Incidental Mutation 'R1015:Atp6v1d'
ID 96196
Institutional Source Beutler Lab
Gene Symbol Atp6v1d
Ensembl Gene ENSMUSG00000021114
Gene Name ATPase, H+ transporting, lysosomal V1 subunit D
Synonyms 1110004P10Rik, lysosomal 34kDa, Atp6m, Vma8, VATD
MMRRC Submission 039119-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1015 (G1)
Quality Score 225
Status Not validated
Chromosome 12
Chromosomal Location 78889756-78908810 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 78896543 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 108 (V108A)
Ref Sequence ENSEMBL: ENSMUSP00000021536 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021536]
AlphaFold P57746
Predicted Effect possibly damaging
Transcript: ENSMUST00000021536
AA Change: V108A

PolyPhen 2 Score 0.698 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000021536
Gene: ENSMUSG00000021114
AA Change: V108A

DomainStartEndE-ValueType
Pfam:ATP-synt_D 15 207 1.2e-76 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000219316
Predicted Effect noncoding transcript
Transcript: ENSMUST00000219377
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 96.1%
  • 20x: 92.4%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c", and d. Additional isoforms of many of the V1 and V0 subunit proteins are encoded by multiple genes or alternatively spliced transcript variants. This gene encodes the V1 domain D subunit protein. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 43 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ap3d1 A G 10: 80,552,323 (GRCm39) V615A probably damaging Het
B3gnt6 C A 7: 97,843,802 (GRCm39) V53L probably benign Het
C8b A G 4: 104,644,157 (GRCm39) K275E probably benign Het
Cage1 T A 13: 38,200,451 (GRCm39) N683I possibly damaging Het
Celsr3 T C 9: 108,710,375 (GRCm39) V1535A probably benign Het
Cep120 C T 18: 53,836,193 (GRCm39) probably null Het
Cep135 T C 5: 76,788,844 (GRCm39) probably null Het
Chd9 T A 8: 91,659,206 (GRCm39) H55Q probably damaging Het
Dmxl2 G A 9: 54,275,049 (GRCm39) T2915I probably benign Het
Eps8l1 A T 7: 4,472,932 (GRCm39) D118V probably damaging Het
Ezhip GTCATCATCATCATC GTCATCATCATCATCATC X: 5,994,645 (GRCm39) probably benign Het
Galnt2 C T 8: 125,063,356 (GRCm39) H359Y probably benign Het
Kdm5d T C Y: 941,687 (GRCm39) V1296A possibly damaging Het
Kif27 T A 13: 58,468,029 (GRCm39) K849N probably damaging Het
Kif5c T A 2: 49,634,377 (GRCm39) D736E probably benign Het
Krt18 T C 15: 101,939,735 (GRCm39) I311T probably benign Het
Lamc2 A T 1: 153,041,945 (GRCm39) V63D possibly damaging Het
Lmbrd1 T A 1: 24,770,959 (GRCm39) C295* probably null Het
Lrrc37 T C 11: 103,436,622 (GRCm39) H754R probably benign Het
Map3k14 T A 11: 103,116,126 (GRCm39) Q767H probably damaging Het
Mapkapk5 T C 5: 121,671,425 (GRCm39) K203E probably benign Het
Mcc C A 18: 44,857,736 (GRCm39) L126F probably benign Het
Mib1 T A 18: 10,726,409 (GRCm39) H35Q probably damaging Het
Myo16 A G 8: 10,440,183 (GRCm39) N412D probably benign Het
Ndst2 T C 14: 20,780,132 (GRCm39) Y36C probably damaging Het
Nfix G A 8: 85,453,155 (GRCm39) R300C probably damaging Het
Nwd2 T C 5: 63,964,154 (GRCm39) I1246T probably damaging Het
Or5d47 T C 2: 87,804,431 (GRCm39) T193A probably benign Het
Or5m9 T C 2: 85,877,426 (GRCm39) I200T possibly damaging Het
Patl1 T C 19: 11,897,737 (GRCm39) V108A probably benign Het
Pdzd2 T C 15: 12,374,594 (GRCm39) E1847G probably damaging Het
Pla2g2f C T 4: 138,481,579 (GRCm39) V57I probably benign Het
Prag1 T C 8: 36,613,697 (GRCm39) V1083A probably damaging Het
Slc3a2 C T 19: 8,685,319 (GRCm39) W227* probably null Het
Snx9 A G 17: 5,970,402 (GRCm39) I379M probably benign Het
Spata31e4 T G 13: 50,855,664 (GRCm39) V434G possibly damaging Het
Tacc2 A G 7: 130,225,795 (GRCm39) K846E probably benign Het
Taf4b T A 18: 14,946,155 (GRCm39) V326E probably damaging Het
Tnrc6c C T 11: 117,612,748 (GRCm39) S462F possibly damaging Het
Trim66 C T 7: 109,054,440 (GRCm39) V1257I probably damaging Het
Urb2 T C 8: 124,756,173 (GRCm39) Y627H probably damaging Het
Usp53 A G 3: 122,727,408 (GRCm39) L1058P probably benign Het
Wdr24 A G 17: 26,047,212 (GRCm39) S702G probably benign Het
Other mutations in Atp6v1d
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00709:Atp6v1d APN 12 78,896,528 (GRCm39) missense probably benign
IGL02319:Atp6v1d APN 12 78,908,230 (GRCm39) missense probably damaging 1.00
IGL03037:Atp6v1d APN 12 78,904,122 (GRCm39) unclassified probably benign
IGL03040:Atp6v1d APN 12 78,904,122 (GRCm39) unclassified probably benign
R1203:Atp6v1d UTSW 12 78,908,214 (GRCm39) missense possibly damaging 0.88
R5470:Atp6v1d UTSW 12 78,892,058 (GRCm39) missense probably benign 0.42
R8479:Atp6v1d UTSW 12 78,896,520 (GRCm39) missense probably benign
R9252:Atp6v1d UTSW 12 78,904,023 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- CCCAGCGTTCAGAACGTGTCATAG -3'
(R):5'- GCACCCTTTTAAAGAGGCAGAGACC -3'

Sequencing Primer
(F):5'- gttcagaacgtgtcatagaacatag -3'
(R):5'- gaggcagagaccaactgag -3'
Posted On 2014-01-05