Mutagenetix > Incidental Mutation

Incidental Mutation 'R8270:Atp5pd'

639460

Institutional Source

Beutler Lab

Gene Symbol

Atp5pd

Ensembl Gene

ENSMUSG00000034566

Gene Name

ATP synthase peripheral stalk subunit d

Synonyms

0610009D10Rik, Atp5h

MMRRC Submission

067694-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.881) question?

Stock #

R8270 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

115306517-115310775 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 115307698 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 91 (D91G)

Ref Sequence

ENSEMBL: ENSMUSP00000046256 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000043931] [ENSMUST00000073791] [ENSMUST00000103035] [ENSMUST00000106533] [ENSMUST00000106537] [ENSMUST00000106539] [ENSMUST00000137754] [ENSMUST00000153983] [ENSMUST00000180072]

AlphaFold

Q9DCX2

Predicted Effect

probably damaging
Transcript: ENSMUST00000043931
AA Change: D91G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000046256
Gene: ENSMUSG00000034566
AA Change: D91G

Domain	Start	End	E-Value	Type
Pfam:Mt_ATP-synt_D	2	161	2.7e-77	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000073791
AA Change: D91G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000086072
Gene: ENSMUSG00000034566
AA Change: D91G

Domain	Start	End	E-Value	Type
Pfam:Mt_ATP-synt_D	2	161	2.7e-77	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000103035

SMART Domains

Protein: ENSMUSP00000099324
Gene: ENSMUSG00000016940

Domain	Start	End	E-Value	Type
low complexity region	8	43	N/A	INTRINSIC
low complexity region	46	71	N/A	INTRINSIC
BTB	72	175	3.45e-19	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000106533

SMART Domains

Protein: ENSMUSP00000102143
Gene: ENSMUSG00000016940

Domain	Start	End	E-Value	Type
low complexity region	8	43	N/A	INTRINSIC
low complexity region	46	71	N/A	INTRINSIC
BTB	72	175	3.45e-19	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000106537
AA Change: D91G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000102147
Gene: ENSMUSG00000034566
AA Change: D91G

Domain	Start	End	E-Value	Type
Pfam:Mt_ATP-synt_D	3	160	5.6e-71	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000106539

SMART Domains

Protein: ENSMUSP00000102149
Gene: ENSMUSG00000018858

Domain	Start	End	E-Value	Type
low complexity region	17	32	N/A	INTRINSIC
PDB:1J26\|A	63	142	8e-49	PDB
SCOP:d1gqea_	98	174	2e-5	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000123345

SMART Domains

Protein: ENSMUSP00000115862
Gene: ENSMUSG00000016940

Domain	Start	End	E-Value	Type
low complexity region	4	39	N/A	INTRINSIC
low complexity region	42	67	N/A	INTRINSIC
BTB	68	171	3.45e-19	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000137754
AA Change: D91G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000121240
Gene: ENSMUSG00000034566
AA Change: D91G

Domain	Start	End	E-Value	Type
Pfam:Mt_ATP-synt_D	2	138	1.8e-64	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000153983

SMART Domains

Protein: ENSMUSP00000116746
Gene: ENSMUSG00000018858

Domain	Start	End	E-Value	Type
low complexity region	17	32	N/A	INTRINSIC
Pfam:RF-1	66	204	1.9e-22	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000180072
AA Change: D91G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000137071
Gene: ENSMUSG00000034566
AA Change: D91G

Domain	Start	End	E-Value	Type
Pfam:Mt_ATP-synt_D	2	161	2.7e-77	PFAM

Coding Region Coverage

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

Validation Efficiency

98% (52/53)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. It is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, which comprises the proton channel. The F1 complex consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled in a ratio of 3 alpha, 3 beta, and a single representative of the other 3. The Fo seems to have nine subunits (a, b, c, d, e, f, g, F6 and 8). This gene encodes the d subunit of the Fo complex. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. In addition, three pseudogenes are located on chromosomes 9, 12 and 15. [provided by RefSeq, Jun 2010]

Allele List at MGI

Other mutations in this stock

Total: 56 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrv1	G	A	13: 81,651,163 (GRCm39)	T3044I	probably damaging	Het
Apbb1ip	C	T	2: 22,765,004 (GRCm39)	P562S	unknown	Het
Arhgap44	A	G	11: 64,912,860 (GRCm39)	M477T	possibly damaging	Het
Arhgef12	T	C	9: 42,882,354 (GRCm39)	T1497A	probably benign	Het
Atp6v0a4	A	G	6: 38,051,164 (GRCm39)	F405L	probably damaging	Het
Bicc1	T	A	10: 70,767,938 (GRCm39)	T893S	probably damaging	Het
Cacna1i	T	A	15: 80,257,835 (GRCm39)	C1122S	probably damaging	Het
Capn7	A	G	14: 31,080,636 (GRCm39)	E369G	probably damaging	Het
Cass4	T	A	2: 172,269,589 (GRCm39)	L557Q	probably damaging	Het
Cdh5	A	G	8: 104,839,672 (GRCm39)	I48V	probably benign	Het
Crisp3	T	C	17: 40,546,813 (GRCm39)	K35R	probably benign	Het
Csde1	G	A	3: 102,946,071 (GRCm39)	A22T	possibly damaging	Het
Ctse	T	C	1: 131,595,877 (GRCm39)	Y190H	probably damaging	Het
Cyp2d34	T	A	15: 82,504,988 (GRCm39)	D24V	possibly damaging	Het
D630045J12Rik	A	T	6: 38,167,658 (GRCm39)	Y981*	probably null	Het
Dclre1a	G	A	19: 56,533,382 (GRCm39)	T404I	possibly damaging	Het
Dmc1	T	C	15: 79,485,746 (GRCm39)	D23G	probably damaging	Het
Dnah8	C	T	17: 31,059,687 (GRCm39)	T4429M	probably damaging	Het
Esf1	A	T	2: 139,997,033 (GRCm39)		probably benign	Het
Fbxl12	C	A	9: 20,550,160 (GRCm39)	R165L	possibly damaging	Het
Fn3k	A	T	11: 121,330,137 (GRCm39)	M107L	probably benign	Het
Fxyd5	A	G	7: 30,740,854 (GRCm39)	L10P	probably damaging	Het
Gm21958	G	A	3: 54,621,633 (GRCm39)		probably benign	Het
Gm4922	C	T	10: 18,659,760 (GRCm39)	D321N	probably benign	Het
Gtf2h3	A	G	5: 124,734,050 (GRCm39)	*310W	probably null	Het
Hapln2	G	A	3: 87,930,851 (GRCm39)	T180I	possibly damaging	Het
Herc1	T	G	9: 66,395,232 (GRCm39)	V4189G	probably damaging	Het
Iqgap1	A	G	7: 80,379,875 (GRCm39)	V1166A	probably damaging	Het
Kcnk10	T	C	12: 98,401,358 (GRCm39)	N439S		Het
Klhl3	A	T	13: 58,260,968 (GRCm39)	M15K		Het
Klk1b26	A	T	7: 43,665,544 (GRCm39)	T151S	probably benign	Het
Krtap5-1	C	A	7: 141,850,199 (GRCm39)	C176F	unknown	Het
Krtap5-3	T	A	7: 141,755,693 (GRCm39)	C177S	unknown	Het
Lrrc37	T	C	11: 103,434,141 (GRCm39)	I3009M	unknown	Het
Map1a	T	C	2: 121,129,501 (GRCm39)	F180L	probably damaging	Het
Mfap5	T	C	6: 122,498,889 (GRCm39)		probably null	Het
Nckap1	T	A	2: 80,355,008 (GRCm39)	H638L	possibly damaging	Het
Optc	C	T	1: 133,832,810 (GRCm39)	V97M	probably benign	Het
Or5p78	T	A	7: 108,212,150 (GRCm39)	I212N	probably benign	Het
Or8b46	T	G	9: 38,450,644 (GRCm39)	M151R	noncoding transcript	Het
Piezo1	A	G	8: 123,228,298 (GRCm39)	Y330H		Het
Ppp1r12b	G	T	1: 134,803,886 (GRCm39)	N424K	probably benign	Het
Prdm5	T	A	6: 65,913,058 (GRCm39)	F580L	probably damaging	Het
Prr27	A	C	5: 87,994,171 (GRCm39)	K348N	possibly damaging	Het
Prr30	A	G	14: 101,435,822 (GRCm39)	Y247H	possibly damaging	Het
Rbks	A	T	5: 31,807,810 (GRCm39)		probably benign	Het
Sec24d	T	C	3: 123,099,535 (GRCm39)	V336A	possibly damaging	Het
Serac1	A	T	17: 6,101,033 (GRCm39)	L457H	probably damaging	Het
Serpina1f	A	G	12: 103,659,757 (GRCm39)	I175T	probably damaging	Het
Smr2l	T	C	5: 88,430,383 (GRCm39)	V93A	possibly damaging	Het
Sspo	A	T	6: 48,426,897 (GRCm39)	H242L	probably benign	Het
Tcaf2	A	T	6: 42,606,958 (GRCm39)	M332K	probably benign	Het
Tnrc6a	T	A	7: 122,769,294 (GRCm39)	N361K	possibly damaging	Het
Trim43b	G	T	9: 88,967,458 (GRCm39)	H393N	possibly damaging	Het
Ush2a	T	C	1: 188,176,838 (GRCm39)	L1334S	probably benign	Het
Usp35	T	C	7: 96,961,551 (GRCm39)	E625G	probably benign	Het

Other mutations in Atp5pd

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00792:Atp5pd	APN	11	115,308,675 (GRCm39)	splice site	probably null
IGL02680:Atp5pd	APN	11	115,306,840 (GRCm39)	critical splice donor site	probably null
IGL03212:Atp5pd	APN	11	115,306,597 (GRCm39)	missense	probably damaging	0.99
R0129:Atp5pd	UTSW	11	115,308,744 (GRCm39)	missense	probably damaging	0.96
R2566:Atp5pd	UTSW	11	115,306,864 (GRCm39)	splice site	probably null
R5283:Atp5pd	UTSW	11	115,306,611 (GRCm39)	missense	probably damaging	1.00
R8103:Atp5pd	UTSW	11	115,306,851 (GRCm39)	missense	possibly damaging	0.88
R8734:Atp5pd	UTSW	11	115,307,689 (GRCm39)	missense	possibly damaging	0.60
R9232:Atp5pd	UTSW	11	115,309,221 (GRCm39)	missense	probably benign	0.36

Predicted Primers

PCR Primer
(F):5'- GCTACTCAGAATTAAGGAAGCTGC -3'
(R):5'- GGGAGGCAAAGTGATCCTTG -3'

Sequencing Primer
(F):5'- GGTGGCACTTGCTTATAATCC -3'
(R):5'- AGGCAAAGTGATCCTTGCTATG -3'

Posted On

2020-07-28