Incidental Mutation 'R2404:Atp9a'
ID 248849
Institutional Source Beutler Lab
Gene Symbol Atp9a
Ensembl Gene ENSMUSG00000027546
Gene Name ATPase, class II, type 9A
Synonyms IIa, Class II
MMRRC Submission 040370-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2404 (G1)
Quality Score 115
Status Validated
Chromosome 2
Chromosomal Location 168476358-168584290 bp(-) (GRCm39)
Type of Mutation critical splice acceptor site
DNA Base Change (assembly) T to A at 168517283 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000136793 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029060] [ENSMUST00000029060] [ENSMUST00000109175] [ENSMUST00000109175] [ENSMUST00000109176] [ENSMUST00000109176] [ENSMUST00000109177] [ENSMUST00000109177] [ENSMUST00000178504] [ENSMUST00000178504] [ENSMUST00000178504] [ENSMUST00000178504]
AlphaFold O70228
Predicted Effect probably null
Transcript: ENSMUST00000029060
SMART Domains Protein: ENSMUSP00000029060
Gene: ENSMUSG00000027546

DomainStartEndE-ValueType
low complexity region 73 88 N/A INTRINSIC
Pfam:E1-E2_ATPase 108 368 7.4e-21 PFAM
Pfam:Hydrolase 385 797 1.5e-19 PFAM
Pfam:HAD 388 794 1.1e-14 PFAM
Pfam:Hydrolase_like2 464 579 3.4e-7 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000029060
SMART Domains Protein: ENSMUSP00000029060
Gene: ENSMUSG00000027546

DomainStartEndE-ValueType
low complexity region 73 88 N/A INTRINSIC
Pfam:E1-E2_ATPase 108 368 7.4e-21 PFAM
Pfam:Hydrolase 385 797 1.5e-19 PFAM
Pfam:HAD 388 794 1.1e-14 PFAM
Pfam:Hydrolase_like2 464 579 3.4e-7 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000109175
SMART Domains Protein: ENSMUSP00000104804
Gene: ENSMUSG00000027546

DomainStartEndE-ValueType
low complexity region 57 72 N/A INTRINSIC
Pfam:E1-E2_ATPase 92 352 7.2e-21 PFAM
Pfam:Hydrolase 369 781 1.4e-19 PFAM
Pfam:HAD 372 778 1.1e-14 PFAM
Pfam:Hydrolase_like2 448 563 3.4e-7 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000109175
SMART Domains Protein: ENSMUSP00000104804
Gene: ENSMUSG00000027546

DomainStartEndE-ValueType
low complexity region 57 72 N/A INTRINSIC
Pfam:E1-E2_ATPase 92 352 7.2e-21 PFAM
Pfam:Hydrolase 369 781 1.4e-19 PFAM
Pfam:HAD 372 778 1.1e-14 PFAM
Pfam:Hydrolase_like2 448 563 3.4e-7 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000109176
SMART Domains Protein: ENSMUSP00000104805
Gene: ENSMUSG00000027546

DomainStartEndE-ValueType
low complexity region 18 57 N/A INTRINSIC
Pfam:PhoLip_ATPase_N 97 163 1.9e-20 PFAM
Pfam:E1-E2_ATPase 166 418 5.8e-13 PFAM
Pfam:Hydrolase 443 855 2.8e-13 PFAM
Pfam:HAD 446 852 2.4e-14 PFAM
Pfam:Cation_ATPase 522 635 1.5e-6 PFAM
Pfam:PhoLip_ATPase_C 869 1098 1.7e-53 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000109176
SMART Domains Protein: ENSMUSP00000104805
Gene: ENSMUSG00000027546

DomainStartEndE-ValueType
low complexity region 18 57 N/A INTRINSIC
Pfam:PhoLip_ATPase_N 97 163 1.9e-20 PFAM
Pfam:E1-E2_ATPase 166 418 5.8e-13 PFAM
Pfam:Hydrolase 443 855 2.8e-13 PFAM
Pfam:HAD 446 852 2.4e-14 PFAM
Pfam:Cation_ATPase 522 635 1.5e-6 PFAM
Pfam:PhoLip_ATPase_C 869 1098 1.7e-53 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000109177
SMART Domains Protein: ENSMUSP00000104806
Gene: ENSMUSG00000027546

DomainStartEndE-ValueType
low complexity region 55 70 N/A INTRINSIC
Pfam:E1-E2_ATPase 90 350 7.2e-21 PFAM
Pfam:Hydrolase 367 779 1.4e-19 PFAM
Pfam:HAD 370 776 1.1e-14 PFAM
Pfam:Hydrolase_like2 446 561 3.3e-7 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000109177
SMART Domains Protein: ENSMUSP00000104806
Gene: ENSMUSG00000027546

DomainStartEndE-ValueType
low complexity region 55 70 N/A INTRINSIC
Pfam:E1-E2_ATPase 90 350 7.2e-21 PFAM
Pfam:Hydrolase 367 779 1.4e-19 PFAM
Pfam:HAD 370 776 1.1e-14 PFAM
Pfam:Hydrolase_like2 446 561 3.3e-7 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140188
Predicted Effect probably null
Transcript: ENSMUST00000178504
SMART Domains Protein: ENSMUSP00000136793
Gene: ENSMUSG00000027546

DomainStartEndE-ValueType
low complexity region 73 88 N/A INTRINSIC
Pfam:E1-E2_ATPase 108 368 7.4e-21 PFAM
Pfam:Hydrolase 385 797 1.5e-19 PFAM
Pfam:HAD 388 794 1.1e-14 PFAM
Pfam:Hydrolase_like2 464 579 3.4e-7 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000178504
SMART Domains Protein: ENSMUSP00000136793
Gene: ENSMUSG00000027546

DomainStartEndE-ValueType
low complexity region 73 88 N/A INTRINSIC
Pfam:E1-E2_ATPase 108 368 7.4e-21 PFAM
Pfam:Hydrolase 385 797 1.5e-19 PFAM
Pfam:HAD 388 794 1.1e-14 PFAM
Pfam:Hydrolase_like2 464 579 3.4e-7 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000178504
SMART Domains Protein: ENSMUSP00000136793
Gene: ENSMUSG00000027546

DomainStartEndE-ValueType
low complexity region 73 88 N/A INTRINSIC
Pfam:E1-E2_ATPase 108 368 7.4e-21 PFAM
Pfam:Hydrolase 385 797 1.5e-19 PFAM
Pfam:HAD 388 794 1.1e-14 PFAM
Pfam:Hydrolase_like2 464 579 3.4e-7 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000178504
SMART Domains Protein: ENSMUSP00000136793
Gene: ENSMUSG00000027546

DomainStartEndE-ValueType
low complexity region 73 88 N/A INTRINSIC
Pfam:E1-E2_ATPase 108 368 7.4e-21 PFAM
Pfam:Hydrolase 385 797 1.5e-19 PFAM
Pfam:HAD 388 794 1.1e-14 PFAM
Pfam:Hydrolase_like2 464 579 3.4e-7 PFAM
Meta Mutation Damage Score 0.9498 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.2%
Validation Efficiency 98% (52/53)
Allele List at MGI
Other mutations in this stock
Total: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933402N03Rik T C 7: 130,740,923 (GRCm39) T98A possibly damaging Het
Aifm2 A G 10: 61,563,974 (GRCm39) I161V probably benign Het
Arhgef26 T C 3: 62,336,336 (GRCm39) M625T possibly damaging Het
Avpr1a T C 10: 122,285,115 (GRCm39) F136L possibly damaging Het
Bcas3 T C 11: 85,245,715 (GRCm39) probably benign Het
Bnc1 A T 7: 81,618,463 (GRCm39) H867Q probably benign Het
Cdh12 C T 15: 21,537,720 (GRCm39) T407I probably damaging Het
Chd5 C T 4: 152,451,791 (GRCm39) T701M probably damaging Het
Dhx57 A G 17: 80,561,733 (GRCm39) V927A probably damaging Het
Dnah2 A G 11: 69,328,047 (GRCm39) F3353L probably damaging Het
Ect2 G A 3: 27,185,999 (GRCm39) P495S probably benign Het
Egfl7 G A 2: 26,479,162 (GRCm39) E25K possibly damaging Het
Gm5117 T C 8: 32,227,306 (GRCm39) noncoding transcript Het
Hbs1l A T 10: 21,171,946 (GRCm39) probably benign Het
Insrr C T 3: 87,709,974 (GRCm39) T309I possibly damaging Het
Kalrn C T 16: 33,810,180 (GRCm39) D2525N possibly damaging Het
Kif12 A C 4: 63,088,790 (GRCm39) L170R probably damaging Het
Krt90 A G 15: 101,463,105 (GRCm39) probably null Het
Mcu A G 10: 59,303,526 (GRCm39) S104P probably damaging Het
Mical3 G A 6: 120,936,789 (GRCm39) P374S probably benign Het
Ncam2 A T 16: 81,287,128 (GRCm39) probably benign Het
Or12e9 A G 2: 87,202,568 (GRCm39) I231V probably benign Het
Or2t47 A T 11: 58,442,546 (GRCm39) I173N probably damaging Het
Or2w1b T C 13: 21,300,012 (GRCm39) L50P probably damaging Het
Or5k17 G A 16: 58,745,998 (GRCm39) S312L probably benign Het
Otud7a A G 7: 63,346,899 (GRCm39) S158G probably benign Het
Phlpp1 C T 1: 106,100,569 (GRCm39) T279M probably benign Het
Pkhd1l1 T G 15: 44,414,216 (GRCm39) W2828G probably damaging Het
Pnma8a A T 7: 16,694,316 (GRCm39) N57I probably damaging Het
Ppp4r4 A G 12: 103,547,749 (GRCm39) probably null Het
Ptprq T C 10: 107,522,460 (GRCm39) Y531C probably damaging Het
Rai1 A G 11: 60,080,750 (GRCm39) T1605A probably benign Het
Satb2 T C 1: 56,987,267 (GRCm39) Y106C probably damaging Het
Sgms1 G A 19: 32,137,072 (GRCm39) R165* probably null Het
Slc19a3 T A 1: 83,000,756 (GRCm39) H87L probably benign Het
Slc4a7 G T 14: 14,733,733 (GRCm38) V54L probably damaging Het
Sp110 A C 1: 85,505,050 (GRCm39) F434C probably benign Het
Spen T C 4: 141,205,216 (GRCm39) N1137S unknown Het
Spice1 T C 16: 44,186,989 (GRCm39) I162T probably benign Het
Spmip1 G A 6: 29,473,390 (GRCm39) R173Q probably benign Het
Sqor A T 2: 122,649,943 (GRCm39) T396S probably benign Het
Tshz3 A T 7: 36,469,805 (GRCm39) Q598L probably damaging Het
Ttc13 C T 8: 125,405,736 (GRCm39) probably benign Het
Ubxn2a T C 12: 4,933,851 (GRCm39) T187A probably benign Het
Usp28 T C 9: 48,948,558 (GRCm39) probably null Het
Zc3h12a T C 4: 125,013,316 (GRCm39) Y516C probably damaging Het
Zfp616 A C 11: 73,975,682 (GRCm39) K650N probably damaging Het
Other mutations in Atp9a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00965:Atp9a APN 2 168,482,600 (GRCm39) missense probably benign 0.24
IGL01594:Atp9a APN 2 168,532,932 (GRCm39) missense probably damaging 1.00
IGL01911:Atp9a APN 2 168,495,481 (GRCm39) missense probably damaging 1.00
IGL02606:Atp9a APN 2 168,494,588 (GRCm39) missense probably damaging 1.00
IGL02639:Atp9a APN 2 168,491,540 (GRCm39) missense probably damaging 1.00
IGL03011:Atp9a APN 2 168,494,552 (GRCm39) missense probably damaging 1.00
IGL03294:Atp9a APN 2 168,531,225 (GRCm39) missense probably benign 0.04
IGL03310:Atp9a APN 2 168,481,879 (GRCm39) missense probably damaging 1.00
R0114:Atp9a UTSW 2 168,552,776 (GRCm39) nonsense probably null
R0194:Atp9a UTSW 2 168,485,805 (GRCm39) missense probably benign 0.00
R0427:Atp9a UTSW 2 168,482,617 (GRCm39) critical splice acceptor site probably null
R0508:Atp9a UTSW 2 168,491,446 (GRCm39) splice site probably null
R1611:Atp9a UTSW 2 168,515,489 (GRCm39) missense probably damaging 1.00
R2120:Atp9a UTSW 2 168,495,457 (GRCm39) missense probably damaging 1.00
R2330:Atp9a UTSW 2 168,481,849 (GRCm39) missense probably benign 0.01
R2348:Atp9a UTSW 2 168,552,746 (GRCm39) splice site probably benign
R2881:Atp9a UTSW 2 168,548,134 (GRCm39) missense probably damaging 1.00
R2882:Atp9a UTSW 2 168,548,134 (GRCm39) missense probably damaging 1.00
R4029:Atp9a UTSW 2 168,531,245 (GRCm39) missense probably damaging 1.00
R4371:Atp9a UTSW 2 168,491,535 (GRCm39) missense probably damaging 1.00
R4411:Atp9a UTSW 2 168,503,853 (GRCm39) missense probably damaging 1.00
R4446:Atp9a UTSW 2 168,523,917 (GRCm39) missense possibly damaging 0.75
R4583:Atp9a UTSW 2 168,531,280 (GRCm39) splice site probably null
R4626:Atp9a UTSW 2 168,481,863 (GRCm39) missense probably damaging 1.00
R4661:Atp9a UTSW 2 168,479,592 (GRCm39) missense possibly damaging 0.52
R4679:Atp9a UTSW 2 168,503,884 (GRCm39) missense possibly damaging 0.95
R4738:Atp9a UTSW 2 168,510,101 (GRCm39) missense probably benign
R5191:Atp9a UTSW 2 168,503,983 (GRCm39) missense possibly damaging 0.51
R5216:Atp9a UTSW 2 168,516,808 (GRCm39) missense probably benign 0.38
R5280:Atp9a UTSW 2 168,481,908 (GRCm39) missense possibly damaging 0.66
R5509:Atp9a UTSW 2 168,481,857 (GRCm39) missense probably damaging 1.00
R5798:Atp9a UTSW 2 168,532,884 (GRCm39) critical splice donor site probably null
R5807:Atp9a UTSW 2 168,495,454 (GRCm39) missense probably damaging 0.98
R5926:Atp9a UTSW 2 168,548,191 (GRCm39) missense probably damaging 1.00
R6046:Atp9a UTSW 2 168,476,790 (GRCm39) missense probably benign 0.42
R6244:Atp9a UTSW 2 168,531,272 (GRCm39) critical splice acceptor site probably null
R6307:Atp9a UTSW 2 168,510,090 (GRCm39) missense probably benign 0.02
R6345:Atp9a UTSW 2 168,518,093 (GRCm39) missense probably damaging 0.99
R6442:Atp9a UTSW 2 168,491,481 (GRCm39) missense probably benign 0.01
R6459:Atp9a UTSW 2 168,509,933 (GRCm39) missense probably damaging 1.00
R6769:Atp9a UTSW 2 168,516,820 (GRCm39) missense probably damaging 1.00
R6771:Atp9a UTSW 2 168,516,820 (GRCm39) missense probably damaging 1.00
R6841:Atp9a UTSW 2 168,496,140 (GRCm39) missense possibly damaging 0.87
R7271:Atp9a UTSW 2 168,576,047 (GRCm39)
R7422:Atp9a UTSW 2 168,490,513 (GRCm39) missense probably damaging 1.00
R7490:Atp9a UTSW 2 168,517,272 (GRCm39) missense probably benign 0.00
R7827:Atp9a UTSW 2 168,547,114 (GRCm39) missense probably benign 0.03
R7833:Atp9a UTSW 2 168,516,777 (GRCm39) missense probably benign 0.02
R7854:Atp9a UTSW 2 168,490,523 (GRCm39) missense probably benign 0.02
R7963:Atp9a UTSW 2 168,516,732 (GRCm39) missense probably damaging 1.00
R8331:Atp9a UTSW 2 168,517,217 (GRCm39) missense probably benign 0.01
R8904:Atp9a UTSW 2 168,547,097 (GRCm39) missense probably benign 0.05
R8914:Atp9a UTSW 2 168,479,420 (GRCm39) critical splice donor site probably null
R9129:Atp9a UTSW 2 168,517,205 (GRCm39) missense probably benign 0.00
R9149:Atp9a UTSW 2 168,575,988 (GRCm39) intron probably benign
R9171:Atp9a UTSW 2 168,485,780 (GRCm39) critical splice donor site probably null
R9189:Atp9a UTSW 2 168,518,060 (GRCm39) critical splice donor site probably null
R9299:Atp9a UTSW 2 168,554,666 (GRCm39) start codon destroyed probably null
R9303:Atp9a UTSW 2 168,517,163 (GRCm39) missense probably benign 0.13
R9305:Atp9a UTSW 2 168,517,163 (GRCm39) missense probably benign 0.13
Predicted Primers PCR Primer
(F):5'- AGCTCACCTGATAGGAATGATG -3'
(R):5'- CGATTTGGCACACTTGTTGCG -3'

Sequencing Primer
(F):5'- CCTGATAGGAATGATGTTGGAAAAC -3'
(R):5'- ACACTTGTTGCGTTTTGAGACAC -3'
Posted On 2014-11-11