Mutagenetix > Incidental Mutation

Incidental Mutation 'R4980:Atg16l1'

384721

Institutional Source

Beutler Lab

Gene Symbol

Atg16l1

Ensembl Gene

ENSMUSG00000026289

Gene Name

autophagy related 16 like 1

Synonyms

WDR30, APG16L, 1500009K01Rik

MMRRC Submission

042575-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4980 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

87683730-87720150 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 87694553 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 77 (S77P)

Ref Sequence

ENSEMBL: ENSMUSP00000120955 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027512] [ENSMUST00000113186] [ENSMUST00000113190] [ENSMUST00000144047]

AlphaFold

Q8C0J2

Predicted Effect

possibly damaging
Transcript: ENSMUST00000027512
AA Change: S139P

PolyPhen 2 Score 0.889 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000027512
Gene: ENSMUSG00000026289
AA Change: S139P

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

possibly damaging
Transcript: ENSMUST00000113186
AA Change: S139P

PolyPhen 2 Score 0.889 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000108811
Gene: ENSMUSG00000026289
AA Change: S139P

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: S139P

PolyPhen 2 Score 0.889 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000108815
Gene: ENSMUSG00000026289
AA Change: S139P

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129431

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

possibly damaging
Transcript: ENSMUST00000144047
AA Change: S77P

PolyPhen 2 Score 0.889 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000120955
Gene: ENSMUSG00000026289
AA Change: S77P

Domain	Start	End	E-Value	Type
Pfam:ATG16	1	145	2.9e-50	PFAM

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 93.8%

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930522L14Rik	A	T	5: 109,885,292 (GRCm39)	C189S	probably damaging	Het
Abcd3	A	T	3: 121,562,917 (GRCm39)		probably null	Het
Adar	T	C	3: 89,638,121 (GRCm39)	S2P	probably benign	Het
Amhr2	T	A	15: 102,362,765 (GRCm39)	S511T	probably benign	Het
Bltp1	T	C	3: 36,997,461 (GRCm39)	S1173P	probably damaging	Het
Cacna1i	T	C	15: 80,232,650 (GRCm39)	F218L	probably damaging	Het
Cd5l	A	T	3: 87,274,908 (GRCm39)	H149L	probably benign	Het
Cdc14a	T	A	3: 116,186,506 (GRCm39)	R92*	probably null	Het
Col19a1	T	C	1: 24,565,564 (GRCm39)	T256A	unknown	Het
Col22a1	C	T	15: 71,673,792 (GRCm39)	A975T	unknown	Het
Cracd	A	T	5: 77,005,421 (GRCm39)	D594V	unknown	Het
Cyp20a1	T	C	1: 60,402,373 (GRCm39)	W153R	probably damaging	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Homo
Dpyd	T	C	3: 118,710,767 (GRCm39)	S392P	probably damaging	Het
Dst	A	T	1: 34,295,369 (GRCm39)	L957F	probably damaging	Het
Emilin2	G	T	17: 71,560,066 (GRCm39)	D970E	possibly damaging	Het
Fbn2	T	C	18: 58,143,703 (GRCm39)	E2784G	probably benign	Het
Fbxw10	T	C	11: 62,738,583 (GRCm39)	I159T	possibly damaging	Het
Fgfr2	T	C	7: 129,802,810 (GRCm39)	Y192C	probably damaging	Het
Gm7298	A	G	6: 121,736,198 (GRCm39)		probably null	Het
Igf2r	C	T	17: 12,922,247 (GRCm39)		probably null	Het
Ints4	T	C	7: 97,151,057 (GRCm39)		probably null	Het
Kcnf1	A	G	12: 17,225,012 (GRCm39)	F403S	possibly damaging	Het
Kif11	C	T	19: 37,375,819 (GRCm39)	Q211*	probably null	Het
Kif13a	A	G	13: 46,906,222 (GRCm39)	S574P	possibly damaging	Het
Kifc3	T	A	8: 95,853,177 (GRCm39)	T60S	probably benign	Het
Krt82	T	C	15: 101,453,534 (GRCm39)	D284G	possibly damaging	Het
Lancl1	T	C	1: 67,043,968 (GRCm39)	Y344C	probably benign	Het
Ltbp3	A	T	19: 5,803,955 (GRCm39)		probably null	Het
Map3k4	A	G	17: 12,490,958 (GRCm39)	F158L	probably damaging	Het
Mast2	A	G	4: 116,174,948 (GRCm39)	Y469H	probably damaging	Het
Mcf2l	T	G	8: 13,034,883 (GRCm39)	F97C	probably damaging	Het
Mpeg1	T	C	19: 12,438,904 (GRCm39)	S121P	probably damaging	Het
Mycbp2	A	T	14: 103,497,821 (GRCm39)		probably null	Het
Myt1l	A	T	12: 29,877,038 (GRCm39)	T230S	unknown	Het
Naa15	T	C	3: 51,366,173 (GRCm39)		probably null	Het
Nans	G	A	4: 46,492,764 (GRCm39)	R64Q	probably benign	Het
Nbea	C	T	3: 55,554,772 (GRCm39)		probably null	Het
Nbea	T	C	3: 55,860,466 (GRCm39)	E1870G	probably benign	Het
Ncapd3	T	C	9: 26,974,591 (GRCm39)	S688P	probably damaging	Het
Nedd4l	G	T	18: 65,213,131 (GRCm39)	E96*	probably null	Het
Or56a5	T	A	7: 104,793,431 (GRCm39)	Y23F	probably benign	Het
Or5b21	A	T	19: 12,839,384 (GRCm39)	M82L	probably benign	Het
Pdxk	A	G	10: 78,287,318 (GRCm39)	L81P	probably damaging	Het
Plec	T	A	15: 76,077,495 (GRCm39)	R269*	probably null	Het
Plec	T	C	15: 76,090,065 (GRCm39)	I92V	probably damaging	Het
Ppara	T	C	15: 85,671,434 (GRCm39)	Y112H	probably damaging	Het
Ppp2r2c	A	T	5: 37,109,732 (GRCm39)	M364L	probably benign	Het
Prag1	A	C	8: 36,606,740 (GRCm39)	H827P	probably damaging	Het
Ptprg	A	G	14: 12,154,421 (GRCm38)	N714S	probably benign	Het
Rbp2	G	A	9: 98,380,894 (GRCm39)	V67I	probably benign	Het
Rictor	T	A	15: 6,811,141 (GRCm39)	Y835N	probably damaging	Het
Ripply2	A	G	9: 86,901,747 (GRCm39)	Q91R	probably damaging	Het
Sap130	C	A	18: 31,782,699 (GRCm39)	H203Q	possibly damaging	Het
Sema4d	T	C	13: 51,865,270 (GRCm39)	Y358C	probably damaging	Het
Serbp1	G	A	6: 67,254,872 (GRCm39)	D294N	probably benign	Het
Slc16a10	A	G	10: 39,956,801 (GRCm39)	W113R	probably damaging	Het
Slc6a6	A	G	6: 91,703,041 (GRCm39)	Y138C	probably damaging	Het
Spag11a	T	C	8: 19,207,962 (GRCm39)	M1T	probably null	Het
Spata20	T	C	11: 94,375,435 (GRCm39)	M120V	probably damaging	Het
Stk32a	A	C	18: 43,447,113 (GRCm39)	K357Q	probably benign	Het
Tasor	T	A	14: 27,183,382 (GRCm39)	L614I	probably benign	Het
Trmo	A	T	4: 46,389,364 (GRCm39)	C10*	probably null	Het
Tsc22d1	T	G	14: 76,655,696 (GRCm39)	V643G	probably benign	Het
Vangl2	A	T	1: 171,837,132 (GRCm39)	L226I	probably damaging	Het
Vps35l	T	A	7: 118,406,232 (GRCm39)	D605E	probably damaging	Het
Wnt3a	A	T	11: 59,140,626 (GRCm39)	C297S	probably damaging	Het
Wwc1	T	C	11: 35,778,930 (GRCm39)	K301E	possibly damaging	Het
Zfhx4	C	T	3: 5,464,039 (GRCm39)	T1399I	possibly damaging	Het
Zswim4	C	T	8: 84,953,296 (GRCm39)		probably null	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
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'- TTACTAGCCGTCTGTGGTCG -3'
(R):5'- TCTGCATTGAGGCGATTGGC -3'

Sequencing Primer
(F):5'- TCGGTAGGCGCTTCATCCTG -3'
(R):5'- GGCTTCTTGGGCCTTCTCAG -3'

Posted On

2016-05-10