Incidental Mutation 'R0129:Atp5pd'
ID 21581
Institutional Source Beutler Lab
Gene Symbol Atp5pd
Ensembl Gene ENSMUSG00000034566
Gene Name ATP synthase peripheral stalk subunit d
Synonyms 0610009D10Rik, Atp5h
MMRRC Submission 038414-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.881) question?
Stock # R0129 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 11
Chromosomal Location 115306517-115310775 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 115308744 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 47 (E47G)
Ref Sequence ENSEMBL: ENSMUSP00000121240 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000043931] [ENSMUST00000073791] [ENSMUST00000103035] [ENSMUST00000106533] [ENSMUST00000106537] [ENSMUST00000137754] [ENSMUST00000180072]
AlphaFold Q9DCX2
Predicted Effect probably benign
Transcript: ENSMUST00000043931
AA Change: E47G

PolyPhen 2 Score 0.431 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000046256
Gene: ENSMUSG00000034566
AA Change: E47G

DomainStartEndE-ValueType
Pfam:Mt_ATP-synt_D 2 161 2.7e-77 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000073791
AA Change: E47G

PolyPhen 2 Score 0.431 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000086072
Gene: ENSMUSG00000034566
AA Change: E47G

DomainStartEndE-ValueType
Pfam:Mt_ATP-synt_D 2 161 2.7e-77 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000103035
SMART Domains Protein: ENSMUSP00000099324
Gene: ENSMUSG00000016940

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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: ENSMUST00000106537
AA Change: E47G

PolyPhen 2 Score 0.431 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000102147
Gene: ENSMUSG00000034566
AA Change: E47G

DomainStartEndE-ValueType
Pfam:Mt_ATP-synt_D 3 160 5.6e-71 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000123345
SMART Domains Protein: ENSMUSP00000115862
Gene: ENSMUSG00000016940

DomainStartEndE-ValueType
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: E47G

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000121240
Gene: ENSMUSG00000034566
AA Change: E47G

DomainStartEndE-ValueType
Pfam:Mt_ATP-synt_D 2 138 1.8e-64 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000180072
AA Change: E47G

PolyPhen 2 Score 0.431 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000137071
Gene: ENSMUSG00000034566
AA Change: E47G

DomainStartEndE-ValueType
Pfam:Mt_ATP-synt_D 2 161 2.7e-77 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138779
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141474
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143856
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137563
Meta Mutation Damage Score 0.7162 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 97.7%
  • 10x: 92.2%
  • 20x: 74.4%
Validation Efficiency 100% (80/80)
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acaa2 A G 18: 74,920,265 (GRCm39) D31G probably damaging Het
Actr2 A G 11: 20,050,939 (GRCm39) probably benign Het
Adcy8 A G 15: 64,618,862 (GRCm39) C764R probably benign Het
Ago4 A C 4: 126,410,976 (GRCm39) F171C possibly damaging Het
Akt2 T C 7: 27,336,395 (GRCm39) F408S probably damaging Het
Ankrd24 T C 10: 81,474,163 (GRCm39) L26P probably damaging Het
Appl1 A T 14: 26,650,600 (GRCm39) M524K probably damaging Het
Arhgef11 T A 3: 87,635,370 (GRCm39) I922N probably damaging Het
Birc6 A G 17: 74,835,755 (GRCm39) D70G probably benign Het
Bola2 G A 7: 126,295,731 (GRCm39) V56M probably damaging Het
Cd300lg A G 11: 101,944,918 (GRCm39) probably null Het
Cdc42bpb A G 12: 111,271,393 (GRCm39) probably benign Het
Ceacam20 A G 7: 19,710,185 (GRCm39) N403S probably damaging Het
Cenpf T C 1: 189,391,847 (GRCm39) M662V probably benign Het
Chd3 C A 11: 69,239,327 (GRCm39) E1607* probably null Het
Chtf18 A T 17: 25,946,285 (GRCm39) Y9* probably null Het
Clta A G 4: 44,032,424 (GRCm39) N200S probably benign Het
Csmd1 G A 8: 16,129,956 (GRCm39) S1722F possibly damaging Het
Cyria C T 12: 12,412,350 (GRCm39) T204I probably damaging Het
Dennd4a T C 9: 64,800,576 (GRCm39) S905P probably damaging Het
Dhx57 T C 17: 80,546,343 (GRCm39) K1347R probably damaging Het
Dmc1 A T 15: 79,480,441 (GRCm39) probably benign Het
Dnhd1 G T 7: 105,370,131 (GRCm39) A4519S probably benign Het
Dnmbp A G 19: 43,838,466 (GRCm39) C1120R probably benign Het
Efs C T 14: 55,154,680 (GRCm39) A427T probably damaging Het
Erich6 T C 3: 58,531,799 (GRCm39) E399G probably damaging Het
Espl1 A G 15: 102,225,083 (GRCm39) T1431A probably benign Het
Fam184b A G 5: 45,690,120 (GRCm39) S830P probably damaging Het
Herc1 T A 9: 66,355,357 (GRCm39) C2203S probably damaging Het
Itpr1 G A 6: 108,326,637 (GRCm39) V120M probably damaging Het
Kcnh7 G A 2: 62,546,503 (GRCm39) T1026I probably benign Het
Kif1b A G 4: 149,345,658 (GRCm39) I394T probably benign Het
Ldlrap1 A C 4: 134,484,733 (GRCm39) V87G probably damaging Het
Lgals12 C T 19: 7,580,403 (GRCm39) V155I probably damaging Het
Limch1 A T 5: 67,116,933 (GRCm39) N116I probably damaging Het
Lonp2 C T 8: 87,361,518 (GRCm39) R232C probably damaging Het
Lrch1 C A 14: 75,073,186 (GRCm39) C151F probably benign Het
Lrig3 A G 10: 125,842,812 (GRCm39) Y579C probably damaging Het
Macf1 T C 4: 123,327,068 (GRCm39) S4808G probably damaging Het
Mapkap1 A T 2: 34,513,494 (GRCm39) K501N probably damaging Het
Mdc1 G T 17: 36,165,337 (GRCm39) R1523L probably benign Het
Mlh3 C T 12: 85,312,914 (GRCm39) probably benign Het
Mul1 T C 4: 138,165,032 (GRCm39) probably benign Het
Mybl2 G A 2: 162,901,411 (GRCm39) probably benign Het
Notch1 G C 2: 26,350,470 (GRCm39) H2223Q probably benign Het
Notch2 C A 3: 98,053,936 (GRCm39) L2200M probably benign Het
Odad3 G T 9: 21,904,848 (GRCm39) R313S probably damaging Het
Or10ak8 A T 4: 118,774,667 (GRCm39) probably null Het
Or12k5 G A 2: 36,895,057 (GRCm39) R190* probably null Het
Or5ae2 T A 7: 84,506,196 (GRCm39) F206L probably benign Het
Or8a1b T C 9: 37,623,236 (GRCm39) Y113C probably damaging Het
Plekhs1 T C 19: 56,465,722 (GRCm39) probably null Het
Ppm1h G A 10: 122,777,260 (GRCm39) G509R probably damaging Het
Ppp2r3c C T 12: 55,345,207 (GRCm39) E94K probably damaging Het
Ppp2r5e T A 12: 75,509,164 (GRCm39) I372F probably damaging Het
Ptprt G A 2: 162,119,990 (GRCm39) T159I probably benign Het
Rab20 A G 8: 11,504,415 (GRCm39) F95S probably damaging Het
Rfc3 A C 5: 151,574,616 (GRCm39) M1R probably null Het
Skp2 A G 15: 9,125,280 (GRCm39) S100P probably damaging Het
Smg5 T C 3: 88,256,540 (GRCm39) S269P probably benign Het
Sspo A T 6: 48,432,352 (GRCm39) T684S probably benign Het
Syt3 A G 7: 44,042,782 (GRCm39) K355E probably damaging Het
Tcp10a A T 17: 7,610,903 (GRCm39) K355N probably damaging Het
Tnrc18 A G 5: 142,750,800 (GRCm39) probably benign Het
Tsfm A G 10: 126,866,339 (GRCm39) L74P probably benign Het
Ttn G C 2: 76,564,609 (GRCm39) N28509K probably damaging Het
Ube2l6 G A 2: 84,629,252 (GRCm39) M1I probably null Het
Vmn2r80 T A 10: 79,005,330 (GRCm39) H322Q probably damaging Het
Zkscan8 A T 13: 21,706,441 (GRCm39) S212T probably benign Het
Other mutations in Atp5pd
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
R8270:Atp5pd UTSW 11 115,307,698 (GRCm39) missense probably damaging 1.00
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'- GCCAAGTGACTGAACCCTGATTCTC -3'
(R):5'- CCATCCTTGATGCTGAACCTGGAAG -3'

Sequencing Primer
(F):5'- GAACCCTGATTCTCTACAGGTG -3'
(R):5'- cccctttacccacttagcc -3'
Posted On 2013-04-11