Incidental Mutation 'R4012:Atg16l1'
ID 311724
Institutional Source Beutler Lab
Gene Symbol Atg16l1
Ensembl Gene ENSMUSG00000026289
Gene Name autophagy related 16 like 1
Synonyms WDR30, APG16L, 1500009K01Rik
MMRRC Submission 040949-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4012 (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 87694629 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 102 (D102G)
Ref Sequence ENSEMBL: ENSMUSP00000120955 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000027512] [ENSMUST00000113186] [ENSMUST00000113190] [ENSMUST00000144047]
AlphaFold Q8C0J2
Predicted Effect probably damaging
Transcript: ENSMUST00000027512
AA Change: D164G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000027512
Gene: ENSMUSG00000026289
AA Change: D164G

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: D164G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108811
Gene: ENSMUSG00000026289
AA Change: D164G

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: D164G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108815
Gene: ENSMUSG00000026289
AA Change: D164G

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: ENSMUST00000129431
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133072
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134603
Predicted Effect probably damaging
Transcript: ENSMUST00000144047
AA Change: D102G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000120955
Gene: ENSMUSG00000026289
AA Change: D102G

DomainStartEndE-ValueType
Pfam:ATG16 1 145 2.9e-50 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137638
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151037
Meta Mutation Damage Score 0.3841 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 93.0%
Validation Efficiency 100% (79/79)
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: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adnp2 G T 18: 80,174,036 (GRCm39) F124L probably benign Het
Aicda A G 6: 122,536,449 (GRCm39) K10E probably benign Het
Als2 A G 1: 59,226,575 (GRCm39) C910R probably benign Het
Ankrd11 T A 8: 123,619,156 (GRCm39) K1565N probably damaging Het
Apol7b T C 15: 77,308,909 (GRCm39) D63G probably damaging Het
Arhgef4 T C 1: 34,764,187 (GRCm39) C1148R possibly damaging Het
Babam2 T C 5: 32,158,782 (GRCm39) V244A probably damaging Het
Brd10 T G 19: 29,720,990 (GRCm39) K622N probably damaging Het
Cars1 G A 7: 143,113,411 (GRCm39) A668V possibly damaging Het
Ccdc168 T C 1: 44,100,129 (GRCm39) D323G possibly damaging Het
Ccdc185 T A 1: 182,576,453 (GRCm39) S79C possibly damaging Het
Ccdc88b G C 19: 6,826,359 (GRCm39) R1119G probably damaging Het
Cebpz A T 17: 79,231,896 (GRCm39) V810E probably damaging Het
Cep120 T C 18: 53,871,654 (GRCm39) T73A probably damaging Het
Chat C A 14: 32,145,269 (GRCm39) C380F possibly damaging Het
Cltc T C 11: 86,648,087 (GRCm39) Q10R probably benign Het
Cripto C T 9: 110,769,781 (GRCm39) M169I probably benign Het
Cst8 T C 2: 148,646,622 (GRCm39) probably benign Het
Cts3 C T 13: 61,715,868 (GRCm39) probably null Het
Cyp4a29 T A 4: 115,105,707 (GRCm39) D136E probably benign Het
Dmxl2 A C 9: 54,286,297 (GRCm39) probably null Het
Dsg4 T A 18: 20,584,919 (GRCm39) V211E possibly damaging Het
Efcab5 C T 11: 77,008,656 (GRCm39) V957I probably damaging Het
Eif4g2 A T 7: 110,673,358 (GRCm39) L807Q possibly damaging Het
Epha4 A G 1: 77,366,731 (GRCm39) probably benign Het
Epm2aip1 A T 9: 111,101,458 (GRCm39) I144F probably benign Het
Erbb4 C T 1: 68,599,735 (GRCm39) R114H probably damaging Het
Fabp3 C T 4: 130,206,180 (GRCm39) T57I probably benign Het
Fam170a C T 18: 50,415,038 (GRCm39) A228V probably damaging Het
Foxred1 A T 9: 35,117,571 (GRCm39) M254K possibly damaging Het
Gm1527 T A 3: 28,952,969 (GRCm39) C90S probably benign Het
Gpr137b T C 13: 13,533,947 (GRCm39) T370A probably benign Het
Gtf2e2 A G 8: 34,245,993 (GRCm39) probably benign Het
Hgsnat A T 8: 26,445,817 (GRCm39) L359* probably null Het
Hhip A T 8: 80,719,223 (GRCm39) C435S probably damaging Het
Hoxa13 T C 6: 52,236,107 (GRCm39) D310G possibly damaging Het
Hspa14 T C 2: 3,513,675 (GRCm39) Y18C probably damaging Het
Ighg1 A G 12: 113,293,270 (GRCm39) V140A probably damaging Het
Ighv1-58 A T 12: 115,275,930 (GRCm39) Y69* probably null Het
Inpp5j A G 11: 3,450,185 (GRCm39) F615L probably benign Het
Kcna1 T A 6: 126,619,873 (GRCm39) Y149F probably benign Het
Kcnj6 A T 16: 94,625,877 (GRCm39) probably null Het
Krtap4-1 G T 11: 99,518,637 (GRCm39) C124* probably null Het
Lama1 T A 17: 68,119,368 (GRCm39) L2615* probably null Het
Lcp2 A T 11: 34,018,439 (GRCm39) I72F probably damaging Het
Med1 T A 11: 98,062,532 (GRCm39) I189F possibly damaging Het
Meioc C T 11: 102,566,654 (GRCm39) R757C probably damaging Het
Mtr T A 13: 12,204,283 (GRCm39) H1171L probably damaging Het
Mtr G C 13: 12,204,284 (GRCm39) H1171D probably damaging Het
Naa12 A G 18: 80,255,339 (GRCm39) D211G probably benign Het
Nlrc5 A G 8: 95,202,620 (GRCm39) Y240C possibly damaging Het
Nsun4 T A 4: 115,908,259 (GRCm39) H767L possibly damaging Het
Pcdha1 T A 18: 37,064,189 (GRCm39) N284K probably benign Het
Pcdhgb8 A C 18: 37,896,414 (GRCm39) S495R probably benign Het
Pramel1 T A 4: 143,123,260 (GRCm39) I79N possibly damaging Het
Prdm6 A T 18: 53,673,390 (GRCm39) E183D possibly damaging Het
Prex2 T C 1: 11,254,740 (GRCm39) F1125L probably benign Het
Prkg2 T C 5: 99,127,674 (GRCm39) I346V possibly damaging Het
Ptprz1 A G 6: 23,002,584 (GRCm39) D1558G probably damaging Het
Pttg1ip2 A C 5: 5,528,955 (GRCm39) L20R probably damaging Het
Qng1 T A 13: 58,529,800 (GRCm39) K271* probably null Het
Rab11fip3 GCTCGTCT GCT 17: 26,287,002 (GRCm39) probably null Het
Rin2 C T 2: 145,702,366 (GRCm39) T354I probably benign Het
S100a6 A G 3: 90,521,508 (GRCm39) D50G probably damaging Het
Shroom3 T A 5: 93,096,342 (GRCm39) probably benign Het
Sipa1l1 G A 12: 82,388,556 (GRCm39) V261M possibly damaging Het
Slc5a4b T A 10: 75,910,826 (GRCm39) I337F probably damaging Het
Smarcc1 A G 9: 109,961,273 (GRCm39) Y30C possibly damaging Het
Swap70 A G 7: 109,880,512 (GRCm39) K576E possibly damaging Het
Syt6 A G 3: 103,532,809 (GRCm39) probably benign Het
Szt2 T C 4: 118,241,097 (GRCm39) I1726V probably benign Het
Thoc1 A G 18: 9,987,651 (GRCm39) K453E possibly damaging Het
Tmem38b A G 4: 53,854,409 (GRCm39) I214V probably benign Het
Tonsl A T 15: 76,521,244 (GRCm39) I354N probably damaging Het
Trappc9 T C 15: 72,903,472 (GRCm39) I303V possibly damaging Het
Trim66 A G 7: 109,057,338 (GRCm39) S1032P probably damaging Het
Tsc22d4 T C 5: 137,756,590 (GRCm39) V6A probably benign Het
Ubtd2 A G 11: 32,449,260 (GRCm39) K36E probably benign Het
Zkscan2 T C 7: 123,097,883 (GRCm39) E171G 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
R4391:Atg16l1 UTSW 1 87,687,842 (GRCm39) missense probably damaging 0.97
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'- AGCTAGATGGACCAGGTGTG -3'
(R):5'- GTCCACTAACTGCAGCTAGATGTC -3'

Sequencing Primer
(F):5'- GGCCAGTGTTCCCATTGCTG -3'
(R):5'- TAGATGTCCCACCTGGAGTC -3'
Posted On 2015-04-29