Incidental Mutation 'R4990:Atg16l1'
ID 386097
Institutional Source Beutler Lab
Gene Symbol Atg16l1
Ensembl Gene ENSMUSG00000026289
Gene Name autophagy related 16 like 1
Synonyms WDR30, APG16L, 1500009K01Rik
MMRRC Submission 042584-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4990 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 87683730-87720150 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 87717091 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Arginine at position 471 (K471R)
Ref Sequence ENSEMBL: ENSMUSP00000108811 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000027512] [ENSMUST00000113186] [ENSMUST00000113190]
AlphaFold Q8C0J2
Predicted Effect probably benign
Transcript: ENSMUST00000027512
AA Change: K490R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000027512
Gene: ENSMUSG00000026289
AA Change: K490R

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 benign
Transcript: ENSMUST00000113186
AA Change: K471R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000108811
Gene: ENSMUSG00000026289
AA Change: K471R

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 benign
Transcript: ENSMUST00000113190
AA Change: K506R

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000108815
Gene: ENSMUSG00000026289
AA Change: K506R

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: ENSMUST00000127884
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137638
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151037
Predicted Effect noncoding transcript
Transcript: ENSMUST00000158656
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.4%
Validation Efficiency
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: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca12 T C 1: 71,334,098 (GRCm39) I1135V possibly damaging Het
Abca14 G A 7: 119,911,388 (GRCm39) R1324K probably benign Het
Amer3 A C 1: 34,627,822 (GRCm39) D687A probably benign Het
Aplnr G A 2: 84,967,721 (GRCm39) V249M probably damaging Het
Cacna1b A G 2: 24,568,886 (GRCm39) probably null Het
Catspere2 A C 1: 177,925,987 (GRCm39) I218L probably benign Het
Ccdc152 A G 15: 3,330,639 (GRCm39) I12T probably benign Het
Cds1 A G 5: 101,946,245 (GRCm39) Y148C probably damaging Het
Cenpe T A 3: 134,962,401 (GRCm39) L1989Q probably damaging Het
Cep295 T C 9: 15,243,434 (GRCm39) Q1674R probably damaging Het
D930020B18Rik C G 10: 121,490,666 (GRCm39) P89A probably damaging Het
D930020B18Rik C T 10: 121,490,667 (GRCm39) P89L probably damaging Het
Dock2 T C 11: 34,586,078 (GRCm39) M535V probably damaging Het
Dscam A G 16: 96,626,715 (GRCm39) V398A probably benign Het
Elmo1 T C 13: 20,526,689 (GRCm39) F413S probably damaging Het
Emb T A 13: 117,401,046 (GRCm39) N198K probably damaging Het
Eno3 A G 11: 70,549,473 (GRCm39) D98G probably damaging Het
Fbp1 C T 13: 63,012,888 (GRCm39) V102I probably benign Het
Fbxw18 T C 9: 109,517,461 (GRCm39) E414G probably damaging Het
Grem2 A G 1: 174,664,379 (GRCm39) C157R probably damaging Het
Hnrnpr G A 4: 136,063,609 (GRCm39) V239I probably damaging Het
Hnrnpr A G 4: 136,056,690 (GRCm39) E230G probably damaging Het
Ipo11 A T 13: 106,997,395 (GRCm39) I688K probably benign Het
Irx4 G T 13: 73,413,626 (GRCm39) R32L probably benign Het
Kcnh7 T C 2: 62,564,632 (GRCm39) N876D probably benign Het
Klk1b26 T A 7: 43,665,673 (GRCm39) probably null Het
Lrp2 G T 2: 69,311,732 (GRCm39) T2582K probably benign Het
Lrriq1 A G 10: 103,036,420 (GRCm39) I911T probably damaging Het
Megf6 A G 4: 154,351,683 (GRCm39) E1132G possibly damaging Het
Mesp1 A G 7: 79,442,669 (GRCm39) Y203H probably damaging Het
Ms4a4a T C 19: 11,356,201 (GRCm39) S29P probably benign Het
Nbeal2 A C 9: 110,463,871 (GRCm39) C1174G probably benign Het
Neb C T 2: 52,145,558 (GRCm39) V2989I probably benign Het
Nkx2-1 T C 12: 56,581,724 (GRCm39) Y41C possibly damaging Het
Nrxn3 T A 12: 89,227,244 (GRCm39) I293N probably damaging Het
Nt5e A G 9: 88,237,646 (GRCm39) N192S probably benign Het
Ntng1 A T 3: 110,042,577 (GRCm39) probably null Het
Or13a17 G A 7: 140,271,360 (GRCm39) E181K probably damaging Het
Or3a1d A G 11: 74,238,023 (GRCm39) I129T probably damaging Het
Or4c110 A T 2: 88,831,816 (GRCm39) I272K probably damaging Het
Or4c15b A T 2: 89,113,671 (GRCm39) probably null Het
Panx1 A G 9: 14,921,513 (GRCm39) Y121H probably damaging Het
Pcsk4 A G 10: 80,161,215 (GRCm39) I233T possibly damaging Het
Pgm3 T A 9: 86,440,465 (GRCm39) I409F probably damaging Het
Plg T C 17: 12,630,397 (GRCm39) Y645H probably benign Het
Pon3 T C 6: 5,221,619 (GRCm39) H337R probably benign Het
Rasa2 A G 9: 96,474,042 (GRCm39) I162T probably benign Het
Ror1 A G 4: 100,299,161 (GRCm39) I845V probably benign Het
Rpl4 T C 9: 64,082,167 (GRCm39) V22A probably benign Het
Ryr3 T C 2: 112,740,318 (GRCm39) N531S probably damaging Het
Ryr3 G T 2: 112,466,122 (GRCm39) Q4746K probably damaging Het
Sbno1 A T 5: 124,538,228 (GRCm39) F571I probably damaging Het
Scarf1 T C 11: 75,416,841 (GRCm39) V761A probably benign Het
Sec22b T G 3: 97,828,427 (GRCm39) probably null Het
Slc45a2 A G 15: 11,001,236 (GRCm39) M112V probably benign Het
Snai3 G A 8: 123,183,071 (GRCm39) T158M possibly damaging Het
Spata31d1a T C 13: 59,850,965 (GRCm39) N388D probably benign Het
Speer1e A T 5: 11,236,381 (GRCm39) E138V probably damaging Het
Sv2b T C 7: 74,767,470 (GRCm39) N642S possibly damaging Het
Svil T A 18: 5,056,810 (GRCm39) I561K probably benign Het
Trappc11 A T 8: 47,943,930 (GRCm39) D1127E probably benign Het
Triobp C A 15: 78,851,205 (GRCm39) A453D probably benign Het
Tubd1 T C 11: 86,448,665 (GRCm39) L295P probably damaging Het
Ulk4 C T 9: 121,021,852 (GRCm39) V620I probably benign Het
Vmn2r39 A G 7: 9,026,675 (GRCm39) I442T probably benign Het
Wwc1 T C 11: 35,767,393 (GRCm39) T413A probably benign Het
Zfp131 A C 13: 120,244,449 (GRCm39) V77G probably damaging Het
Zfyve26 T C 12: 79,334,607 (GRCm39) D137G probably 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
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
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'- AATAATAGGCTAGGGACATAGTTCC -3'
(R):5'- GAGCCGCATTTGAATCCAG -3'

Sequencing Primer
(F):5'- GGACATAGTTCCTGCCCCTTGAAG -3'
(R):5'- GCATTTGAATCCAGGCGCAC -3'
Posted On 2016-05-10