Y	probably damaging	Het
Or5w1b	C	T	2: 87,475,534 (GRCm39)	W311*	probably null	Het
Perm1	G	T	4: 156,303,192 (GRCm39)	V579L	probably benign	Het
Phyhipl	A	G	10: 70,404,788 (GRCm39)	V140A	probably benign	Het
Pip5k1c	T	A	10: 81,144,842 (GRCm39)	S228T	probably damaging	Het
Plekhn1	T	G	4: 156,309,268 (GRCm39)	T213P	probably damaging	Het
Pomt2	A	T	12: 87,163,303 (GRCm39)		probably null	Het
Ptn	T	A	6: 36,718,284 (GRCm39)	H127L	probably benign	Het
Ptprk	A	T	10: 28,462,015 (GRCm39)	M1193L	probably benign	Het
Ptpru	G	A	4: 131,527,023 (GRCm39)	P650S	probably benign	Het
Pum2	T	A	12: 8,783,390 (GRCm39)	L613Q	probably damaging	Het
Rapgef6	A	G	11: 54,582,446 (GRCm39)	T1458A	probably damaging	Het
Sap130	C	T	18: 31,810,462 (GRCm39)	A470V	probably benign	Het
Sertad2	C	A	11: 20,598,116 (GRCm39)	P104Q	probably benign	Het
Sfrp4	A	T	13: 19,814,414 (GRCm39)	M324L	unknown	Het
Sh3bp4	A	G	1: 89,073,156 (GRCm39)	N668S	probably benign	Het
Snx30	C	A	4: 59,894,653 (GRCm39)	D410E	probably benign	Het
Spata31	C	A	13: 65,069,319 (GRCm39)	S489*	probably null	Het
Taok3	T	A	5: 117,366,050 (GRCm39)	M367K	probably benign	Het
Tfap2a	T	C	13: 40,874,850 (GRCm39)	N254D	possibly damaging	Het
Tgtp1	T	G	11: 48,877,867 (GRCm39)	L279F	possibly damaging	Het
Tmpo	A	G	10: 90,999,172 (GRCm39)	F205S	probably damaging	Het
Tmprss5	A	T	9: 49,023,517 (GRCm39)	I218L	probably benign	Het
Tti2	A	G	8: 31,641,224 (GRCm39)	E116G	probably benign	Het
Vmn2r59	A	T	7: 41,695,205 (GRCm39)	N402K	possibly damaging	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
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'- AAAACCTATGGGCTGGAGCG -3'
(R):5'- CACCCTTGTTCTAGCAGACTGC -3'

Sequencing Primer
(F):5'- CCAGAGTGAGTGGGGCTG -3'
(R):5'- AGACTGCGTTGTCCTTCCAG -3'

Posted On

2019-06-07