Incidental Mutation 'R1489:Atg9a'
ID 163574
Institutional Source Beutler Lab
Gene Symbol Atg9a
Ensembl Gene ENSMUSG00000033124
Gene Name autophagy related 9A
Synonyms Apg9l1
MMRRC Submission 039541-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1489 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 75157509-75168654 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 75162734 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Valine at position 427 (D427V)
Ref Sequence ENSEMBL: ENSMUSP00000139641 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000040689] [ENSMUST00000186744] [ENSMUST00000188347] [ENSMUST00000189702] [ENSMUST00000189665]
AlphaFold Q68FE2
Predicted Effect probably damaging
Transcript: ENSMUST00000040689
AA Change: D427V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000047449
Gene: ENSMUSG00000033124
AA Change: D427V

DomainStartEndE-ValueType
transmembrane domain 70 92 N/A INTRINSIC
transmembrane domain 126 148 N/A INTRINSIC
Pfam:APG9 173 530 3.4e-134 PFAM
low complexity region 588 599 N/A INTRINSIC
low complexity region 607 621 N/A INTRINSIC
Blast:HELICc 692 733 1e-13 BLAST
low complexity region 734 755 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000185727
Predicted Effect probably benign
Transcript: ENSMUST00000186744
Predicted Effect noncoding transcript
Transcript: ENSMUST00000187601
Predicted Effect probably benign
Transcript: ENSMUST00000187785
Predicted Effect probably damaging
Transcript: ENSMUST00000188347
AA Change: D427V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000139731
Gene: ENSMUSG00000033124
AA Change: D427V

DomainStartEndE-ValueType
transmembrane domain 70 92 N/A INTRINSIC
transmembrane domain 126 148 N/A INTRINSIC
Pfam:APG9 172 533 2.4e-140 PFAM
low complexity region 588 599 N/A INTRINSIC
low complexity region 607 621 N/A INTRINSIC
Blast:HELICc 692 733 1e-13 BLAST
low complexity region 734 755 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000189702
AA Change: D427V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000139641
Gene: ENSMUSG00000033124
AA Change: D427V

DomainStartEndE-ValueType
transmembrane domain 70 92 N/A INTRINSIC
transmembrane domain 126 148 N/A INTRINSIC
Pfam:APG9 172 533 2.4e-140 PFAM
low complexity region 588 599 N/A INTRINSIC
low complexity region 607 621 N/A INTRINSIC
Blast:HELICc 692 733 1e-13 BLAST
low complexity region 734 755 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000189820
AA Change: D419V
Predicted Effect noncoding transcript
Transcript: ENSMUST00000188430
Predicted Effect probably benign
Transcript: ENSMUST00000189665
SMART Domains Protein: ENSMUSP00000140012
Gene: ENSMUSG00000033124

DomainStartEndE-ValueType
transmembrane domain 70 92 N/A INTRINSIC
transmembrane domain 126 148 N/A INTRINSIC
Meta Mutation Damage Score 0.9677 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.9%
Validation Efficiency 96% (52/54)
MGI Phenotype PHENOTYPE: Mice homozygous for a null mutation all die within 1 day of birth and display impaired autophagy. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2700097O09Rik A G 12: 55,106,295 (GRCm39) S143P possibly damaging Het
4930522H14Rik T C 4: 109,362,654 (GRCm39) K218E possibly damaging Het
Abcb1a T A 5: 8,736,300 (GRCm39) probably null Het
Adam39 A G 8: 41,278,031 (GRCm39) T141A possibly damaging Het
Adam6b T A 12: 113,455,071 (GRCm39) S629R probably benign Het
Ap3b2 C A 7: 81,113,438 (GRCm39) E924* probably null Het
Armc3 A T 2: 19,314,858 (GRCm39) Y856F probably benign Het
Asap1 A G 15: 64,044,579 (GRCm39) L142P probably damaging Het
Atl2 G A 17: 80,160,135 (GRCm39) A17V probably benign Het
Atxn2l A T 7: 126,095,639 (GRCm39) S379T probably damaging Het
C1ql3 G T 2: 13,015,453 (GRCm39) P69Q possibly damaging Het
Cap2 A T 13: 46,763,111 (GRCm39) I114F probably damaging Het
Ccdc168 A G 1: 44,096,950 (GRCm39) F1383L probably benign Het
Ccdc168 T C 1: 44,100,667 (GRCm39) I144V probably benign Het
Cox16 T C 12: 81,521,389 (GRCm39) N135S probably null Het
Dnajc13 A T 9: 104,108,234 (GRCm39) H180Q possibly damaging Het
Dpy19l3 A T 7: 35,424,835 (GRCm39) Y73* probably null Het
Duox2 T A 2: 122,123,877 (GRCm39) M436L probably benign Het
Exoc6 T A 19: 37,585,568 (GRCm39) M481K possibly damaging Het
Fbxw2 GCCCCC GCCCCCCCC 2: 34,702,829 (GRCm39) probably benign Het
Fmn1 T A 2: 113,195,557 (GRCm39) V419E unknown Het
Fndc4 T C 5: 31,450,795 (GRCm39) *232W probably null Het
Foxc1 C T 13: 31,992,595 (GRCm39) R469* probably null Het
Fsip2 A G 2: 82,810,155 (GRCm39) H2158R probably benign Het
Ghdc C T 11: 100,659,083 (GRCm39) G373D probably benign Het
Gm10330 A T 12: 23,830,032 (GRCm39) S50T probably benign Het
Hlx G T 1: 184,464,184 (GRCm39) A52D probably damaging Het
Lonrf1 A G 8: 36,690,108 (GRCm39) V650A probably damaging Het
Map1a T C 2: 121,130,918 (GRCm39) V578A possibly damaging Het
Mbd3 C G 10: 80,229,740 (GRCm39) D190H probably damaging Het
Mcpt9 T C 14: 56,264,976 (GRCm39) K175R probably benign Het
Mia3 A G 1: 183,120,121 (GRCm39) S85P probably benign Het
Myrip T C 9: 120,261,595 (GRCm39) F403L probably damaging Het
Nox4 A G 7: 86,954,097 (GRCm39) Y134C probably damaging Het
Numb A G 12: 83,842,217 (GRCm39) L642P probably damaging Het
Pappa A T 4: 65,099,185 (GRCm39) Y568F possibly damaging Het
Pdzrn4 T C 15: 92,575,593 (GRCm39) L333P probably benign Het
Prl A T 13: 27,241,619 (GRCm39) S3C probably damaging Het
Ptprc T C 1: 138,047,824 (GRCm39) T60A possibly damaging Het
Rbm10 C T X: 20,503,903 (GRCm39) probably benign Het
Slc7a7 C T 14: 54,646,103 (GRCm39) R120H probably damaging Het
Smpd1 T C 7: 105,205,761 (GRCm39) probably null Het
Spta1 A G 1: 174,058,891 (GRCm39) E1942G probably damaging Het
Tmem38a A G 8: 73,333,479 (GRCm39) Y66C probably damaging Het
Tnnt1 A T 7: 4,510,524 (GRCm39) Y232* probably null Het
Tpte T C 8: 22,839,405 (GRCm39) probably null Het
Virma T C 4: 11,521,164 (GRCm39) V907A probably damaging Het
Vmn1r174 C T 7: 23,453,981 (GRCm39) Q216* probably null Het
Zswim3 T C 2: 164,661,901 (GRCm39) V127A probably benign Het
Other mutations in Atg9a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01464:Atg9a APN 1 75,167,010 (GRCm39) missense probably damaging 1.00
IGL02041:Atg9a APN 1 75,159,748 (GRCm39) missense possibly damaging 0.47
IGL03367:Atg9a APN 1 75,164,601 (GRCm39) missense probably benign 0.18
PIT4494001:Atg9a UTSW 1 75,164,597 (GRCm39) nonsense probably null
R0054:Atg9a UTSW 1 75,161,143 (GRCm39) missense probably damaging 1.00
R0054:Atg9a UTSW 1 75,161,143 (GRCm39) missense probably damaging 1.00
R0408:Atg9a UTSW 1 75,161,939 (GRCm39) missense probably damaging 1.00
R0520:Atg9a UTSW 1 75,163,178 (GRCm39) nonsense probably null
R0653:Atg9a UTSW 1 75,166,972 (GRCm39) missense probably damaging 0.96
R0666:Atg9a UTSW 1 75,161,734 (GRCm39) missense probably damaging 0.99
R0961:Atg9a UTSW 1 75,163,390 (GRCm39) missense probably damaging 0.99
R1490:Atg9a UTSW 1 75,162,389 (GRCm39) missense possibly damaging 0.70
R1692:Atg9a UTSW 1 75,166,999 (GRCm39) missense probably benign 0.04
R1997:Atg9a UTSW 1 75,166,270 (GRCm39) missense probably benign 0.33
R2005:Atg9a UTSW 1 75,162,635 (GRCm39) missense probably benign 0.18
R2172:Atg9a UTSW 1 75,162,329 (GRCm39) missense probably damaging 0.99
R4004:Atg9a UTSW 1 75,163,095 (GRCm39) missense probably damaging 1.00
R4105:Atg9a UTSW 1 75,162,603 (GRCm39) missense probably damaging 1.00
R5010:Atg9a UTSW 1 75,162,704 (GRCm39) splice site probably null
R5220:Atg9a UTSW 1 75,162,372 (GRCm39) missense probably damaging 1.00
R5898:Atg9a UTSW 1 75,162,916 (GRCm39) missense probably damaging 1.00
R6295:Atg9a UTSW 1 75,161,702 (GRCm39) missense probably benign 0.01
R6390:Atg9a UTSW 1 75,164,625 (GRCm39) missense probably damaging 1.00
R7312:Atg9a UTSW 1 75,164,736 (GRCm39) missense probably damaging 1.00
R7729:Atg9a UTSW 1 75,161,204 (GRCm39) missense probably benign 0.34
R8111:Atg9a UTSW 1 75,164,366 (GRCm39) missense probably damaging 1.00
R8210:Atg9a UTSW 1 75,163,009 (GRCm39) missense probably damaging 1.00
R8210:Atg9a UTSW 1 75,161,927 (GRCm39) missense probably damaging 1.00
R8256:Atg9a UTSW 1 75,163,563 (GRCm39) missense possibly damaging 0.88
R8319:Atg9a UTSW 1 75,162,342 (GRCm39) nonsense probably null
R8321:Atg9a UTSW 1 75,162,342 (GRCm39) nonsense probably null
R8382:Atg9a UTSW 1 75,162,342 (GRCm39) nonsense probably null
R8406:Atg9a UTSW 1 75,167,028 (GRCm39) missense probably damaging 1.00
R8482:Atg9a UTSW 1 75,162,870 (GRCm39) missense probably damaging 0.99
R8855:Atg9a UTSW 1 75,161,867 (GRCm39) missense probably damaging 1.00
R8866:Atg9a UTSW 1 75,161,867 (GRCm39) missense probably damaging 1.00
R9381:Atg9a UTSW 1 75,162,726 (GRCm39) missense probably benign
R9441:Atg9a UTSW 1 75,163,086 (GRCm39) missense possibly damaging 0.92
R9442:Atg9a UTSW 1 75,163,086 (GRCm39) missense possibly damaging 0.92
R9448:Atg9a UTSW 1 75,162,849 (GRCm39) missense probably benign 0.35
R9608:Atg9a UTSW 1 75,161,739 (GRCm39) missense possibly damaging 0.52
R9703:Atg9a UTSW 1 75,162,431 (GRCm39) missense probably damaging 0.98
RF021:Atg9a UTSW 1 75,159,273 (GRCm39) missense probably damaging 0.96
Z1176:Atg9a UTSW 1 75,163,203 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCACTCACTGCCTTGTACTGGAAG -3'
(R):5'- TCAATGAGCTGGAGCATGAGCTG -3'

Sequencing Primer
(F):5'- AGAGCTGGGCAAACTCGTC -3'
(R):5'- CAAGAATGGTGCCTTCTTCG -3'
Posted On 2014-03-28