Mutagenetix > Incidental Mutation

Incidental Mutation 'R5010:Atg9a'

390406

Institutional Source

Beutler Lab

Gene Symbol

Atg9a

Ensembl Gene

ENSMUSG00000033124

Gene Name

autophagy related 9A

Synonyms

Apg9l1

MMRRC Submission

042601-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5010 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

75180860-75192196 bp(-) (GRCm38)

Type of Mutation

splice site

DNA Base Change (assembly)

A to T at 75186060 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040689] [ENSMUST00000186744] [ENSMUST00000188347] [ENSMUST00000189665] [ENSMUST00000189702]

AlphaFold

Q68FE2

Predicted Effect

probably damaging
Transcript: ENSMUST00000040689
AA Change: L437Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000047449
Gene: ENSMUSG00000033124
AA Change: L437Q

Domain	Start	End	E-Value	Type
transmembrane domain	70	92	N/A	INTRINSIC
transmembrane domain	126	148	N/A	INTRINSIC
Pfam:APG9	173	530	3.4e-134	PFAM
low complexity region	588	599	N/A	INTRINSIC
low complexity region	607	621	N/A	INTRINSIC
Blast:HELICc	692	733	1e-13	BLAST
low complexity region	734	755	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000185727

Predicted Effect

probably benign
Transcript: ENSMUST00000186744

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000187601

Predicted Effect

probably null
Transcript: ENSMUST00000187785

Predicted Effect

probably null
Transcript: ENSMUST00000187785

Predicted Effect

probably damaging
Transcript: ENSMUST00000188347
AA Change: L437Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000139731
Gene: ENSMUSG00000033124
AA Change: L437Q

Domain	Start	End	E-Value	Type
transmembrane domain	70	92	N/A	INTRINSIC
transmembrane domain	126	148	N/A	INTRINSIC
Pfam:APG9	172	533	2.4e-140	PFAM
low complexity region	588	599	N/A	INTRINSIC
low complexity region	607	621	N/A	INTRINSIC
Blast:HELICc	692	733	1e-13	BLAST
low complexity region	734	755	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000188430

Predicted Effect

probably benign
Transcript: ENSMUST00000189665

SMART Domains

Protein: ENSMUSP00000140012
Gene: ENSMUSG00000033124

Domain	Start	End	E-Value	Type
transmembrane domain	70	92	N/A	INTRINSIC
transmembrane domain	126	148	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000189702
AA Change: L437Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000139641
Gene: ENSMUSG00000033124
AA Change: L437Q

Domain	Start	End	E-Value	Type
transmembrane domain	70	92	N/A	INTRINSIC
transmembrane domain	126	148	N/A	INTRINSIC
Pfam:APG9	172	533	2.4e-140	PFAM
low complexity region	588	599	N/A	INTRINSIC
low complexity region	607	621	N/A	INTRINSIC
Blast:HELICc	692	733	1e-13	BLAST
low complexity region	734	755	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000189820
AA Change: L429Q

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

Meta Mutation Damage Score

0.9213

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.6%

Validation Efficiency

98% (65/66)

MGI Phenotype

PHENOTYPE: Mice homozygous for a null mutation all die within 1 day of birth and display impaired autophagy. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810065E05Rik	C	T	11: 58,422,804	A86V	possibly damaging	Het
9430097D07Rik	A	G	2: 32,574,428		probably benign	Het
Actr5	T	A	2: 158,635,363	D411E	probably benign	Het
Ang5	A	G	14: 43,962,845	D122G	probably benign	Het
C530008M17Rik	G	C	5: 76,657,834		probably benign	Het
Dctd	C	T	8: 48,137,414		probably benign	Het
Ddx11	G	A	17: 66,147,722	V642M	possibly damaging	Het
Dis3l2	G	A	1: 86,760,321	V100I	probably benign	Het
Echdc2	T	C	4: 108,172,131	V111A	probably benign	Het
Egr1	A	G	18: 34,863,658	T498A	probably benign	Het
Exosc3	T	C	4: 45,317,702	K200R	possibly damaging	Het
Exosc8	T	C	3: 54,729,223	D229G	probably benign	Het
Ext1	T	A	15: 53,092,412	I430F	probably damaging	Het
Fbxw22	T	C	9: 109,403,424	N31S	probably benign	Het
Gja8	T	C	3: 96,919,849	T166A	probably benign	Het
Gm21814	T	A	6: 149,583,618		noncoding transcript	Het
Gm21915	T	A	9: 40,670,648	H12Q	probably benign	Het
Gm597	A	G	1: 28,777,862	I363T	possibly damaging	Het
Hgsnat	G	A	8: 25,947,960	R527*	probably null	Het
Iqgap2	A	G	13: 95,673,743	F731S	probably benign	Het
Jchain	T	C	5: 88,522,505	H85R	probably damaging	Het
Kcnb2	T	C	1: 15,312,962	C171R	probably benign	Het
Kcnk3	C	A	5: 30,622,805	R400S	possibly damaging	Het
Klhl28	C	T	12: 64,957,227	E171K	probably damaging	Het
Lrrfip2	T	C	9: 111,223,972	I375T	possibly damaging	Het
Mccc1	T	C	3: 35,979,017	N326S	probably benign	Het
Med13l	T	C	5: 118,593,550	V97A	possibly damaging	Het
Mertk	C	A	2: 128,784,000	T685K	probably benign	Het
Msh2	C	A	17: 87,723,413	A906E	probably benign	Het
Myom2	G	A	8: 15,083,310	V401M	probably damaging	Het
Nme5	A	C	18: 34,578,685	M1R	probably null	Het
Nop2	T	C	6: 125,133,763	S68P	probably benign	Het
Notch1	A	T	2: 26,476,114	D809E	possibly damaging	Het
Olfr292	T	C	7: 86,694,585	I43T	possibly damaging	Het
Ppat	C	T	5: 76,928,678		probably benign	Het
Prss23	T	A	7: 89,510,214	M216L	probably benign	Het
Psg18	A	T	7: 18,349,354	V171D	probably damaging	Het
Psg28	A	G	7: 18,427,891	V229A	probably damaging	Het
Qser1	T	C	2: 104,787,831	N879D	possibly damaging	Het
Rpap1	T	C	2: 119,770,041	N879S	probably benign	Het
Rusc2	T	C	4: 43,415,926	S411P	probably damaging	Het
Rxfp2	T	A	5: 150,067,360	W519R	probably damaging	Het
Scpep1	T	A	11: 88,941,349	Q185L	probably benign	Het
Serpinb11	A	G	1: 107,379,649	N270S	probably benign	Het
Serpinb6d	T	A	13: 33,671,444	M367K	probably benign	Het
Skint10	T	G	4: 112,727,672	I213L	probably benign	Het
Skint5	T	C	4: 113,546,537	T1163A	unknown	Het
Slamf9	A	T	1: 172,476,213	I42L	possibly damaging	Het
Slc1a3	T	C	15: 8,650,846		probably benign	Het
Smad6	T	A	9: 63,953,900	Q371L	possibly damaging	Het
Snx31	A	T	15: 36,555,324	V26E	probably damaging	Het
Taf4b	A	G	18: 14,822,172	N594S	possibly damaging	Het
Tanc2	T	C	11: 105,780,092	S172P	probably damaging	Het
Tas2r110	T	A	6: 132,868,475	Y156*	probably null	Het
Tbc1d20	G	A	2: 152,293,936		probably benign	Het
Timm50	A	T	7: 28,306,859	D272E	probably benign	Het
Ttn	T	G	2: 76,900,511		probably benign	Het
Vps13c	T	A	9: 67,916,379	F1362I	probably benign	Het
Vwf	T	C	6: 125,566,257	S154P	probably benign	Het
Zfp445	T	C	9: 122,852,345	R844G	probably benign	Het

Other mutations in Atg9a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01464:Atg9a	APN	1	75190366	missense	probably damaging	1.00
IGL02041:Atg9a	APN	1	75183104	missense	possibly damaging	0.47
IGL03367:Atg9a	APN	1	75187957	missense	probably benign	0.18
PIT4494001:Atg9a	UTSW	1	75187953	nonsense	probably null
R0054:Atg9a	UTSW	1	75184499	missense	probably damaging	1.00
R0054:Atg9a	UTSW	1	75184499	missense	probably damaging	1.00
R0408:Atg9a	UTSW	1	75185295	missense	probably damaging	1.00
R0520:Atg9a	UTSW	1	75186534	nonsense	probably null
R0653:Atg9a	UTSW	1	75190328	missense	probably damaging	0.96
R0666:Atg9a	UTSW	1	75185090	missense	probably damaging	0.99
R0961:Atg9a	UTSW	1	75186746	missense	probably damaging	0.99
R1489:Atg9a	UTSW	1	75186090	missense	probably damaging	1.00
R1490:Atg9a	UTSW	1	75185745	missense	possibly damaging	0.70
R1692:Atg9a	UTSW	1	75190355	missense	probably benign	0.04
R1997:Atg9a	UTSW	1	75189626	missense	probably benign	0.33
R2005:Atg9a	UTSW	1	75185991	missense	probably benign	0.18
R2172:Atg9a	UTSW	1	75185685	missense	probably damaging	0.99
R4004:Atg9a	UTSW	1	75186451	missense	probably damaging	1.00
R4105:Atg9a	UTSW	1	75185959	missense	probably damaging	1.00
R5220:Atg9a	UTSW	1	75185728	missense	probably damaging	1.00
R5898:Atg9a	UTSW	1	75186272	missense	probably damaging	1.00
R6295:Atg9a	UTSW	1	75185058	missense	probably benign	0.01
R6390:Atg9a	UTSW	1	75187981	missense	probably damaging	1.00
R7312:Atg9a	UTSW	1	75188092	missense	probably damaging	1.00
R7729:Atg9a	UTSW	1	75184560	missense	probably benign	0.34
R8111:Atg9a	UTSW	1	75187722	missense	probably damaging	1.00
R8210:Atg9a	UTSW	1	75185283	missense	probably damaging	1.00
R8210:Atg9a	UTSW	1	75186365	missense	probably damaging	1.00
R8256:Atg9a	UTSW	1	75186919	missense	possibly damaging	0.88
R8319:Atg9a	UTSW	1	75185698	nonsense	probably null
R8321:Atg9a	UTSW	1	75185698	nonsense	probably null
R8382:Atg9a	UTSW	1	75185698	nonsense	probably null
R8406:Atg9a	UTSW	1	75190384	missense	probably damaging	1.00
R8482:Atg9a	UTSW	1	75186226	missense	probably damaging	0.99
R8855:Atg9a	UTSW	1	75185223	missense	probably damaging	1.00
R8866:Atg9a	UTSW	1	75185223	missense	probably damaging	1.00
R9381:Atg9a	UTSW	1	75186082	missense	probably benign
R9441:Atg9a	UTSW	1	75186442	missense	possibly damaging	0.92
R9442:Atg9a	UTSW	1	75186442	missense	possibly damaging	0.92
R9448:Atg9a	UTSW	1	75186205	missense	probably benign	0.35
R9608:Atg9a	UTSW	1	75185095	missense	possibly damaging	0.52
R9703:Atg9a	UTSW	1	75185787	missense	probably damaging	0.98
RF021:Atg9a	UTSW	1	75182629	missense	probably damaging	0.96
Z1176:Atg9a	UTSW	1	75186559	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ACGATGGGACTCAGCAACTC -3'
(R):5'- GATGAAGATGTGTTAGCTGTGGAAC -3'

Sequencing Primer
(F):5'- AGGTTACCCGCAAGCAGGAC -3'
(R):5'- CACGTCCTCACCACGGTC -3'

Posted On

2016-06-06