Mutagenetix > Incidental Mutation

Incidental Mutation 'R8782:Atg16l1'

670292

Institutional Source

Beutler Lab

Gene Symbol

Atg16l1

Ensembl Gene

ENSMUSG00000026289

Gene Name

autophagy related 16 like 1

Synonyms

WDR30, APG16L, 1500009K01Rik

MMRRC Submission

068630-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8782 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

87683730-87720150 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 87714010 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 474 (T474A)

Ref Sequence

ENSEMBL: ENSMUSP00000108815 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027512] [ENSMUST00000113186] [ENSMUST00000113190]

AlphaFold

Q8C0J2

Predicted Effect

possibly damaging
Transcript: ENSMUST00000027512
AA Change: T458A

PolyPhen 2 Score 0.915 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000027512
Gene: ENSMUSG00000026289
AA Change: T458A

Domain	Start	End	E-Value	Type
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: T439A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000108811
Gene: ENSMUSG00000026289
AA Change: T439A

Domain	Start	End	E-Value	Type
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

possibly damaging
Transcript: ENSMUST00000113190
AA Change: T474A

PolyPhen 2 Score 0.758 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000108815
Gene: ENSMUSG00000026289
AA Change: T474A

Domain	Start	End	E-Value	Type
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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

99% (73/74)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930563M21Rik	A	G	9: 55,910,242 (GRCm39)		probably null	Het
Abhd16b	G	T	2: 181,136,208 (GRCm39)	R370L	probably benign	Het
Acox2	T	A	14: 8,250,035 (GRCm38)	T342S	probably damaging	Het
Adamts12	A	T	15: 11,237,678 (GRCm39)	Q329L	probably damaging	Het
Aimp1	T	C	3: 132,373,242 (GRCm39)	M233V	possibly damaging	Het
Atp1a1	T	C	3: 101,501,533 (GRCm39)	T57A	possibly damaging	Het
Bcat2	A	G	7: 45,234,917 (GRCm39)	D205G	probably benign	Het
Brd1	G	T	15: 88,614,834 (GRCm39)	C20*	probably null	Het
Camsap2	T	C	1: 136,204,957 (GRCm39)	M519V		Het
Caprin1	T	A	2: 103,603,133 (GRCm39)	T477S	probably benign	Het
Cdk5rap2	G	T	4: 70,161,712 (GRCm39)	Q1516K	possibly damaging	Het
Cep97	T	C	16: 55,726,084 (GRCm39)	D673G	probably benign	Het
Chat	A	T	14: 32,146,155 (GRCm39)	D339E	probably benign	Het
Col28a1	G	A	6: 8,175,227 (GRCm39)	S207F	unknown	Het
Commd10	T	A	18: 47,096,809 (GRCm39)	L72Q	probably damaging	Het
Crim1	T	C	17: 78,508,306 (GRCm39)	C37R	probably damaging	Het
Csgalnact1	T	A	8: 68,811,307 (GRCm39)	K454N	probably damaging	Het
Ctif	G	T	18: 75,654,868 (GRCm39)	H219Q	probably benign	Het
Ddx10	A	T	9: 53,146,588 (GRCm39)	F211L	probably damaging	Het
Dhrs2	A	T	14: 55,473,538 (GRCm39)	I66F	possibly damaging	Het
Dmtf1	A	T	5: 9,179,168 (GRCm39)	D343E	probably damaging	Het
Dync2i1	C	T	12: 116,205,332 (GRCm39)	R419H	probably damaging	Het
Fam120b	A	T	17: 15,622,472 (GRCm39)	Q150L	probably damaging	Het
Fam217a	G	A	13: 35,095,033 (GRCm39)	P242L	probably benign	Het
Gcnt2	A	G	13: 41,072,229 (GRCm39)	T291A	probably damaging	Het
Gm14305	T	G	2: 176,413,213 (GRCm39)	C368W	possibly damaging	Het
Gpr158	A	G	2: 21,404,149 (GRCm39)	D307G	probably damaging	Het
Hcls1	A	G	16: 36,777,663 (GRCm39)	M261V	probably benign	Het
Hmcn1	A	G	1: 150,540,636 (GRCm39)	M2891T	probably benign	Het
Ighv1-31	A	T	12: 114,793,305 (GRCm39)	W5R	possibly damaging	Het
Impg2	A	G	16: 56,079,818 (GRCm39)	T541A	probably damaging	Het
Ints1	A	T	5: 139,744,952 (GRCm39)	L1452Q	probably benign	Het
Kcnc2	T	A	10: 112,292,437 (GRCm39)	S542T	probably benign	Het
Kif18a	C	T	2: 109,127,118 (GRCm39)	R351C	probably damaging	Het
Lactbl1	T	G	4: 136,358,329 (GRCm39)	L100R	possibly damaging	Het
Loxl3	T	C	6: 83,025,051 (GRCm39)	S260P	probably benign	Het
Lrba	A	T	3: 86,549,976 (GRCm39)	Y2315F	probably benign	Het
Lrrc32	A	T	7: 98,148,270 (GRCm39)	N350I	probably damaging	Het
Lyn	C	A	4: 3,783,055 (GRCm39)	F429L	probably damaging	Het
Matk	A	G	10: 81,098,294 (GRCm39)	K402E	probably damaging	Het
Mau2	T	C	8: 70,485,845 (GRCm39)	E121G	possibly damaging	Het
Mrgprx2	A	G	7: 48,132,299 (GRCm39)	L173P	probably damaging	Het
Mroh1	A	G	15: 76,298,496 (GRCm39)	T369A	possibly damaging	Het
Myh6	A	G	14: 55,187,357 (GRCm39)	L1308P	possibly damaging	Het
Nbeal2	T	C	9: 110,459,873 (GRCm39)	D1895G	probably benign	Het
Ncr1	A	G	7: 4,340,763 (GRCm39)	T6A	probably benign	Het
Neb	T	A	2: 52,078,785 (GRCm39)	E5819D	probably benign	Het
Neurod4	T	C	10: 130,106,948 (GRCm39)	N109D	probably damaging	Het
Nsd2	A	T	5: 34,000,485 (GRCm39)	M1L	probably benign	Het
Nwd2	A	G	5: 63,882,540 (GRCm39)	Y64C	probably damaging	Het
Olfm2	T	A	9: 20,579,501 (GRCm39)	N417Y	probably damaging	Het
Oog3	T	A	4: 143,885,962 (GRCm39)	D212V	probably benign	Het
Or13c25	T	A	4: 52,911,693 (GRCm39)	M34L	probably benign	Het
Or5p1	A	T	7: 107,916,296 (GRCm39)	H65L	probably damaging	Het
Parp1	A	G	1: 180,417,127 (GRCm39)	K637R	probably benign	Het
Pcdhga3	T	C	18: 37,807,865 (GRCm39)	L106P	probably damaging	Het
Pdk4	T	C	6: 5,494,962 (GRCm39)	N67S	possibly damaging	Het
Plcxd3	A	G	15: 4,546,250 (GRCm39)	T85A	probably benign	Het
Plxna1	T	C	6: 89,300,220 (GRCm39)	Y1621C	probably damaging	Het
Pnliprp1	T	A	19: 58,719,025 (GRCm39)	M108K	probably damaging	Het
Pou3f1	GCACCACCACCACCACCAC	GCACCACCACCACCAC	4: 124,552,807 (GRCm39)		probably benign	Het
Prl8a1	A	T	13: 27,758,011 (GRCm39)	C233S	probably damaging	Het
R3hdm2	T	G	10: 127,293,521 (GRCm39)	S142A	probably damaging	Het
Sgo2a	T	A	1: 58,056,616 (GRCm39)		probably benign	Het
Sh3tc1	A	T	5: 35,871,548 (GRCm39)	M328K	possibly damaging	Het
Sim1	A	G	10: 50,772,165 (GRCm39)	E58G	probably benign	Het
Slc35e3	A	G	10: 117,580,798 (GRCm39)	Y169H	probably damaging	Het
Slc8a1	T	C	17: 81,955,442 (GRCm39)	D532G	probably damaging	Het
Speer4a1	T	A	5: 26,241,754 (GRCm39)	H124L	probably benign	Het
Stab2	T	A	10: 86,735,685 (GRCm39)	T1299S	probably benign	Het
Tesmin	T	C	19: 3,445,965 (GRCm39)	V237A	probably benign	Het
Trappc11	A	T	8: 47,951,701 (GRCm39)	I984N	probably benign	Het
Ube2q2	G	A	9: 55,070,354 (GRCm39)		probably null	Het
Vmn1r169	A	G	7: 23,277,403 (GRCm39)	D265G	possibly damaging	Het
Vps13b	G	T	15: 35,422,483 (GRCm39)	V148L	possibly damaging	Het
Vwce	T	C	19: 10,615,491 (GRCm39)	V124A	probably benign	Het
Zc3h15	G	A	2: 83,491,787 (GRCm39)	R292H	probably benign	Het

Other mutations in Atg16l1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
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'- TCCTTTCAGTCTGAGGAGCG -3'
(R):5'- AATGACGCTGGACCCAGAAG -3'

Sequencing Primer
(F):5'- AGTCTGAGGAGCGCTGGG -3'
(R):5'- GCTGGACCCAGAAGACTACTTTG -3'

Posted On

2021-04-30