Incidental Mutation 'R4391:Atg16l1'
ID 326351
Institutional Source Beutler Lab
Gene Symbol Atg16l1
Ensembl Gene ENSMUSG00000026289
Gene Name autophagy related 16 like 1
Synonyms WDR30, APG16L, 1500009K01Rik
MMRRC Submission 041682-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4391 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 87683730-87720150 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 87687842 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 62 (D62G)
Ref Sequence ENSEMBL: ENSMUSP00000108815 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000027512] [ENSMUST00000113186] [ENSMUST00000113190] [ENSMUST00000144047]
AlphaFold Q8C0J2
Predicted Effect probably damaging
Transcript: ENSMUST00000027512
AA Change: D62G

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000027512
Gene: ENSMUSG00000026289
AA Change: D62G

DomainStartEndE-ValueType
Pfam:ATG16 13 207 1.3e-63 PFAM
low complexity region 237 246 N/A INTRINSIC
WD40 311 350 7.05e-9 SMART
WD40 355 394 7.28e-2 SMART
WD40 397 436 1.07e-8 SMART
WD40 439 475 3.7e0 SMART
WD40 478 516 5.35e-1 SMART
WD40 519 562 1.2e-2 SMART
WD40 565 605 6.89e-3 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000113186
AA Change: D62G

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000108811
Gene: ENSMUSG00000026289
AA Change: D62G

DomainStartEndE-ValueType
Pfam:ATG16 13 207 3.7e-64 PFAM
low complexity region 237 246 N/A INTRINSIC
low complexity region 257 271 N/A INTRINSIC
WD40 292 331 7.05e-9 SMART
WD40 336 375 7.28e-2 SMART
WD40 378 417 1.07e-8 SMART
WD40 420 456 3.7e0 SMART
WD40 459 497 5.35e-1 SMART
WD40 500 543 1.2e-2 SMART
WD40 546 586 6.89e-3 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000113190
AA Change: D62G

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000108815
Gene: ENSMUSG00000026289
AA Change: D62G

DomainStartEndE-ValueType
Pfam:ATG16 16 206 6.5e-49 PFAM
low complexity region 237 246 N/A INTRINSIC
low complexity region 295 306 N/A INTRINSIC
WD40 327 366 7.05e-9 SMART
WD40 371 410 7.28e-2 SMART
WD40 413 452 1.07e-8 SMART
WD40 455 491 3.7e0 SMART
WD40 494 532 5.35e-1 SMART
WD40 535 578 1.2e-2 SMART
WD40 581 621 6.89e-3 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133072
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134603
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137638
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151037
Predicted Effect probably benign
Transcript: ENSMUST00000144047
SMART Domains Protein: ENSMUSP00000120955
Gene: ENSMUSG00000026289

DomainStartEndE-ValueType
Pfam:ATG16 1 145 2.9e-50 PFAM
Meta Mutation Damage Score 0.2691 question?
Coding Region Coverage
  • 1x: 99.6%
  • 3x: 98.6%
  • 10x: 96.4%
  • 20x: 91.6%
Validation Efficiency 100% (40/40)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is part of a large protein complex that is necessary for autophagy, the major process by which intracellular components are targeted to lysosomes for degradation. Defects in this gene are a cause of susceptibility to inflammatory bowel disease type 10 (IBD10). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jun 2010]
PHENOTYPE: Null homozygotes have a cellular defect in autophagy that results in lethality during the neonatal starvation period. Mice homozygous for hypomorphic alleles have Paneth cells with aberrant, disorganized granules similar to those found in patients with Crohn's disease. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 35 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
6030469F06Rik A T 12: 31,234,622 (GRCm39) noncoding transcript Het
Actn2 C T 13: 12,305,634 (GRCm39) R394Q probably damaging Het
Atp2b1 A G 10: 98,839,076 (GRCm39) T635A probably benign Het
Chil4 G A 3: 106,111,043 (GRCm39) P284S possibly damaging Het
Dnah1 G A 14: 31,016,792 (GRCm39) T1575I probably damaging Het
Dnah7b A G 1: 46,376,754 (GRCm39) probably null Het
Dnajc12 A G 10: 63,242,838 (GRCm39) T37A probably benign Het
Efcab5 T A 11: 76,981,284 (GRCm39) N1354I probably damaging Het
Epas1 T C 17: 87,117,091 (GRCm39) L218P probably benign Het
Fbxw15 T A 9: 109,397,300 (GRCm39) probably benign Het
Filip1l C A 16: 57,391,155 (GRCm39) S581* probably null Het
Focad T A 4: 88,104,195 (GRCm39) I358K probably damaging Het
Gm382 T A X: 125,968,942 (GRCm39) S376T probably benign Het
Gpsm1 C T 2: 26,214,009 (GRCm39) R179C probably damaging Het
Hjurp A G 1: 88,194,283 (GRCm39) probably benign Het
Homer3 G A 8: 70,742,793 (GRCm39) probably null Het
Krt39 C T 11: 99,405,578 (GRCm39) A441T probably benign Het
Nrdc T A 4: 108,903,841 (GRCm39) N662K probably damaging Het
Obox5 C T 7: 15,491,899 (GRCm39) Q105* probably null Het
Or56a3b T A 7: 104,770,793 (GRCm39) M43K possibly damaging Het
Or5af1 T A 11: 58,722,841 (GRCm39) V287D possibly damaging Het
Or8c13 A T 9: 38,091,645 (GRCm39) V158D probably damaging Het
Pcdhb5 T A 18: 37,455,789 (GRCm39) L723Q possibly damaging Het
Pou3f3 G T 1: 42,736,618 (GRCm39) A105S unknown Het
Ppp1r3d C T 2: 178,055,880 (GRCm39) D41N probably damaging Het
Ppp4r1 A G 17: 66,131,749 (GRCm39) N497S probably benign Het
Rad54b T G 4: 11,615,570 (GRCm39) N859K probably benign Het
Sh3bp2 C T 5: 34,707,062 (GRCm39) S29L probably benign Het
Smarcad1 A T 6: 65,033,443 (GRCm39) N142I probably benign Het
Sp140l1 G A 1: 85,062,852 (GRCm39) probably benign Het
Stat3 G A 11: 100,796,378 (GRCm39) probably benign Het
Stmn3 T C 2: 180,950,576 (GRCm39) R77G probably benign Het
Ugt1a1 CAGAGAGAGAGAGA CAGAGAGAGAGA 1: 88,139,706 (GRCm39) probably benign Het
Vmn2r79 A G 7: 86,651,099 (GRCm39) H166R possibly damaging Het
Xlr3a T C X: 72,135,450 (GRCm39) I87V possibly damaging Het
Other mutations in Atg16l1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00092:Atg16l1 APN 1 87,693,119 (GRCm39) missense possibly damaging 0.68
IGL00861:Atg16l1 APN 1 87,702,560 (GRCm39) missense probably damaging 1.00
IGL01065:Atg16l1 APN 1 87,713,653 (GRCm39) missense probably damaging 0.99
IGL01068:Atg16l1 APN 1 87,702,546 (GRCm39) missense probably damaging 1.00
IGL01140:Atg16l1 APN 1 87,702,575 (GRCm39) missense probably benign 0.03
R0023:Atg16l1 UTSW 1 87,717,187 (GRCm39) missense probably benign 0.00
R0023:Atg16l1 UTSW 1 87,717,187 (GRCm39) missense probably benign 0.00
R0650:Atg16l1 UTSW 1 87,709,421 (GRCm39) missense possibly damaging 0.93
R0655:Atg16l1 UTSW 1 87,694,551 (GRCm39) missense probably damaging 1.00
R1421:Atg16l1 UTSW 1 87,714,080 (GRCm39) splice site probably benign
R1549:Atg16l1 UTSW 1 87,701,910 (GRCm39) missense probably benign
R2202:Atg16l1 UTSW 1 87,694,737 (GRCm39) missense probably benign 0.03
R2204:Atg16l1 UTSW 1 87,694,737 (GRCm39) missense probably benign 0.03
R3689:Atg16l1 UTSW 1 87,713,626 (GRCm39) missense probably damaging 1.00
R4012:Atg16l1 UTSW 1 87,694,629 (GRCm39) missense probably damaging 1.00
R4839:Atg16l1 UTSW 1 87,693,896 (GRCm39) missense probably damaging 0.99
R4935:Atg16l1 UTSW 1 87,694,764 (GRCm39) missense possibly damaging 0.69
R4980:Atg16l1 UTSW 1 87,694,553 (GRCm39) missense possibly damaging 0.89
R4990:Atg16l1 UTSW 1 87,717,091 (GRCm39) missense probably benign 0.00
R5011:Atg16l1 UTSW 1 87,701,902 (GRCm39) nonsense probably null
R5457:Atg16l1 UTSW 1 87,702,813 (GRCm39) missense probably damaging 0.96
R5897:Atg16l1 UTSW 1 87,713,719 (GRCm39) critical splice donor site probably null
R6289:Atg16l1 UTSW 1 87,683,937 (GRCm39) missense probably damaging 0.99
R6437:Atg16l1 UTSW 1 87,718,370 (GRCm39) missense probably damaging 1.00
R6727:Atg16l1 UTSW 1 87,702,576 (GRCm39) missense possibly damaging 0.68
R6923:Atg16l1 UTSW 1 87,702,078 (GRCm39) splice site probably null
R7423:Atg16l1 UTSW 1 87,714,023 (GRCm39) missense probably damaging 1.00
R7475:Atg16l1 UTSW 1 87,687,805 (GRCm39) missense possibly damaging 0.89
R8493:Atg16l1 UTSW 1 87,706,704 (GRCm39) missense probably damaging 1.00
R8742:Atg16l1 UTSW 1 87,694,620 (GRCm39) missense probably damaging 1.00
R8782:Atg16l1 UTSW 1 87,714,010 (GRCm39) missense possibly damaging 0.76
R9035:Atg16l1 UTSW 1 87,693,167 (GRCm39) critical splice donor site probably null
R9071:Atg16l1 UTSW 1 87,683,907 (GRCm39) intron probably benign
R9282:Atg16l1 UTSW 1 87,707,906 (GRCm39) missense possibly damaging 0.70
R9706:Atg16l1 UTSW 1 87,713,977 (GRCm39) missense possibly damaging 0.64
Predicted Primers PCR Primer
(F):5'- AGTTCCTAGACTGCTGCATGC -3'
(R):5'- TGAGCGCCTACAATCACTG -3'

Sequencing Primer
(F):5'- ACTGCTGCATGCGACGAAG -3'
(R):5'- TCACTGCAAGAGCTGAAGAC -3'
Posted On 2015-07-06