Incidental Mutation 'R5569:Atpaf2'
ID 435550
Institutional Source Beutler Lab
Gene Symbol Atpaf2
Ensembl Gene ENSMUSG00000042709
Gene Name ATP synthase mitochondrial F1 complex assembly factor 2
Synonyms ATP12, ATP12p
MMRRC Submission 043126-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5569 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 60291452-60309283 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 60307706 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tryptophan to Arginine at position 11 (W11R)
Ref Sequence ENSEMBL: ENSMUSP00000135761 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070681] [ENSMUST00000108721] [ENSMUST00000139477] [ENSMUST00000145532]
AlphaFold Q91YY4
Predicted Effect probably benign
Transcript: ENSMUST00000070681
SMART Domains Protein: ENSMUSP00000064926
Gene: ENSMUSG00000018415

DomainStartEndE-ValueType
low complexity region 8 20 N/A INTRINSIC
Pfam:Vac_ImportDeg 38 206 3.4e-66 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000108721
AA Change: W11R

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000104361
Gene: ENSMUSG00000042709
AA Change: W11R

DomainStartEndE-ValueType
low complexity region 16 29 N/A INTRINSIC
Pfam:ATP12 56 177 7.9e-43 PFAM
low complexity region 227 237 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138696
Predicted Effect probably benign
Transcript: ENSMUST00000139477
SMART Domains Protein: ENSMUSP00000135441
Gene: ENSMUSG00000018415

DomainStartEndE-ValueType
low complexity region 8 20 N/A INTRINSIC
Pfam:Vac_ImportDeg 37 209 3.7e-70 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141987
Predicted Effect probably damaging
Transcript: ENSMUST00000145532
AA Change: W11R

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000135761
Gene: ENSMUSG00000042709
AA Change: W11R

DomainStartEndE-ValueType
low complexity region 16 29 N/A INTRINSIC
Pfam:ATP12 56 154 9.3e-34 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154387
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156966
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.3%
  • 20x: 94.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an assembly factor for the F(1) component of the mitochondrial ATP synthase. This protein binds specifically to the F1 alpha subunit and is thought to prevent this subunit from forming nonproductive homooligomers during enzyme assembly. This gene is located within the Smith-Magenis syndrome region on chromosome 17. An alternatively spliced transcript variant has been described, but its biological validity has not been determined. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acad10 A G 5: 121,764,143 (GRCm39) S929P probably damaging Het
Ackr3 A G 1: 90,142,563 (GRCm39) T341A probably benign Het
Acox3 A G 5: 35,760,377 (GRCm39) Y431C probably damaging Het
Adamtsl2 G A 2: 26,992,845 (GRCm39) V653M probably damaging Het
Anks6 T C 4: 47,045,007 (GRCm39) K300E probably damaging Het
Ap5z1 A T 5: 142,460,206 (GRCm39) D495V probably damaging Het
Atm A T 9: 53,427,750 (GRCm39) Y453* probably null Het
Bhmt1b A C 18: 87,775,392 (GRCm39) Y305S probably damaging Het
Capn1 T A 19: 6,063,690 (GRCm39) T129S probably benign Het
Catspere2 A T 1: 177,939,162 (GRCm39) K678N possibly damaging Het
Cdh17 A G 4: 11,816,990 (GRCm39) I800M probably damaging Het
Cfap206 C T 4: 34,724,892 (GRCm39) R69Q probably damaging Het
Cp T C 3: 20,033,041 (GRCm39) Y623H probably damaging Het
Dcaf5 A T 12: 80,386,975 (GRCm39) Y384N probably damaging Het
Dhx9 A T 1: 153,342,838 (GRCm39) C555S possibly damaging Het
Dlg2 A G 7: 91,617,388 (GRCm39) T317A probably benign Het
Dsp C T 13: 38,376,628 (GRCm39) T1471I probably benign Het
Ebf1 A G 11: 44,883,228 (GRCm39) M489V possibly damaging Het
Enpp3 T C 10: 24,654,719 (GRCm39) D230G probably damaging Het
Eri3 T C 4: 117,506,553 (GRCm39) M294T possibly damaging Het
Fat1 T A 8: 45,492,873 (GRCm39) V3842E probably damaging Het
Fermt1 T A 2: 132,757,123 (GRCm39) Y569F possibly damaging Het
Fscn1 A G 5: 142,946,799 (GRCm39) D199G probably benign Het
Glce A G 9: 61,977,485 (GRCm39) V133A probably benign Het
Gtf2h3 C T 5: 124,722,360 (GRCm39) T121I probably benign Het
Hk1 A G 10: 62,122,220 (GRCm39) S520P probably benign Het
Ighv12-3 A G 12: 114,330,555 (GRCm39) V7A probably benign Het
Ighv6-7 C A 12: 114,419,476 (GRCm39) A43S probably damaging Het
Inf2 A G 12: 112,568,113 (GRCm39) I222V possibly damaging Het
Kmo T A 1: 175,482,688 (GRCm39) N337K probably benign Het
Mcf2l C T 8: 13,055,481 (GRCm39) R611W probably damaging Het
Mipep A T 14: 61,040,383 (GRCm39) H301L probably damaging Het
Mprip A T 11: 59,651,789 (GRCm39) E1831V probably damaging Het
Mrgpra3 T C 7: 47,239,759 (GRCm39) T56A probably benign Het
Mtmr14 G A 6: 113,217,246 (GRCm39) V53I probably damaging Het
Mycbp2 A T 14: 103,372,679 (GRCm39) W4056R probably damaging Het
Myl2 A T 5: 122,244,783 (GRCm39) D151V possibly damaging Het
Myo5c A T 9: 75,180,792 (GRCm39) D727V probably damaging Het
Or10s1 A G 9: 39,985,593 (GRCm39) M1V probably null Het
Or1e22 A T 11: 73,377,518 (GRCm39) I44N probably damaging Het
Or2ag12 A T 7: 106,277,690 (GRCm39) M1K probably null Het
Or56b1b T A 7: 108,164,772 (GRCm39) M77L probably benign Het
Or9s18 A G 13: 65,300,793 (GRCm39) T252A possibly damaging Het
Pabpc1l C T 2: 163,885,474 (GRCm39) T409I probably benign Het
Pcgf1 C T 6: 83,056,686 (GRCm39) R81* probably null Het
Pcgf2 A G 11: 97,583,193 (GRCm39) probably null Het
Phf14 T A 6: 11,934,015 (GRCm39) N292K probably damaging Het
Plin4 T C 17: 56,409,147 (GRCm39) T1358A probably benign Het
Pomgnt1 T C 4: 116,013,164 (GRCm39) S423P probably damaging Het
Prep G A 10: 44,973,533 (GRCm39) V214I probably benign Het
Ptger1 T C 8: 84,394,961 (GRCm39) probably null Het
Pus7 C T 5: 23,953,832 (GRCm39) G415D probably benign Het
Rbm44 C T 1: 91,096,460 (GRCm39) P940S probably damaging Het
Ripor1 A T 8: 106,344,147 (GRCm39) D427V probably damaging Het
Rp1 A G 1: 4,415,460 (GRCm39) I1884T probably damaging Het
Rpl15-ps6 T C 15: 52,341,624 (GRCm39) noncoding transcript Het
Serinc2 T C 4: 130,172,272 (GRCm39) R7G probably benign Het
Serpina6 A C 12: 103,620,719 (GRCm39) F10C possibly damaging Het
Skint5 T A 4: 113,545,903 (GRCm39) probably null Het
Slc66a3 T A 12: 17,045,629 (GRCm39) I114F possibly damaging Het
Slc6a4 A T 11: 76,914,081 (GRCm39) I544F possibly damaging Het
Spdye4b T C 5: 143,188,176 (GRCm39) M223T probably benign Het
Tbc1d17 A T 7: 44,497,755 (GRCm39) V39D probably damaging Het
Thbs3 T A 3: 89,126,770 (GRCm39) Y295N probably damaging Het
Themis G A 10: 28,657,887 (GRCm39) E152K possibly damaging Het
Tmem131 A T 1: 36,838,419 (GRCm39) I1502N probably benign Het
Tmem43 T A 6: 91,454,336 (GRCm39) M41K probably benign Het
Tmprss6 A C 15: 78,324,503 (GRCm39) W771G probably damaging Het
Trp53tg5 T C 2: 164,313,256 (GRCm39) T140A probably benign Het
Uchl1 A G 5: 66,844,216 (GRCm39) E206G probably damaging Het
Vash2 A G 1: 190,692,488 (GRCm39) V229A possibly damaging Het
Vmn1r192 C A 13: 22,371,384 (GRCm39) A279S possibly damaging Het
Vmn1r32 T C 6: 66,530,156 (GRCm39) R207G probably damaging Het
Vmn2r14 T A 5: 109,368,261 (GRCm39) M244L probably benign Het
Vwa5b2 T A 16: 20,414,089 (GRCm39) H236Q probably damaging Het
Zfp652 C T 11: 95,640,116 (GRCm39) P14S probably benign Het
Zfp668 G A 7: 127,466,995 (GRCm39) R194* probably null Het
Zgrf1 G T 3: 127,354,674 (GRCm39) V98L probably benign Het
Other mutations in Atpaf2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00479:Atpaf2 APN 11 60,300,410 (GRCm39) critical splice donor site probably null
IGL00504:Atpaf2 APN 11 60,296,629 (GRCm39) missense probably damaging 1.00
IGL01941:Atpaf2 APN 11 60,294,724 (GRCm39) missense probably benign 0.01
IGL02960:Atpaf2 APN 11 60,296,650 (GRCm39) missense probably damaging 0.99
IGL03082:Atpaf2 APN 11 60,294,670 (GRCm39) missense probably damaging 0.99
R1103:Atpaf2 UTSW 11 60,294,776 (GRCm39) missense probably benign 0.06
R4782:Atpaf2 UTSW 11 60,295,238 (GRCm39) missense probably damaging 0.99
R5180:Atpaf2 UTSW 11 60,296,695 (GRCm39) missense possibly damaging 0.69
R5947:Atpaf2 UTSW 11 60,296,708 (GRCm39) splice site probably benign
R6388:Atpaf2 UTSW 11 60,307,833 (GRCm39) start gained probably benign
R8206:Atpaf2 UTSW 11 60,295,304 (GRCm39) missense probably damaging 0.97
R8359:Atpaf2 UTSW 11 60,298,129 (GRCm39) missense probably damaging 1.00
Z1176:Atpaf2 UTSW 11 60,307,601 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- CGTCAGAAACCTTCCTCCAG -3'
(R):5'- GCGAGCACGTTTATGATGCTG -3'

Sequencing Primer
(F):5'- ACCTTCCTCCAGGTGAGC -3'
(R):5'- AGCACGTTTATGATGCTGATTGAC -3'
Posted On 2016-10-24